From da30dfff516fd4c6a367d398e3f4ccbc2a620471 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Aug 2020 16:07:04 +0200 Subject: [PATCH 0001/2365] {compiler} GCC 10.2.0 + binutils 2.35 --- .../b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb | 28 ++++++++++ .../binutils/binutils-2.35-GCCcore-10.2.0.eb | 35 +++++++++++++ .../f/flex/flex-2.6.4-GCCcore-10.2.0.eb | 34 +++++++++++++ easybuild/easyconfigs/g/GCC/GCC-10.2.0.eb | 22 ++++++++ .../easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 51 +++++++++++++++++++ .../help2man-1.47.16-GCCcore-10.2.0.eb | 25 +++++++++ .../m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 33 ++++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb | 26 ++++++++++ 8 files changed, 254 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..55d04ef9b9 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.7.1' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1dd952839cf0d5a8178c691eeae40dc48fa50d18dcce648b1ad9ae0195367d13'] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.35', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4f2b121412 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +name = 'binutils' +version = '2.35' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['binutils-2.34-readd-avx512-vmovd.patch'] +checksums = [ + 'a3ac62bae4f339855b5449cfa9b49df90c635adbd67ecb8a0e7f3ae86a058da6', # binutils-2.35.tar.gz + '45ecf7f5d198dd446d1a2e2a4d46b2747eb6fb8f2bfa18d7d42769e710e85716', # binutils-2.34-readd-avx512-vmovd.patch +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.11'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d6bae199dd --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.7.1'), + ('help2man', '1.47.16'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.35', '', True), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-10.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-10.2.0.eb new file mode 100644 index 0000000000..45f4144c99 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '10.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', '2.35', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0cac7b1b4a --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '10.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.0.tar.bz2', + 'mpfr-4.1.0.tar.bz2', + 'mpc-1.1.0.tar.gz', + 'isl-0.22.1.tar.bz2', +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz + 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea', # gmp-6.2.0.tar.bz2 + 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 + '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz + '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch + '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.35'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..16eb74c38c --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.16' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['3ef8580c5b86e32ca092ce8de43df204f5e6f714b0cd32bc6237e6cd0f34a8f4'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.35', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..50594f87ec --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['M4-1.4.18_glibc_2.28.patch'] +checksums = [ + 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz + 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.35', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c26c13b8e5 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.35', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 4f809fa4ae4947a9b53fd99f561cc11d86dd3e7a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Sep 2020 22:21:17 +0200 Subject: [PATCH 0002/2365] {lang}[GCCcore/10.2.0] Perl v5.32.0 --- .../e/expat/expat-2.2.9-GCCcore-10.2.0.eb | 33 + .../libreadline-8.0-GCCcore-10.2.0.eb | 41 + .../n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 41 + .../p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 1747 +++++++++++++++++ 4 files changed, 1862 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fdcc804030 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.9' + +homepage = 'https://libexpat.github.io' + +description = """ + Expat is an XML parser library written in C. It is a stream-oriented parser + in which an application registers handlers for things the parser might find + in the XML document (like start tags) +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f1063084dc4302a427dabcca499c8312b3a32a29b7d2506653ecc8f950a9a237'] + +builddependencies = [('binutils', '2.35')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cb086a8416 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.0' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['e339f51971478d369f8a053a330a190781acb9864cf4c541060f12078948e461'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('ncurses', '6.2'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a3839f2181 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.2' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] + +builddependencies = [('binutils', '2.35')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # default build + local_common_configopts, + # the UTF-8 enabled version (ncursesw) + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +local_libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cdcbceba52 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -0,0 +1,1747 @@ +name = 'Perl' +version = '5.32.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('zlib', '1.2.11'), # for Net::SSLeay + ('expat', '2.2.9'), # for XML::Parser + ('ncurses', '6.2'), # for Term::ReadLine::Gnu + ('libreadline', '8.0'), # for Term::ReadLine::Gnu +] + +# OpenSSL is required for Net::SSLeay +osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# !! order of extensions is important !! +# extensions updated on Sept 13th 2019 +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['1e0050fcd6789a2179ec0db282bf1e90fb92be35d1171588bd9c47d52d959cf5'], + }), + ('ExtUtils::InstallPaths', '0.012', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], + }), + ('Test::Harness', '3.42', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['0fd90d4efea82d6e262e6933759e85d27cbcfa4091b14bf4042ae20bab528e53'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Test::Fatal', '0.016', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7283d430f2ba2030b8cd979ae3039d3f1b2ec3dde1a11ca6ae09f992a66f788f'], + }), + ('Test::Warnings', '0.030', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['89a4947ddf1564ae01122275584433d7f6c4370370bcf3768922d796956ae24f'], + }), + ('File::ShareDir', '1.116', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['59d90bfdf98c4656ff4173e62954ea8cf0de66565e35d108ecd7050596cb8328'], + }), + ('File::ShareDir::Install', '0.13', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['45befdf0d95cbefe7c25a1daf293d85f780d6d2576146546e6828aad26e580f9'], + }), + ('DateTime::Locale', '1.26', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1e43152a7ca4585a335958da0dd5e430b95a820f6de6456df26e7ec2a6649792'], + }), + ('DateTime::TimeZone', '2.39', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['65a49083bf465b42c6a65df575efaceb87b5ba5a997d4e91e6ddba57190c8fca'], + }), + ('Test::Requires', '0.11', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': ['4b88de549597eecddf7c3c38a4d0204a16f59ad804577b671896ac04e24e040f'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], + }), + ('Module::Build', '0.4231', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7e0f4c692c1740c1ac84ea14d7ea3d8bc798b2fb26c09877229e04f430b2b717'], + }), + ('Module::Runtime', '0.016', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': ['68302ec646833547d410be28e09676db75006f4aa58a11f3bdb44ffe99f0f024'], + }), + ('Try::Tiny', '0.30', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['da5bd0d5c903519bbf10bb9ba0cb7bcac0563882bcfe4503aee3fb143eddef6b'], + }), + ('Params::Validate', '1.29', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['49a68dfb430bea028042479111d19068e08095e5a467e320b7ab7bde3d729733'], + }), + ('List::MoreUtils', '0.428', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['713e0945d5f16e62d81d5f3da2b6a7b14a4ce439f6d3a7de74df1fd166476cc2'], + }), + ('Exporter::Tiny', '1.002002', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['00f0b95716b18157132c6c118ded8ba31392563d19e490433e9a65382e707101'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['38220d04f02e3a803193c2575a1644cce0b95ad4b95c19eb932b94e2647ef678'], + }), + ('DateTime', '1.52', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['67828b6172b23d9534b8f2a593b05caa6240737a3b2246f3e1fe4e015dbc3dfc'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['9a48433f86e08ce18e03526e2982de52162eb909d19735460f07eefcaf463ea6'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + 'checksums': ['4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e'], + }), + ('Git', '0.42', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + 'checksums': ['9469a9f398f3a2bf2b0500566ee41d3ff6fae460412a137185767a1cc4783a6d'], + }), + ('Tree::DAG_Node', '1.31', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['1c8ba69772568b3758054247097512c550efe31517c329fb65eef7afccc9d304'], + }), + ('Template', '3.009', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['d6ad23bbf637a59b5dfd1ac006460dfcb185982e4852cde77150fbd085f1f5b6'], + }), + ('DBI', '1.643', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'], + }), + ('DBD::SQLite', '1.64', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['f4ae8f7b50842305566aadd90f7bfd12a9e32b6c603a9b1c1529e73eb82aff01'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': ['11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8'], + }), + ('Archive::Extract', '0.86', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['9acd09cdb8e8cf0b6d08210a3b80342300c89a359855319bf6b00c14c4aab687'], + }), + ('DBIx::Simple', '1.37', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + 'checksums': ['46d311aa2ce08907401c56119658426dbb044c5a40de73d9a7b79bf50390cae3'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + 'checksums': ['f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5'], + }), + ('File::Spec', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('Test::Simple', '1.302177', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['9fbf263096d893d7f8e0dcb0ea0dfe8d62b973b86e6360f43b54080bd2974554'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + 'checksums': ['a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d'], + }), + ('IO::Stringy', '2.113', { + 'source_tmpl': 'IO-Stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['51220fcaf9f66a639b69d251d7b0757bf4202f4f9debd45bdd341a6aca62fe4e'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1'], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "GRANTM"'], + 'checksums': ['66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0'], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': ['47e995859f8dd0413aa3f22d350c4a62da652e854267aa0586ae544ae2bae5ef'], + }), + ('XML::SAX', '1.02', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['4506c387043aa6a77b455f00f57409f3720aa7e553495ab2535263b4ed1ea12a'], + }), + ('Test::LeakTrace', '0.16', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['5f089eed915f1ec8c743f6d2777c3ecd0ca01df2f7b9e10038d316952583e403'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533'], + }), + ('Text::Aligner', '0.16', { + 'source_tmpl': 'Text-Aligner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['5c857dbce586f57fa3d7c4ebd320023ab3b2963b2049428ae01bd3bc4f215725'], + }), + ('Text::Table', '1.134', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['bacf429b18b7c0b22c088219055063e3902749531d488ebd7b17eab7757cd10b'], + }), + ('MIME::Types', '2.17', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['e04ed7d42f1ff3150a303805f2689c28f80b92c511784d4641cb7f040d3e8ff6'], + }), + ('File::Copy::Recursive', '0.45', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['d3971cf78a8345e38042b208bb7b39cb695080386af629f4a04ffd6549df1157'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': ['7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77'], + }), + ('Capture::Tiny', '0.48', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['6c23113e87bad393308c90a207013e505f659274736638d8c79bac9c67cc3e19'], + }), + ('File::Copy::Recursive::Reduced', '0.006', { + 'source_tmpl': 'File-Copy-Recursive-Reduced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['e618f993a69f4355205c58fffff6982609f28b47f646ec6e244e41b5c6707e2c'], + }), + ('Module::Build::XSUtil', '0.19', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + 'checksums': ['9063b3c346edeb422807ffe49ffb23038c4f900d4a77b845ce4b53d97bf29400'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + 'checksums': ['0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "DARREN"'], + 'checksums': ['0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843'], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['ec28c7e1d9e67c45eca197077f7cdc41ead1bb4c538c7f02a3296a4bb92f608b'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + 'checksums': ['c36fd2b68d48c2e17417bf2873c78820f3ae02460fdf5976b8eeab887d59e16c'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 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'source_tmpl': 'Pod-Escapes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], + }), + ('if', '0.0608', { + 'source_tmpl': 'if-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], + }), + ('Test', '1.26', { + 'source_tmpl': 'Test-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['f7701bd28e05e7f82fe9a181bbab38f53fa6aeae48d2a810da74d1b981d4f392'], + }), + ('ExtUtils::Constant', '0.25', { + 'source_tmpl': 'ExtUtils-Constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['6933d0e963b62281ef7561068e6aecac8c4ac2b476b2bba09ab0b90fbac9d757'], + }), + ('ExtUtils::CBuilder', '0.280234', { + 'source_tmpl': 'ExtUtils-CBuilder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AM/AMBS'], + 'checksums': ['d80095ea1f28b4908cbedacead63f61f762472bba898281449dad782deecf1c3'], + }), + ('Carp::Heavy', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('IO::Handle', '1.42', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('IO::Seekable', '1.42', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('Pod::Simple', '3.40', { + 'source_tmpl': 'Pod-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KH/KHW'], + 'checksums': ['063a8cb9d8abd84fd64c3e9581addf96a6b0f77a2048a1846c3a6b14269a040d'], + }), + ('IO::File', '1.42', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('IO::Select', '1.42', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('IO::Socket', '1.42', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('Socket', '2.030', { + 'source_tmpl': 'Socket-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['2573571d0db6ab98b5472a371c4acb24fe53d890f920e43aab49a0eeabe6da67'], + }), + ('Time::Local', '1.30', { + 'source_tmpl': 'Time-Local-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c7744f6b2986b946d3e2cf034df371bee16cdbafe53e945abb1a542c4f8920cb'], + }), + ('Storable', '3.15', { + 'source_tmpl': 'Storable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['fc3dad06cb2e6fc86a2f2abc5b5491d9da328ca3e6b6306559c224521db174da'], + }), + ('ExtUtils::ParseXS', '3.35', { + 'source_tmpl': 'ExtUtils-ParseXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['41def0511278a2a8ba9afa25ccab45b0453f75e7fd774e8644b5f9a57cc4ee1c'], + }), + ('Pod::Man', '4.14', { + 'source_tmpl': 'podlators-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'], + 'checksums': ['7af1c41de34b2e4dbff700a29d7387549c2b6cf16142214450c924707ddb0f82'], + }), + ('Mozilla::CA', '20200520', { + 'source_tmpl': 'Mozilla-CA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABH'], + 'checksums': ['b3ca0002310bf24a16c0d5920bdea97a2f46e77e7be3e7377e850d033387c726'], + }), + ('Test::More', '1.302177', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['9fbf263096d893d7f8e0dcb0ea0dfe8d62b973b86e6360f43b54080bd2974554'], + }), + ('Test::RequiresInternet', '0.05', { + 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN'], + 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], + }), + ('LWP::Protocol::https', '6.09', { + 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['16cfe1a511690b066db5667c8714802ee2b9c5d28a31a3e7bd36fbc70a3af592'], + }), + ('Module::Load', '0.34', { + 'source_tmpl': 'Module-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['7f5b0c4d3cc8ba867639bff61ad857a940970ea246dd3b0a6729dd7fc84059f3'], + }), + ('Module::Load::Conditional', '0.72', { + 'source_tmpl': 'Module-Load-Conditional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['36938936c501aa708aa17b12a67c2fb7157e88a2e3ec03da5fcf59069f654e5b'], + }), + ('parent', '0.238', { + 'source_tmpl': 'parent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['38f58fdef3e28a194c9c8d0dc5d02672faf93c069f40c5bcb1fabeadbbc4d2d1'], + }), + ('Net::Domain', '3.11', { + 'source_tmpl': 'libnet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['2fab1e4d6e565c77f6e845368790de65cb2f966fcd9bb56a41d0e7b5851a52d3'], + }), + ('Scalar::Util', '1.55', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['4d2bdc1c72a7bc4d69d6a5cc85bc7566497c3b183c6175b832784329d58feb4b'], + }), + ('Text::ParseWords', '3.30', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': ['85e0238179dd43997e58c66bd51611182bc7d533505029a2db0d3232edaff5e8'], + }), + ('Encode', '3.07', { + 'source_tmpl': 'Encode-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], + 'checksums': ['34a4ec9b574b7a6c6132c4ab3ded490fd600bc7ce382124aeda58bb1e112910f'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], + }), + ('Data::Dumper', '2.173', { + 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], + }), + ('Cwd', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['7f863566a6a9cb93eda93beadb77d9aa04b9304d769cea3bb921b9a91b3a1eb9'], + }), + ('ExtUtils::CppGuess', '0.21', { + 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['ff629178321a1e591b83f809712593eae4408a413aa448654bce59b156f24153'], + }), + ('XSLoader', '0.24', { + 'source_tmpl': 'XSLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], + 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], + }), + ('AutoLoader', '5.74', { + 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], + }), + ('URI::Escape', '1.76', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['b2c98e1d50d6f572483ee538a6f4ccc8d9185f91f0073fd8af7390898254413e'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], + }), + ('MCE::Mutex', '1.874', { + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], + 'checksums': ['d809e3018475115ad7eccb8bef49bde3bf3e75abbbcd80564728bbcfab86d3d0'], + }), + ('Text::CSV_XS', '1.44', { + 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['c4812ddca8e2654736c44bc2ce60b27a428a1bc4d5364b0ed1fad3609c8f9bc4'], + }), + ('DBD::CSV', '0.55', { + 'source_tmpl': 'DBD-CSV-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['4670028e46df9a3c2791740445e8a4c82840b6667cee5dd796bc5a6ad9266ddb'], + }), + ('Array::Transpose', '0.06', { + 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], + 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], + }), + ('Config::Simple', '4.58', { + 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], + 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], + }), +] + +moduleclass = 'lang' From cde9302b4db063f896afc8949f28420c3f0c0f2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Sep 2020 09:30:13 +0200 Subject: [PATCH 0003/2365] fix date when extensions were updated in Perl 5.32.0 easyconfig --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index cdcbceba52..c5b2d9d251 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ dependencies = [ osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # !! order of extensions is important !! -# extensions updated on Sept 13th 2019 +# extensions updated on Aug 21st 2020 exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', From 88f13b5681307fd836a19a92f9f7e47944043f60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Sep 2020 11:08:19 +0200 Subject: [PATCH 0004/2365] fix broken source URLs for extensions included in Perl 5.32.0 easyconfig --- .../p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index c5b2d9d251..26aa3e5ed5 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -248,7 +248,7 @@ exts_list = [ }), ('XML::SAX::Base', '1.09', { 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "GRANTM"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], 'checksums': ['66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0'], }), ('XML::NamespaceSupport', '1.12', { @@ -318,7 +318,7 @@ exts_list = [ }), ('Template::Plugin::Number::Format', '1.06', { 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "DARREN"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], 'checksums': ['0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843'], }), ('HTML::Parser', '3.72', { @@ -583,7 +583,7 @@ exts_list = [ }), ('XML::Bare', '0.53', { 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "CODECHILD"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], 'checksums': ['865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd'], }), ('Dist::CheckConflicts', '0.11', { @@ -728,7 +728,7 @@ exts_list = [ }), ('Time::Piece::MySQL', '0.06', { 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "KASEI"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], 'checksums': ['319601feec17fae344988a5ee91cfc6a0bcfe742af77dba254724c3268b2a60f'], }), ('Package::Stash::XS', '0.29', { @@ -913,7 +913,7 @@ exts_list = [ }), ('UNIVERSAL::moniker', '0.08', { 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "KASEI"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], 'checksums': ['94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c'], }), ('Exception::Class', '1.44', { @@ -1299,7 +1299,7 @@ exts_list = [ }), ('MooseX::Types::Perl', '0.101343', { 'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "RJBS"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['f084beaf3c33209c68d05d4dbc24c25d604a6458b9738d96dceb086c8ef1325a'], }), ('Role::Tiny', '2.001004', { @@ -1399,7 +1399,7 @@ exts_list = [ }), ('Config::INI', '0.025', { 'source_tmpl': 'Config-INI-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "RJBS"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['628bf76d5b91f89dde22d4813ec033026ebf71b772bb61ccda909da00c869732'], }), ('String::Truncate', '1.100602', { @@ -1514,7 +1514,7 @@ exts_list = [ }), ('Params::Check', '0.38', { 'source_tmpl': 'Params-Check-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "BINGOS"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], 'checksums': ['f0c9d33876c36b1bca1475276d26d2efaf449b256d7cc8118fae012e89a26290'], }), ('Locale::Maketext::Simple', '0.21', { From dab07a76e9eb06057cf7568043f38dd520e8b231 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Sep 2020 11:09:56 +0200 Subject: [PATCH 0005/2365] also fix source URLs for Array::Utils --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 26aa3e5ed5..83f5087b9a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -1189,7 +1189,7 @@ exts_list = [ }), ('Array::Utils', '0.5', { 'source_tmpl': 'Array-Utils-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZM/ZMIJ'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZM/ZMIJ/Array'], 'checksums': ['89dd1b7fcd9b4379492a3a77496e39fe6cd379b773fd03a6b160dd26ede63770'], }), ('File::Grep', '0.02', { From 87009deb5cc25814b827977859260696b447183a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Sep 2020 11:12:25 +0200 Subject: [PATCH 0006/2365] also fix source URLs for Tie::Function --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 83f5087b9a..5ec6cca0e6 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -313,7 +313,7 @@ exts_list = [ }), ('Tie::Function', '0.02', { 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], 'checksums': ['0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117'], }), ('Template::Plugin::Number::Format', '1.06', { From 691cb1db40d0ac129b315e02e3f4e2a947693094 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Sep 2020 17:27:54 +0200 Subject: [PATCH 0007/2365] {devel}[GCCcore/10.2.0] Autotools v20200321 --- .../Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb | 41 +++++++++++++++++ .../Automake-1.16.2-GCCcore-10.2.0.eb | 44 +++++++++++++++++++ .../Autotools-20200321-GCCcore-10.2.0.eb | 24 ++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb | 32 ++++++++++++++ 4 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20200321-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c5f974ed99 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] + +builddependencies = [ + ('binutils', '2.35'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.32.0'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..161cd23bf2 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.2' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] + +builddependencies = [ + ('binutils', '2.35'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.32.0'), +] + +dependencies = [ + ('Autoconf', '2.69'), +] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20200321-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20200321-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..748c84f8d6 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20200321-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20200321' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.16.2'), # 20200321 + ('libtool', '2.4.6'), # 20150215 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dd1e6e9fa2 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From 91598c869e2a2d94163197d60b042b26bc02191c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Sep 2020 19:05:20 +0200 Subject: [PATCH 0008/2365] fix SHA256 checksum for Automake 1.16.2 --- .../easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb index 161cd23bf2..94d0fe0023 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] +checksums = ['b2f361094b410b4acbf4efba7337bdb786335ca09eb2518635a09fb7319ca5c1'] builddependencies = [ ('binutils', '2.35'), From 271124f42903638191f4640a609866e425adcc6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2020 16:45:46 +0200 Subject: [PATCH 0009/2365] {lib}[GCCcore/10.2.0] UCX v1.9.0 --- .../numactl/numactl-2.0.13-GCCcore-10.2.0.eb | 34 ++++++++++++++ .../pkg-config-0.29.2-GCCcore-10.2.0.eb | 34 ++++++++++++++ .../u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 3 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9de001385a --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.13' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['97ee012b2f294903530424b4ff7f28bcaad6a356897ce8777383f87e5c2e325d'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1103527815 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [('binutils', '2.35')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0c81fb441b --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.9.0' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['a7a2c8841dc0d5444088a4373dc9b9cc68dbffcd917c1eba92ca8ed8e5e635fb'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('numactl', '2.0.13'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From b909f2629bcf7e17e561452dc0fdc93734040b14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 11:32:27 +0200 Subject: [PATCH 0010/2365] {system}[GCCcore/10.2.0] hwloc 2.2.0 + deps --- .../h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb | 48 +++++++++++++++++++ .../libpciaccess-0.16-GCCcore-10.2.0.eb | 26 ++++++++++ .../libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb | 28 +++++++++++ .../x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 48 +++++++++++++++++++ .../xorg-macros-1.19.2-GCCcore-10.2.0.eb | 37 ++++++++++++++ 5 files changed, 187 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ddabd3a738 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.2.0' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake +# cfr. https://github.com/open-mpi/hwloc/issues/315 +toolchainopts = {'vectorize': False} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2defba03ddd91761b858cbbdc2e3a6e27b44e94696dbfa21380191328485a433'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('numactl', '2.0.13'), + ('libxml2', '2.9.10'), + ('libpciaccess', '0.16'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7e7b8c982a --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.16' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['84413553994aef0070cf420050aa5c0a51b1956b404920e21b81e96db6a61a27'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..38a25e4b1a --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.10' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..264331a9b0 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU LGPLv2.1+ +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.5' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['XZ-5.2.2_compat-libs.patch'] +checksums = [ + '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 + '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch +] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21', '', True), + ('binutils', '2.35'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..55d95bd126 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.2' + +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['326e51a5d673e3d9cc7f139aee469a11e18ea060b1d06c22694612e68a2089b1'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From 0aac8f735f67c5d73b38d743764a3e4bd765e7fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 11:36:23 +0200 Subject: [PATCH 0011/2365] {lib}[GCCcore/10.2.0] OpenMPI v4.0.5, libevent v2.1.12, libfabric v1.11.0, PMIx 3.1.5 --- .../libevent-2.1.12-GCCcore-10.2.0.eb | 37 +++++++++++++++ .../libfabric-1.11.0-GCCcore-10.2.0.eb | 40 ++++++++++++++++ .../o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 32 +++++++++++++ .../p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 4 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..22b850f842 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3518074350 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.11.0' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'ofiwg' +source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9938abf628e7ea8dcf60a94a4b62d499fbc0dbc6733478b6db2e6a373c80d58f'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb new file mode 100644 index 0000000000..15b78eb63e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -0,0 +1,32 @@ +name = 'OpenMPI' +version = '4.0.5' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('libevent', '2.1.12'), + ('UCX', '1.9.0'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..efe2a2d3ed --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '3.1.5' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['88934195174455df478b996313095df25b51d0caf5a5cce01b22f0ccdc6c5cf7'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' From 9eba8da85bd2efdcff0b1af539e8294597400b17 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 9 Oct 2020 10:56:27 +0100 Subject: [PATCH 0012/2365] Add new DB for GCCcore 10.2.0 and Perl: DB_File requires DB as a dep --- .../d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ .../p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 1 + 2 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..35c967bb55 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +# EasyBuild easyconfig +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# download via +# https://www.oracle.com/technetwork/products/berkeleydb/downloads/, +# requires registration +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 5ec6cca0e6..18b17c57ec 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('expat', '2.2.9'), # for XML::Parser ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.0'), # for Term::ReadLine::Gnu + ('DB', '18.1.40'), # for DB_File ] # OpenSSL is required for Net::SSLeay From 84af52cf2285a297a5e6a6ea96bd9db8b14ed8fe Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 9 Oct 2020 11:02:06 +0100 Subject: [PATCH 0013/2365] checksums --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb index 35c967bb55..3437dbddff 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} # https://www.oracle.com/technetwork/products/berkeleydb/downloads/, # requires registration sources = [SOURCELOWER_TAR_GZ] +checksums = ['0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8'] builddependencies = [('binutils', '2.35')] From 7f77048ce70c2285440856b2f1ef2f9442e02ee4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 9 Oct 2020 14:46:10 +0100 Subject: [PATCH 0014/2365] patch out installation attempt of missing docs --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb index 3437dbddff..d2d28cd5ff 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} # https://www.oracle.com/technetwork/products/berkeleydb/downloads/, # requires registration sources = [SOURCELOWER_TAR_GZ] -checksums = ['0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8'] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] builddependencies = [('binutils', '2.35')] From ab5d73c78c84703de60c8ab6948da6b4abb66836 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 9 Oct 2020 15:06:55 +0100 Subject: [PATCH 0015/2365] checksums --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb index d2d28cd5ff..d57cfc30de 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -15,6 +15,10 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} # requires registration sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] builddependencies = [('binutils', '2.35')] From 2146c5453cb963e40f2bb5ac0ce407219f38375d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 10 Oct 2020 19:20:43 +0100 Subject: [PATCH 0016/2365] Switch to homebrew mirror for DB source --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb index d57cfc30de..6b601fe0f4 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -10,10 +10,10 @@ description = """Berkeley DB enables the development of custom data management toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -# download via -# https://www.oracle.com/technetwork/products/berkeleydb/downloads/, -# requires registration -sources = [SOURCELOWER_TAR_GZ] +# use Homebrew source mirror to allow auto-downloading source tarball +# (Oracle website - https://www.oracle.com/technetwork/products/berkeleydb/downloads/ - requires reigstration) +source_urls = ['https://bintray.com/homebrew/mirror/download_file?file_path='] +sources = [{'download_filename': 'berkeley-db-%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] patches = ['%(name)s-%(version)s_fix_doc_install.patch'] checksums = [ '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz From 8b7487ac76c4ed6c540823817de4aaf6e921bbf8 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 17:38:24 +0200 Subject: [PATCH 0017/2365] adding easyconfigs: bzip2-1.0.8-GCCcore-10.2.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ec886cad08 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-1.0.6-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + + +moduleclass = 'tools' From fdeafae431750960a74e8d6a9931d1862e93e208 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 17:41:24 +0200 Subject: [PATCH 0018/2365] adding easyconfigs: SQLite-3.33.0-GCCcore-10.2.0.eb --- .../s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ffffe1f458 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: https://hpcbios.readthedocs.org/en/latest/ +# # + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.33.0' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/2020/'] +sources = ['%%(namelower)s-autoconf-%s000.tar.gz' % (''.join(version.split('.')))] +checksums = ['106a2c48c7f75a298a7557bcc0d5f4f454e5b43811cc738b7ca294d6956bbb15'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('libreadline', '8.0'), + ('Tcl', '8.6.10'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' From 6cae7cabc79126cca4b78b7864d47e17df5c07d4 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 17:42:03 +0200 Subject: [PATCH 0019/2365] adding easyconfigs: Tcl-8.6.10-GCCcore-10.2.0.eb --- .../t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5cd77d8338 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.10' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['5196dbf6638e3df8d5c87b5815c8c2b758496eb6f0e41446596c9a4e638d87ed'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' From 785a4311af5ea1c283cb6d058ad7daf6b561db63 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 18:44:24 +0200 Subject: [PATCH 0020/2365] Include sanity check command --- .../easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb index ffffe1f458..3243496e8a 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb @@ -44,4 +44,8 @@ sanity_check_paths = { 'dirs': ['lib/pkgconfig'], } +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + moduleclass = 'devel' From 9fc720b263d6a12f13d6d71ad8c10fe4451fe752 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 19:33:06 +0200 Subject: [PATCH 0021/2365] adding easyconfigs: GMP-6.2.0-GCCcore-10.2.0.eb --- .../g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b1f3baccd6 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.2.0' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' From 80acafb3e1c39eed0a37189be1d362d2812ed26e Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 20:25:09 +0200 Subject: [PATCH 0022/2365] Use same filename method as 3.31.1 --- easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb index 3243496e8a..272f12272d 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb @@ -14,6 +14,7 @@ easyblock = 'ConfigureMake' name = 'SQLite' version = '3.33.0' +local_filename_version = '3330000' homepage = 'https://www.sqlite.org/' description = "SQLite: SQL Database Engine in a C Library" @@ -22,7 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} source_urls = ['https://www.%(namelower)s.org/2020/'] -sources = ['%%(namelower)s-autoconf-%s000.tar.gz' % (''.join(version.split('.')))] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] checksums = ['106a2c48c7f75a298a7557bcc0d5f4f454e5b43811cc738b7ca294d6956bbb15'] builddependencies = [ From 2d6a7cb91ecc9d75b9748217882f6f217f487c8c Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 20:27:04 +0200 Subject: [PATCH 0023/2365] adding easyconfigs: libffi-3.3-GCCcore-10.2.0.eb --- .../l/libffi/libffi-3.3-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6ccf73557b --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.3' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'ftp://sourceware.org/pub/%(name)s/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/%(name)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['72fba7922703ddfa7a028d513ac15a85c8d54c8d67f55fa5a4802885dc652056'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 851a42ecad2a268e2632c780d9bcc4382b58e0dd Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 22:09:27 +0200 Subject: [PATCH 0024/2365] adding easyconfigs: Python-2.7.18-GCCcore-10.2.0.eb, Python-3.8.4-GCCcore-10.2.0.eb --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 299 ++++++++++++++++++ 1 file changed, 299 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b17ca55ddc --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -0,0 +1,299 @@ +name = 'Python' +version = '2.7.18' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +dependencies = [ + ('binutils', '2.35'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('SQLite', '3.33.0'), + ('GMP', '6.2.0'), # required for pycrypto + ('libffi', '3.3'), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 13 October 2020 +exts_list = [ + ('setuptools', '44.1.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'use_pip': False, + 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], + }), + ('pip', '20.2.3', { + 'use_pip': False, + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), + ('wheel', '0.35.1', { + 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('paycheck', '1.0.2', { + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.5.0', { + 'checksums': ['14bfd98f51c78a3dd22a1ef45cf194ad79eee4a19e8e1a0d5c7f8e81ffe182ea'], + }), + ('Cython', '0.29.21', { + 'checksums': ['e57acb89bd55943c8d8bf813763d20b9099cc7165c0f16b707631a7654be9cad'], + }), + ('six', '1.15.0', { + 'checksums': ['30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259'], + }), + ('toml', '0.10.1', { + 'checksums': ['926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f'], + }), + ('setuptools_scm', '4.1.2', { + 'checksums': ['a8994582e716ec690f33fec70cca0f85bd23ec974e3f783233e4879090a7faa8'], + }), + ('python-dateutil', '2.8.1', { + 'modulename': 'dateutil', + 'checksums': ['73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c'], + }), + ('decorator', '4.4.2', { + 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], + 'checksums': [ + 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz + # pycrypto-2.6.1_remove-usr-include.patch + '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', + ], + }), + ('ecdsa', '0.16.0', { + 'checksums': ['494c6a853e9ed2e9be33d160b41d47afc50a6629b993d2b9c5ad7bb226add892'], + }), + ('enum34', '1.1.10', { + 'modulename': 'enum', + 'checksums': ['cce6a7477ed816bd2542d03d53db9f0db935dd013b70f336a95c73979289f248'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.4.0', { + 'checksums': ['f4f6e119474e58e04a2b1af817eb585b4fd72bdd89b998624712b5c99be7641c'], + }), + ('idna', '2.10', { + 'checksums': ['b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6'], + }), + ('pycparser', '2.20', { + 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], + }), + ('cffi', '1.14.3', { + 'checksums': ['f92f789e4f9241cd262ad7a555ca2c648a98178a953af117ef7fad46aa1d5591'], + }), + ('cryptography', '3.1.1', { + 'checksums': ['9d9fc6a16357965d282dd4ab6531013935425d0dc4950df2e0cf2a1b1ac1017d'], + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.4.0', { + 'modulename': 'nacl', + 'checksums': ['54e9a2c849c742006516ad56a88f5c74bf2ce92c9f67435187c3c5953b346505'], + }), + ('bcrypt', '3.1.7', { + 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], + }), + ('paramiko', '2.7.2', { + 'checksums': ['7f36f4ba2c0d81d219f4595e35f70d56cc94f9ac40a6acdf51d6ca210ce65035'], + }), + ('pyparsing', '2.4.7', { + 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], + }), + ('netifaces', '0.10.9', { + 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], + }), + ('netaddr', '0.8.0', { + 'checksums': ['d6cc57c7a07b1d9d2e917aa8b36ae8ce61c35ba3fcd1b83ca31c5a0ee2b5a243'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '3.0.5', { + 'checksums': ['83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3'], + }), + ('pytz', '2020.1', { + 'checksums': ['c35965d010ce31b23eeb663ed3cc8c906275d6be1a34393a1d73a41febf4a048'], + }), + ('bitstring', '3.1.7', { + 'checksums': ['fdf3eb72b229d2864fb507f8f42b1b2c57af7ce5fec035972f9566de440a864a'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.1', { + 'source_tmpl': 'distlib-%(version)s.zip', + 'checksums': ['edf6116872c863e1aa9d5bb7cb5e05a022c519a4594dc703843343a9ddd9bff1'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('importlib_resources', '3.0.0', { + 'checksums': ['19f745a6eca188b490b1428c8d1d4a0d2368759f32370ea8fb89cad2ab1106c3'], + }), + ('virtualenv', '20.0.34', { + 'checksums': ['4bf0e2bf99d33b123a895a5a244f0d7adb2a92171c6bbb31c3e2db235624abf1'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.14.1', { + 'checksums': ['0630eea4f5664c463f23fbf5dcfc54a2bc6168902719fa8e19daf033022786c8'], + }), + ('chardet', '3.0.4', { + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2020.6.20', { + 'checksums': ['5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3'], + }), + ('urllib3', '1.25.10', { + 'checksums': ['91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a'], + }), + ('requests', '2.24.0', { + 'checksums': ['b3559a131db72c33ee969480840fff4bb6dd111de7dd27c8ee1f820f4f00231b'], + }), + ('xlrd', '1.2.0', { + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('py_expression_eval', '0.3.10', { + 'checksums': ['43038326b686df697f9533895184c15d18769e215abbd8bcecaea607483f35b3'], + }), + ('tabulate', '0.8.7', { + 'checksums': ['db2723a20d04bcda8522165c73eea7c300eda74e0ce852d9022e0159d7895007'], + }), + ('ujson', '2.0.3', { + 'checksums': ['bd2deffc983827510e5145fb66e4cc0f577480c62fe0b4882139f8f7d27ae9a3'], + }), + ('atomicwrites', '1.4.0', { + 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], + }), + ('py', '1.9.0', { + 'checksums': ['9ca6883ce56b4e8da7e79ac18787889fa5206c79dcc67fb065376cd2fe03f342'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.5', { + 'checksums': ['6cd9a47b597b37cc57de1c05e56fb1a1c9cc9fab04fe78c29acd090418529868'], + }), + ('zipp', '1.2.0', { + 'checksums': ['c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1'], + }), + ('configparser', '4.0.2', { + 'checksums': ['c7d282687a5308319bf3d2e7706e575c635b0a470342641c93bea0ea3b5331df'], + }), + ('contextlib2', '0.6.0.post1', { + 'checksums': ['01f490098c18b19d2bd5bb5dc445b2054d2fa97f09a4280ba2c5f3c394c8162e'], + }), + ('importlib_metadata', '2.0.0', { + 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('more-itertools', '5.0.0', { + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + ('attrs', '20.2.0', { + 'modulename': 'attr', + 'checksums': ['26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594'], + }), + ('wcwidth', '0.2.5', { + 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], + }), + ('pytest', '4.6.11', { + 'checksums': ['50fa82392f2120cc3ec2ca0a75ee615be4c479e66669789771f1758332be4353'], + }), + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], + }), + ('sphinxcontrib-websupport', '1.1.2', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['1501befb0fdf1d1c29a800fdbf4ef5dc5369377300ddbdd16d2cd40e54c6eefc'], + }), + ('Pygments', '2.5.2', { + 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], + }), + ('imagesize', '1.2.0', { + 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], + }), + ('docutils', '0.16', { + 'checksums': ['c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc'], + }), + ('snowballstemmer', '2.0.0', { + 'checksums': ['df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52'], + }), + ('Babel', '2.8.0', { + 'checksums': ['1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38'], + }), + ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.7.4.3', { + 'checksums': ['1187fb9c82fd670d10aa07bbb6cfcfe4bdda42d6fab8d5134f04e8c4d0b71cc9'], + }), + ('Sphinx', '1.8.5', { + 'checksums': ['c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('psutil', '5.7.2', { + 'checksums': ['90990af1c3c67195c44c9a889184f84f5b2320dce3ee3acbd054e3ba0b4a7beb'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('singledispatch', '3.4.0.3', { + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('sortedcontainers', '2.2.2', { + 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), +] + +moduleclass = 'lang' From 6c4e206a11281601065585342e0a2bd1c5714750 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 22:31:18 +0200 Subject: [PATCH 0025/2365] adding easyconfigs: intltool-0.51.0-GCCcore-10.2.0.eb --- .../intltool-0.51.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8c601251e7 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Perl', '5.32.0'), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' From fb849e6ce82e2cdb3ed2be1aef88e1c66f6e93f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 22:32:11 +0200 Subject: [PATCH 0026/2365] adding easyconfigs: CMake-3.18.4-GCCcore-10.2.0.eb, cURL-7.72.0-GCCcore-10.2.0.eb, bzip2-1.0.8-GCCcore-10.2.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb | 28 +++++++++++ .../c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb | 35 +++++++++++++ .../c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb | 49 +++++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ec886cad08 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-1.0.6-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e31b9c6094 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +name = 'CMake' +version = '3.18.4' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['597c61358e6a92ecbfad42a9b5321ddd801fc7e7eca08441307c9138382d4f77'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.72.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1d'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..319edd1d92 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.72.0' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d4d5899a3868fbb6ae1856c3e55a32ce35913de3956d1973caccd37bd0174fa2'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1d') +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +configopts = '--with-zlib' +# configopts += '--with-ssl=$EBROOTOPENSSL' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' From 596cdebf5047ae5ee0667a1832d183bc50173ee5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 21:58:01 +0200 Subject: [PATCH 0027/2365] {toolchain} foss/2020b (WIP) --- .../f/FFTW/FFTW-3.3.8-gompi-2020b.eb | 17 ++++++++++++ easybuild/easyconfigs/f/foss/foss-2020b.eb | 27 +++++++++++++++++++ easybuild/easyconfigs/g/gompi/gompi-2020b.eb | 20 ++++++++++++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2020b.eb | 21 +++++++++++++++ .../ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb | 21 +++++++++++++++ 5 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2020b.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2020b.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompi-2020b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompi-2020b.eb new file mode 100644 index 0000000000..d866eed7b5 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompi-2020b.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2020b.eb b/easybuild/easyconfigs/f/foss/foss-2020b.eb new file mode 100644 index 0000000000..f423f25efa --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2020b' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '10.2.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.0.5', '', ('GCC', local_gccver)), + ('OpenBLAS', '0.3.10', '', ('GCC', local_gccver)), + ('FFTW', '3.3.8', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.1.0', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2020b.eb b/easybuild/easyconfigs/g/gompi/gompi-2020b.eb new file mode 100644 index 0000000000..2738c8a249 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2020b.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2020b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '10.2.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.0.5', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2020b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2020b.eb new file mode 100644 index 0000000000..ff80fe6d13 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2020b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb new file mode 100644 index 0000000000..af6cec3942 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb @@ -0,0 +1,21 @@ +name = 'ScaLAPACK' +version = '2.1.0' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6', # scalapack-2.1.0.tgz + 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch +] + +dependencies = [('OpenBLAS', '0.3.10')] + +moduleclass = 'numlib' From 13e4e0722fad1737617a6a0ff1e4a1d9f5e79e1b Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 14 Oct 2020 12:56:46 +0200 Subject: [PATCH 0028/2365] adding easyconfigs: libpng-1.6.37-GCCcore-10.2.0.eb, freetype-2.10.3-GCCcore-10.2.0.eb, util-linux-2.36-GCCcore-10.2.0.eb, fontconfig-2.13.92-GCCcore-10.2.0.eb, gperf-3.1-GCCcore-10.2.0.eb --- .../fontconfig-2.13.92-GCCcore-10.2.0.eb | 39 ++++++++++++++++++ .../freetype-2.10.3-GCCcore-10.2.0.eb | 37 +++++++++++++++++ .../g/gperf/gperf-3.1-GCCcore-10.2.0.eb | 31 ++++++++++++++ .../l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb | 31 ++++++++++++++ .../util-linux-2.36-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 5 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.36-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..077c89c6a4 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.13.92' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3406a05b83a42231e3df68d02bc0a0cf47b3f2e8f11c8ede62267daf5f130016'] + +builddependencies = [ + ('binutils', '2.35'), + ('gperf', '3.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('expat', '2.2.9'), + ('freetype', '2.10.3'), + ('util-linux', '2.36'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..85cc3b228e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +name = 'freetype' +version = '2.10.3' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9dfb4e11efd6e460a87b1991a64bc69344ee7dc219d9b29e7faabc1c168ce8b0'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..570faad38a --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.35'), +] + + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1ed15d2e2e --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.37' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['daeb2620d829575513e35fecc83f0d3791a620b9b93d800b763542ece9390fb4'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +local_majminver = ''.join(version.split('.')[:2]) + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.36-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.36-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..93640fcd1d --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.36-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.36' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['82942cd877a989f6d12d4ce2c757fb67ec53d8c5cd9af0537141ec5f84a2eea3'] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From a15e3e2b355e7811bb1e9baaceb0dc1d18e04d57 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 14 Oct 2020 14:13:26 +0200 Subject: [PATCH 0029/2365] Remove trailing whitespace --- .../f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb index 077c89c6a4..5e691036a5 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ dependencies = [ ('expat', '2.2.9'), - ('freetype', '2.10.3'), + ('freetype', '2.10.3'), ('util-linux', '2.36'), ] From 424ba7f25220e5d14db293b2b4e6820ebce32e80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 13:58:16 +0200 Subject: [PATCH 0030/2365] use OS_PKG_OPENSSL_DEV constant in cURL 7.72.0 and CMake 3.18.4 easyconfigs + bump version for commented out OpenSSL dep --- .../easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb | 6 ++---- easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb | 6 ++---- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb index e31b9c6094..d16e78407b 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb @@ -25,11 +25,9 @@ dependencies = [ ('cURL', '7.72.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.1d'), + # ('OpenSSL', '1.1.1h'), ] -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] +osdependencies = [OS_PKG_OPENSSL_DEV] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb index 319edd1d92..c745d57b96 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb @@ -29,12 +29,10 @@ dependencies = [ ('zlib', '1.2.11'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.1d') + # ('OpenSSL', '1.1.1h') ] -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] +osdependencies = [OS_PKG_OPENSSL_DEV] configopts = '--with-zlib' # configopts += '--with-ssl=$EBROOTOPENSSL' From 159eeff3e89afa5231a19185900fbbcbd2301b4d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 15:14:03 +0200 Subject: [PATCH 0031/2365] add libarchive dep to CMake 3.18.4 --- .../c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb | 1 + .../libarchive-3.4.3-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 2 files changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb index d16e78407b..adcb0b84ea 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb @@ -23,6 +23,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.8'), ('cURL', '7.72.0'), + ('libarchive', '3.4.3'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.1.1h'), diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..56c058b302 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.4.3' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ee1e749213c108cb60d53147f18c31a73d6717d7e3d2481c157e1b34c881ea39'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' From 50ed6b9a55e20dbccf90eb601ef468ecfe9716e3 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 14 Oct 2020 21:57:06 +0200 Subject: [PATCH 0032/2365] Include poetry and other common extensions into core bundles --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 126 +++++++++++++++++- 1 file changed, 122 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index b17ca55ddc..fae6a3ac0e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -38,15 +38,15 @@ exts_default_options = { # order is important! # package versions updated 13 October 2020 exts_list = [ + ('pip', '20.2.3', { + 'use_pip': False, + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', 'use_pip': False, 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], }), - ('pip', '20.2.3', { - 'use_pip': False, - 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], - }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], }), @@ -101,6 +101,9 @@ exts_list = [ 'modulename': 'enum', 'checksums': ['cce6a7477ed816bd2542d03d53db9f0db935dd013b70f336a95c73979289f248'], }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), ('ipaddress', '1.0.23', { 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], }), @@ -276,6 +279,12 @@ exts_list = [ ('Sphinx', '1.8.5', { 'checksums': ['c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08'], }), + ('sphinx-bootstrap-theme', '0.7.1', { + 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), ('click', '7.1.2', { 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], }), @@ -294,6 +303,115 @@ exts_list = [ ('intervaltree', '3.1.0', { 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], }), + ('entrypoints', '0.3', { + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('functools32', '3.2.3-2', { + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), + ('futures', '3.3.0', { + 'checksums': ['7e033af76a5e35f58e56da7a91e687706faf4e7bdfb2cbc3f2cca6b9bcda9794'], + }), + ('glob2', '0.6', { + 'checksums': ['f5b0a686ff21f820c4d3f0c4edd216704cea59d79d00fa337e244a2f2ff83ed6'], + }), + ('importlib-metadata', '1.7.0', { + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83'], + }), + ('subprocess32', '3.5.4', { + 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('regex', '2020.10.11', { + 'checksums': ['463e770c48da76a8da82b8d4a48a541f314e0df91cbb6d873a341dbe578efafd'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('pylev', '1.3.0', { + 'checksums': ['063910098161199b81e453025653ec53556c1be7165a9b7c50be2f4d57eae1c3'], + }), + ('pastel', '0.2.1', { + 'use_pip': False, + 'checksums': ['e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d'], + }), + ('clikit', '0.6.2', { + 'use_pip': False, + 'checksums': ['442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59'], + }), + ('SecretStorage', '2.3.1', { + 'checksums': ['3af65c87765323e6f64c83575b05393f9e003431959c9395d1791d51497f29b6'], + }), + ('keyring', '18.0.1', { + 'checksums': ['67d6cc0132bd77922725fae9f18366bb314fd8f95ff4d323a4df41890a96a838'], + }), + ('keyrings.alt', '3.2.0', { + 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], + }), + ('tomlkit', '0.7.0', { + 'use_pip': False, + 'checksums': ['ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618'], + }), + ('shellingham', '1.3.2', { + 'checksums': ['576c1982bea0ba82fb46c36feb951319d7f42214a82634233f58b40d858a751e'], + }), + ('requests-toolbelt', '0.9.1', { + 'checksums': ['968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0'], + }), + ('pyrsistent', '0.16.1', { + 'checksums': ['aa2ae1c2e496f4d6777f869ea5de7166a8ccb9c2e06ebcf6c7ff1b670c98c5ef'], + }), + ('pkginfo', '1.5.0.1', { + 'checksums': ['7424f2c8511c186cd5424bbf31045b77435b37a8d604990b79d4e70d741148bb'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('cleo', '0.8.1', { + 'use_pip': False, + 'checksums': ['3d0e22d30117851b45970b6c14aca4ab0b18b1b53c8af57bed13208147e4069f'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.0', { + 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], + }), + ('CacheControl', '0.12.6', { + 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], + }), + ('ptyprocess', '0.6.0', { + 'use_pip': False, + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.0.0', { + 'checksums': ['6a664ff389b9f45382536f8fa1611a0cb4d2de7c5a5c885db1f0c600cd11fbd5'], + }), + ('poetry', '1.1.3', { + 'checksums': ['49eae89e2c44b0323214d0bbcefc21ebe3a19baa44db98eefabd4db9e82c7253'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), ] moduleclass = 'lang' From 8cbbf6ec37727d3d277017a47a6e06bfb6879384 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 15 Oct 2020 19:10:38 +0200 Subject: [PATCH 0033/2365] Remove problematic python2 packages --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 39 +++++++------------ 1 file changed, 15 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index fae6a3ac0e..95c964e8dd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -38,15 +38,15 @@ exts_default_options = { # order is important! # package versions updated 13 October 2020 exts_list = [ - ('pip', '20.2.3', { - 'use_pip': False, - 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], - }), ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', 'use_pip': False, 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], }), + ('pip', '20.2.3', { + 'use_pip': False, + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], }), @@ -223,8 +223,9 @@ exts_list = [ ('contextlib2', '0.6.0.post1', { 'checksums': ['01f490098c18b19d2bd5bb5dc445b2054d2fa97f09a4280ba2c5f3c394c8162e'], }), - ('importlib_metadata', '2.0.0', { - 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], + ('importlib-metadata', '1.7.0', { + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83'], }), ('pluggy', '0.13.1', { 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], @@ -236,6 +237,10 @@ exts_list = [ 'modulename': 'attr', 'checksums': ['26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594'], }), + ('backports.functools-lru-cache', '1.6.1', { + 'source_tmpl': 'backports.functools_lru_cache-%(version)s.tar.gz', + 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], + }), ('wcwidth', '0.2.5', { 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], }), @@ -303,9 +308,6 @@ exts_list = [ ('intervaltree', '3.1.0', { 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], }), - ('entrypoints', '0.3', { - 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], - }), ('functools32', '3.2.3-2', { 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), @@ -315,10 +317,6 @@ exts_list = [ ('glob2', '0.6', { 'checksums': ['f5b0a686ff21f820c4d3f0c4edd216704cea59d79d00fa337e244a2f2ff83ed6'], }), - ('importlib-metadata', '1.7.0', { - 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', - 'checksums': ['90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83'], - }), ('subprocess32', '3.5.4', { 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], }), @@ -342,14 +340,9 @@ exts_list = [ 'use_pip': False, 'checksums': ['442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59'], }), - ('SecretStorage', '2.3.1', { - 'checksums': ['3af65c87765323e6f64c83575b05393f9e003431959c9395d1791d51497f29b6'], - }), - ('keyring', '18.0.1', { - 'checksums': ['67d6cc0132bd77922725fae9f18366bb314fd8f95ff4d323a4df41890a96a838'], - }), - ('keyrings.alt', '3.2.0', { - 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], + ('entrypoints', '0.3', { + 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), ('tomlkit', '0.7.0', { 'use_pip': False, @@ -403,11 +396,9 @@ exts_list = [ 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('poetry-core', '1.0.0', { + 'modulename': 'poetry.core', 'checksums': ['6a664ff389b9f45382536f8fa1611a0cb4d2de7c5a5c885db1f0c600cd11fbd5'], }), - ('poetry', '1.1.3', { - 'checksums': ['49eae89e2c44b0323214d0bbcefc21ebe3a19baa44db98eefabd4db9e82c7253'], - }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], From 5d0d13c0777ef4b1201545b78dd6d33f4446f7b0 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 15 Oct 2020 19:30:58 +0200 Subject: [PATCH 0034/2365] Remove module check for 'futures' --- easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index 95c964e8dd..f8b07e20ea 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -312,6 +312,7 @@ exts_list = [ 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('futures', '3.3.0', { + 'modulename': False, 'checksums': ['7e033af76a5e35f58e56da7a91e687706faf4e7bdfb2cbc3f2cca6b9bcda9794'], }), ('glob2', '0.6', { From bd1e63760119b249fe4d52690c5eb399e0ed584e Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 16 Oct 2020 09:26:27 +0200 Subject: [PATCH 0035/2365] Address some review comments on python3 --- .../p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 434 ++++++++++++++++++ .../u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb | 52 +++ 2 files changed, 486 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..356b5e89b9 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -0,0 +1,434 @@ +name = 'Python' +version = '3.8.6' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21'] + +dependencies = [ + ('UnZip', '6.0'), +] + +dependencies = [ + ('binutils', '2.35'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('SQLite', '3.33.0'), + ('XZ', '5.2.5'), + ('GMP', '6.2.0'), # required for pycrypto + ('libffi', '3.3'), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +# symlink 'pip' command to 'pip3' that is included with Python installation +# required so we can update pip to version included in extensions, using pip +installopts = " && ln -s %(installdir)s/bin/pip3 %(installdir)s/bin/pip" + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + + +# order is important! +# package versions updated 13 October 2020 +exts_list = [ + ('pip', '20.2.3', { + 'use_pip': False, + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), + ('setuptools', '50.3.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['39060a59d91cf5cf403fa3bacbb52df4205a8c3585e0b9ba4b30e0e19d4c4b18'], + }), + ('wheel', '0.35.1', { + 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('paycheck', '1.0.2', { + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.5.0', { + 'checksums': ['14bfd98f51c78a3dd22a1ef45cf194ad79eee4a19e8e1a0d5c7f8e81ffe182ea'], + }), + ('Cython', '0.29.21', { + 'checksums': ['e57acb89bd55943c8d8bf813763d20b9099cc7165c0f16b707631a7654be9cad'], + }), + ('six', '1.15.0', { + 'checksums': ['30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259'], + }), + ('toml', '0.10.1', { + 'checksums': ['926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f'], + }), + ('setuptools_scm', '4.1.2', { + 'checksums': ['a8994582e716ec690f33fec70cca0f85bd23ec974e3f783233e4879090a7faa8'], + }), + ('python-dateutil', '2.8.1', { + 'modulename': 'dateutil', + 'checksums': ['73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c'], + }), + ('decorator', '4.4.2', { + 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], + 'checksums': [ + 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz + # pycrypto-2.6.1_remove-usr-include.patch + '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', + ], + }), + ('ecdsa', '0.16.0', { + 'checksums': ['494c6a853e9ed2e9be33d160b41d47afc50a6629b993d2b9c5ad7bb226add892'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.4.0', { + 'checksums': ['f4f6e119474e58e04a2b1af817eb585b4fd72bdd89b998624712b5c99be7641c'], + }), + ('idna', '2.10', { + 'checksums': ['b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6'], + }), + ('pycparser', '2.20', { + 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], + }), + ('cffi', '1.14.3', { + 'checksums': ['f92f789e4f9241cd262ad7a555ca2c648a98178a953af117ef7fad46aa1d5591'], + }), + ('cryptography', '3.1.1', { + 'checksums': ['9d9fc6a16357965d282dd4ab6531013935425d0dc4950df2e0cf2a1b1ac1017d'], + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.4.0', { + 'modulename': 'nacl', + 'checksums': ['54e9a2c849c742006516ad56a88f5c74bf2ce92c9f67435187c3c5953b346505'], + }), + ('bcrypt', '3.2.0', { + 'checksums': ['5b93c1726e50a93a033c36e5ca7fdcd29a5c7395af50a6892f5d9e7c6cfbfb29'], + }), + ('paramiko', '2.7.2', { + 'checksums': ['7f36f4ba2c0d81d219f4595e35f70d56cc94f9ac40a6acdf51d6ca210ce65035'], + }), + ('pyparsing', '2.4.7', { + 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], + }), + ('netifaces', '0.10.9', { + 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], + }), + ('netaddr', '0.8.0', { + 'checksums': ['d6cc57c7a07b1d9d2e917aa8b36ae8ce61c35ba3fcd1b83ca31c5a0ee2b5a243'], + }), + ('mock', '4.0.2', { + 'checksums': ['dd33eb70232b6118298d516bbcecd26704689c386594f0f3c4f13867b2c56f72'], + }), + ('pytz', '2020.1', { + 'checksums': ['c35965d010ce31b23eeb663ed3cc8c906275d6be1a34393a1d73a41febf4a048'], + }), + ('bitstring', '3.1.7', { + 'checksums': ['fdf3eb72b229d2864fb507f8f42b1b2c57af7ce5fec035972f9566de440a864a'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.1', { + 'source_tmpl': 'distlib-%(version)s.zip', + 'checksums': ['edf6116872c863e1aa9d5bb7cb5e05a022c519a4594dc703843343a9ddd9bff1'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('virtualenv', '20.0.34', { + 'checksums': ['4bf0e2bf99d33b123a895a5a244f0d7adb2a92171c6bbb31c3e2db235624abf1'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.17.0', { + 'checksums': ['9e284edd6be6b71883a63c9b7f124738a3c16195513ad940eae7e3438de885d5'], + }), + ('chardet', '3.0.4', { + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2020.6.20', { + 'checksums': ['5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3'], + }), + ('urllib3', '1.25.10', { + 'checksums': ['91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a'], + }), + ('requests', '2.24.0', { + 'checksums': ['b3559a131db72c33ee969480840fff4bb6dd111de7dd27c8ee1f820f4f00231b'], + }), + ('xlrd', '1.2.0', { + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('py_expression_eval', '0.3.10', { + 'checksums': ['43038326b686df697f9533895184c15d18769e215abbd8bcecaea607483f35b3'], + }), + ('tabulate', '0.8.7', { + 'checksums': ['db2723a20d04bcda8522165c73eea7c300eda74e0ce852d9022e0159d7895007'], + }), + ('ujson', '4.0.1', { + 'checksums': ['26cf6241b36ff5ce4539ae687b6b02673109c5e3efc96148806a7873eaa229d3'], + }), + ('atomicwrites', '1.4.0', { + 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], + }), + ('py', '1.9.0', { + 'checksums': ['9ca6883ce56b4e8da7e79ac18787889fa5206c79dcc67fb065376cd2fe03f342'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.5', { + 'checksums': ['6cd9a47b597b37cc57de1c05e56fb1a1c9cc9fab04fe78c29acd090418529868'], + }), + ('zipp', '3.3.0', { + 'checksums': ['64ad89efee774d1897a58607895d80789c59778ea02185dd846ac38394a8642b'], + }), + ('importlib_metadata', '2.0.0', { + 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('more-itertools', '8.5.0', { + 'checksums': ['6f83822ae94818eae2612063a5101a7311e68ae8002005b5e05f03fd74a86a20'], + }), + ('attrs', '20.2.0', { + 'modulename': 'attr', + 'checksums': ['26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594'], + }), + ('wcwidth', '0.2.5', { + 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], + }), + ('iniconfig', '1.0.1', { + 'checksums': ['e5f92f89355a67de0595932a6c6c02ab4afddc6fcdc0bfc5becd0d60884d3f69'], + }), + ('pytest', '6.1.1', { + 'checksums': ['8f593023c1a0f916110285b6efd7f99db07d59546e3d8c36fc60e2ab05d3be92'], + }), + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], + }), + ('sphinxcontrib-websupport', '1.2.4', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['4edf0223a0685a7c485ae5a156b6f529ba1ee481a1417817935b20bde1956232'], + }), + ('Pygments', '2.7.1', { + 'checksums': ['926c3f319eda178d1bd90851e4317e6d8cdb5e292a3386aac9bd75eca29cf9c7'], + }), + ('imagesize', '1.2.0', { + 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], + }), + ('docutils', '0.16', { + 'checksums': ['c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc'], + }), + ('snowballstemmer', '2.0.0', { + 'checksums': ['df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52'], + }), + ('Babel', '2.8.0', { + 'checksums': ['1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38'], + }), + ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('sphinxcontrib-applehelp', '1.0.2', { + 'modulename': 'sphinxcontrib.applehelp', + 'checksums': ['a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58'], + }), + ('sphinxcontrib-devhelp', '1.0.2', { + 'modulename': 'sphinxcontrib.devhelp', + 'checksums': ['ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4'], + }), + ('sphinxcontrib-htmlhelp', '1.0.3', { + 'modulename': 'sphinxcontrib.htmlhelp', + 'checksums': ['e8f5bb7e31b2dbb25b9cc435c8ab7a79787ebf7f906155729338f3156d93659b'], + }), + ('sphinxcontrib-jsmath', '1.0.1', { + 'modulename': 'sphinxcontrib.jsmath', + 'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'], + }), + ('sphinxcontrib-qthelp', '1.0.3', { + 'modulename': 'sphinxcontrib.qthelp', + 'checksums': ['4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72'], + }), + ('sphinxcontrib-serializinghtml', '1.1.4', { + 'modulename': 'sphinxcontrib.serializinghtml', + 'checksums': ['eaa0eccc86e982a9b939b2b82d12cc5d013385ba5eadcc7e4fed23f4405f77bc'], + }), + ('Sphinx', '3.2.1', { + 'checksums': ['321d6d9b16fa381a5306e5a0b76cd48ffbc588e6340059a729c6fdd66087e0e8'], + }), + ('sphinx-bootstrap-theme', '0.7.1', { + 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('psutil', '5.7.0', { + 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('sortedcontainers', '2.2.2', { + 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('flit-core', '3.0.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['a465052057e2d6d957e6850e9915245adedfc4fd0dd5737d0791bf3132417c2d'], + }), + ('flit', '3.0.0', { + 'checksums': ['b4fe0f84a1ffbf125d003e253ec98c0b6e3e31290b31fba3ad22d28588c20893'], + }), + ('regex', '2020.10.11', { + 'checksums': ['463e770c48da76a8da82b8d4a48a541f314e0df91cbb6d873a341dbe578efafd'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('crashtest', '0.3.1', { + 'use_pip': False, + 'checksums': ['42ca7b6ce88b6c7433e2ce47ea884e91ec93104a4b754998be498a8e6c3d37dd'], + }), + ('pylev', '1.3.0', { + 'checksums': ['063910098161199b81e453025653ec53556c1be7165a9b7c50be2f4d57eae1c3'], + }), + ('pastel', '0.2.1', { + 'use_pip': False, + 'checksums': ['e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d'], + }), + ('clikit', '0.6.2', { + 'use_pip': False, + 'checksums': ['442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59'], + }), + ('jeepney', '0.4.3', { + 'use_pip': False, + 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], + }), + ('SecretStorage', '3.1.2', { + 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], + }), + ('keyring', '21.4.0', { + 'modulename': False, + 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], + }), + ('keyrings.alt', '4.0.0', { + 'modulename': False, + 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], + }), + ('tomlkit', '0.7.0', { + 'use_pip': False, + 'checksums': ['ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618'], + }), + ('shellingham', '1.3.2', { + 'checksums': ['576c1982bea0ba82fb46c36feb951319d7f42214a82634233f58b40d858a751e'], + }), + ('requests-toolbelt', '0.9.1', { + 'checksums': ['968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0'], + }), + ('pyrsistent', '0.17.3', { + 'checksums': ['2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e'], + }), + ('pkginfo', '1.5.0.1', { + 'checksums': ['7424f2c8511c186cd5424bbf31045b77435b37a8d604990b79d4e70d741148bb'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('cleo', '0.8.1', { + 'use_pip': False, + 'checksums': ['3d0e22d30117851b45970b6c14aca4ab0b18b1b53c8af57bed13208147e4069f'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.0', { + 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], + }), + ('CacheControl', '0.12.6', { + 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], + }), + ('ptyprocess', '0.6.0', { + 'use_pip': False, + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.0.0', { + 'modulename': 'poetry.core', + 'checksums': ['6a664ff389b9f45382536f8fa1611a0cb4d2de7c5a5c885db1f0c600cd11fbd5'], + }), + ('poetry', '1.1.3', { + 'checksums': ['49eae89e2c44b0323214d0bbcefc21ebe3a19baa44db98eefabd4db9e82c7253'], + }), + ('fsspec', '0.8.4', { + 'checksums': ['e1e494d4814f6804769f3c7bfd7a722a15113cc0339d14755297f09306b8f21f'], + }), + ('threadpoolctl', '2.1.0', { + 'checksums': ['ddc57c96a38beb63db45d6c159b5ab07b6bced12c45a1f07b2b92f272aebfa6b'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..43ecaaf041 --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' +buildopts += 'LF2="$LDFLAGS" ' +# Note: CF is multiple lines +buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' +buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' +buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From a9f3c425824df9b9f4859b57fec64f94d75b7c23 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 16 Oct 2020 11:08:56 +0200 Subject: [PATCH 0036/2365] Fix various things. --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 17 ++++++++++++++++- .../p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 18 +++++++++--------- 2 files changed, 25 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index f8b07e20ea..9328a9011b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -36,7 +36,7 @@ exts_default_options = { } # order is important! -# package versions updated 13 October 2020 +# package versions updated 13 October 2020, to the most recent versions still supporting Python 2.x exts_list = [ ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', @@ -345,6 +345,18 @@ exts_list = [ 'use_pip': False, 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), + ('SecretStorage', '2.3.1', { + 'modulename': False, # Doesn't work properly under Python2, but is required for keyring + 'checksums': ['3af65c87765323e6f64c83575b05393f9e003431959c9395d1791d51497f29b6'], + }), + ('keyring', '18.0.1', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['67d6cc0132bd77922725fae9f18366bb314fd8f95ff4d323a4df41890a96a838'], + }), + ('keyrings.alt', '3.2.0', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], + }), ('tomlkit', '0.7.0', { 'use_pip': False, 'checksums': ['ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618'], @@ -400,6 +412,9 @@ exts_list = [ 'modulename': 'poetry.core', 'checksums': ['6a664ff389b9f45382536f8fa1611a0cb4d2de7c5a5c885db1f0c600cd11fbd5'], }), + ('poetry', '1.1.3', { + 'checksums': ['49eae89e2c44b0323214d0bbcefc21ebe3a19baa44db98eefabd4db9e82c7253'], + }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 356b5e89b9..4371dc3f09 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -8,11 +8,11 @@ description = """Python is a programming language that lets you work more quickl toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.%(namelower)s.org/ftp/%(namelower)s/%(version)s/'] +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21'] -dependencies = [ +builddependencies = [ ('UnZip', '6.0'), ] @@ -166,6 +166,9 @@ exts_list = [ ('filelock', '3.0.12', { 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], }), + ('importlib_metadata', '2.0.0', { + 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], + }), ('virtualenv', '20.0.34', { 'checksums': ['4bf0e2bf99d33b123a895a5a244f0d7adb2a92171c6bbb31c3e2db235624abf1'], }), @@ -214,9 +217,6 @@ exts_list = [ ('zipp', '3.3.0', { 'checksums': ['64ad89efee774d1897a58607895d80789c59778ea02185dd846ac38394a8642b'], }), - ('importlib_metadata', '2.0.0', { - 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], - }), ('pluggy', '0.13.1', { 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], }), @@ -303,8 +303,8 @@ exts_list = [ ('click', '7.1.2', { 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], }), - ('psutil', '5.7.0', { - 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], + ('psutil', '5.7.2', { + 'checksums': ['90990af1c3c67195c44c9a889184f84f5b2320dce3ee3acbd054e3ba0b4a7beb'], }), ('future', '0.18.2', { 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], @@ -354,11 +354,11 @@ exts_list = [ 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], }), ('keyring', '21.4.0', { - 'modulename': False, + 'modulename': False, # Doesn't work properly if HOME directory contains keys 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], }), ('keyrings.alt', '4.0.0', { - 'modulename': False, + 'modulename': False, # Doesn't work properly if HOME directory contains keys 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], }), ('tomlkit', '0.7.0', { From ece46b1eff8933589a8096ce3e52baa7dc6b2f36 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 16 Oct 2020 15:14:51 +0200 Subject: [PATCH 0037/2365] adding easyconfigs: Meson-0.55.3-GCCcore-10.2.0.eb, Ninja-1.10.1-GCCcore-10.2.0.eb --- .../m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ .../n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb | 29 +++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..deecc4136f --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.55.3' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6bed2a25a128bbabe97cf40f63165ebe800e4fcb46db8ab7ef5c2b5789f092a5'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Ninja', '1.10.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..82f318c76b --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.10.1' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a6b6f7ac360d4aabd54e299cc1d8fa7b234cd81b9401693da21221c62569a23e'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +moduleclass = 'tools' From a321d535e5729e33980023dbd6fac8e2481a3e40 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 14:24:14 +0200 Subject: [PATCH 0038/2365] adding easyconfigs: gettext-0.21-GCCcore-10.2.0.eb, X11-20201008-GCCcore-10.2.0.eb, Tk-8.6.10-GCCcore-10.2.0.eb, Tkinter-3.8.6-GCCcore-10.2.0.eb --- .../g/gettext/gettext-0.21-GCCcore-10.2.0.eb | 32 +++ .../t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb | 40 ++++ .../t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb | 24 ++ .../x/X11/X11-20201008-GCCcore-10.2.0.eb | 210 ++++++++++++++++++ 4 files changed, 306 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..97c0fd6787 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['66415634c6e8c3fa8b71362879ec7575e27da43da562c798a8a2f223e6e47f5c'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c72c3a8465 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.10' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + '63df418a859d0a463347f95ded5cd88a3dd3aaa1ceecaeee362194bc30f3e386', # tk8.6.10-src.tar.gz + '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch +] + +builddependencies = [('binutils', '2.35')] +dependencies = [ + ('Tcl', version), + ('X11', '20201008'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d6a0368905 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +name = 'Tkinter' +version = '3.8.6' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] + +builddependencies = [ + ('binutils', '2.35'), + ('libffi', '3.3'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Tk', '8.6.10'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b5b09e0694 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -0,0 +1,210 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20201008' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('Bison', '3.7.1'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('intltool', '0.51.0'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.13.92'), + ('freetype', '2.10.3'), + ('zlib', '1.2.11'), + ('xorg-macros', '1.19.2'), + ('libpciaccess', '0.16'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2020.1', { # 2020-04-14 + 'checksums': ['6265b11b125df2f4853eec4895b14067d5621f813553fa077bebef20d7542418'], + }), + ('libXau', '1.0.9', { # 2019-02-10 + 'checksums': ['1f123d8304b082ad63a9e89376400a3b1d4c29e67e3ea07b3f659cccca690eea'], + }), + ('libXdmcp', '1.1.3', { # 2019-03-16 + 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], + }), + ('xcb-proto', '1.14.1', { # 2020-10-08 + 'checksums': ['85cd21e9d9fbc341d0dbf11eace98d55d7db89fda724b0e598855fcddf0944fd'], + }), + ('libxcb', '1.14', { # 2020-02-22 + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2c7fcddd1da34d9b238c9caeda20d3bd7486456fc50b3cc6567185dbd5b0ad02'], + }), + ('xtrans', '1.4.0', { # 2019-03-16 + 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], + }), + ('libxkbcommon', '1.0.1', { # 2020-09-11 + 'easyblock': 'MesonNinja', + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'checksums': ['57c3630cdc38fb4734cd57fa349e92244f5ae3862813e533cedbd86721a0b6f2'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.6.12', { # 2020-08-24 + 'checksums': ['0fce5fc0a24a3dc728174eccd0cb8d6a1b37a2ec1654bd5628c84e5bc200d594'], + }), + ('libXext', '1.3.4', { # 2019-03-16 + 'checksums': ['8ef0789f282826661ff40a8eef22430378516ac580167da35cc948be9041aac1'], + }), + ('libFS', '1.0.8', { # 2019-03-10 + 'checksums': ['e3da723257f4f4c0c629aec402e0a36fbec66a9418f70d24a159cb0470ec83d2'], + }), + ('libICE', '1.0.10', { # 2019-07-14 + 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], + }), + ('libSM', '1.2.3', { # 2018-10-10 + 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], + }), + ('libXScrnSaver', '1.2.3', { # 2018-07-05 + 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], + }), + ('libXt', '1.2.0', { # 2019-06-21 + 'checksums': ['d4bee88898fc5e1dc470e361430c72fbc529b9cdbbb6c0ed3affea3a39f97d8d'], + }), + ('libXmu', '1.1.3', { # 2019-03-16 + 'checksums': ['5bd9d4ed1ceaac9ea023d86bf1c1632cd3b172dce4a193a72a94e1d9df87a62e'], + }), + ('libXpm', '3.5.13', { # 2019-12-13 + 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], + }), + ('libXaw', '1.0.13', { # 2015-05-01 + 'checksums': ['7e74ac3e5f67def549722ff0333d6e6276b8becd9d89615cda011e71238ab694'], + }), + ('libXfixes', '5.0.3', { # 2016-10-04 + 'checksums': ['9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570'], + }), + ('libXcomposite', '0.4.5', { # 2019-03-11 + 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], + }), + ('libXrender', '0.9.10', { # 2016-10-04 + 'checksums': ['770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf'], + }), + ('libXcursor', '1.2.0', { # 2019-03-11 + 'checksums': ['ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8'], + }), + ('libXdamage', '1.1.5', { # 2019-03-11 + 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], + }), + ('libfontenc', '1.1.4', { # 2019-02-20 + 'checksums': ['895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.4', { # 2019-09-14 + 'checksums': ['74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a'], + }), + ('libXft', '2.3.3', { # 2019-03-16 + 'checksums': ['3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701'], + }), + ('libXi', '1.7.10', { # 2019-06-19 + 'checksums': ['b51e106c445a49409f3da877aa2f9129839001b24697d75a54e5c60507e9a5e3'], + }), + ('libXinerama', '1.1.4', { # 2018-07-05 + 'checksums': ['64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18'], + }), + ('libXrandr', '1.5.2', { # 2019-03-16 + 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], + }), + ('libXres', '1.2.0', { # 2017-10-11 + 'checksums': ['5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a'], + }), + ('libXtst', '1.2.3', { # 2016-10-04 + 'checksums': ['a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2'], + }), + ('libXv', '1.0.11', { # 2016-10-04 + 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], + }), + ('libXvMC', '1.0.12', { # 2019-09-24 + 'checksums': ['024c9ec4f001f037eeca501ee724c7e51cf287eb69ced8c6126e16e7fa9864b5'], + }), + ('libXxf86dga', '1.1.5', { # 2019-03-16 + 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], + }), + ('libXxf86vm', '1.1.4', { # 2015-02-24 + 'checksums': ['5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99'], + }), + ('libdmx', '1.1.4', { # 2018-05-14 + 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], + }), + ('libxkbfile', '1.1.0', { # 2019-03-16 + 'checksums': ['2a92adda3992aa7cbad758ef0b8dfeaedebb49338b772c64ddf369d78c1c51d3'], + }), + ('libxshmfence', '1.3', { # 2018-02-26 + 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.0', { # 2014-10-15 + 'checksums': ['cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42'], + }), + ('xcb-util-keysyms', '0.4.0', { # 2014-10-01 + 'checksums': ['0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96'], + }), + ('xcb-util-renderutil', '0.3.9', { # 2014-06-13 + 'checksums': ['55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5'], + }), + ('xcb-util-wm', '0.4.1', { # 2014-02-19 + 'checksums': ['038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334'], + }), + ('xcb-util-cursor', '0.1.3', { # 2016-05-12 + 'checksums': ['a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8'], + }), + ('xkeyboard-config', '2.28', { # 2019-10-19 + 'checksums': ['4424ffaafdf9f09dea69a317709353c4e2b19f69b2405effadce0bac3bdebdff'], + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.3', { # 2015-02-21 + 'checksums': ['f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c'], + }), + ('xbitmaps', '1.1.2', { # 2018-03-10 + 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From dc1a4dcad8c143529859189da883de6d3b37e421 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 14:45:40 +0200 Subject: [PATCH 0039/2365] Update checksum in Tkinter --- easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb index d6a0368905..c015497455 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb @@ -9,6 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.python.org/ftp/python/%(version)s/'] sources = ['Python-%(version)s.tgz'] +checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21'] builddependencies = [ ('binutils', '2.35'), From fb3579d18d215dfc92249252c520cf2b6d4ea0ea Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 15:36:13 +0200 Subject: [PATCH 0040/2365] Fix checksum in gettext --- easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb index 97c0fd6787..e0d0f8a84f 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['66415634c6e8c3fa8b71362879ec7575e27da43da562c798a8a2f223e6e47f5c'] +checksums = ['c77d0da3102aec9c07f43671e60611ebff89a996ef159497ce8e59d075786b12'] builddependencies = [('binutils', '2.35')] From ecb7794d4e6132baeffdf14f2ec583bfa3b5c4e4 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 15:50:37 +0200 Subject: [PATCH 0041/2365] Fix checksum on extension in X11 --- .../x/X11/X11-20201008-GCCcore-10.2.0.eb | 35 ++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb index b5b09e0694..3b1816070c 100644 --- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -16,6 +16,39 @@ source_urls = [ XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] +checksums = [ + '9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570', # libXfixes-5.0.3.tar.gz + '581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c', # libXcomposite-0.4.5.tar.gz + '770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf', # libXrender-0.9.10.tar.gz + 'ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8', # libXcursor-1.2.0.tar.gz + '630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019', # libXdamage-1.1.5.tar.gz + '895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41', # libfontenc-1.1.4.tar.gz + '59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e', # libXfont-1.5.4.tar.gz + '74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a', # libXfont2-2.0.4.tar.gz + '3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701', # libXft-2.3.3.tar.gz + 'b51e106c445a49409f3da877aa2f9129839001b24697d75a54e5c60507e9a5e3', # libXi-1.7.10.tar.gz + '64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18', # libXinerama-1.1.4.tar.gz + '3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e', # libXrandr-1.5.2.tar.gz + '5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a', # libXres-1.2.0.tar.gz + 'a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2', # libXtst-1.2.3.tar.gz + 'c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1', # libXv-1.0.11.tar.gz + '024c9ec4f001f037eeca501ee724c7e51cf287eb69ced8c6126e16e7fa9864b5', # libXvMC-1.0.12.tar.gz + '715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69', # libXxf86dga-1.1.5.tar.gz + '5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99', # libXxf86vm-1.1.4.tar.gz + '4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925', # libdmx-1.1.4.tar.gz + '2a92adda3992aa7cbad758ef0b8dfeaedebb49338b772c64ddf369d78c1c51d3', # libxkbfile-1.1.0.tar.gz + '7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c', # libxshmfence-1.3.tar.gz + '0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7', # xcb-util-0.4.0.tar.gz + 'cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42', # xcb-util-image-0.4.0.tar.gz + '0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96', # xcb-util-keysyms-0.4.0.tar.gz + '55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5', # xcb-util-renderutil-0.3.9.tar.gz + '038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334', # xcb-util-wm-0.4.1.tar.gz + 'a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8', # xcb-util-cursor-0.1.3.tar.gz + '4424ffaafdf9f09dea69a317709353c4e2b19f69b2405effadce0bac3bdebdff', # xkeyboard-config-2.28.tar.gz + 'e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc', # printproto-1.0.5.tar.gz + 'f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c', # libXp-1.0.3.tar.gz + '27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265', # xbitmaps-1.1.2.tar.gz +] builddependencies = [ ('binutils', '2.35'), @@ -70,7 +103,7 @@ components = [ ('libxkbcommon', '1.0.1', { # 2020-09-11 'easyblock': 'MesonNinja', 'sources': ['libxkbcommon-%(version)s.tar.xz'], - 'checksums': ['57c3630cdc38fb4734cd57fa349e92244f5ae3862813e533cedbd86721a0b6f2'], + 'checksums': ['ab68b25341c99f2218d7cf3dad459c1827f411219901ade05bbccbdb856b6c8d'], 'preconfigopts': '', 'configopts': '-Denable-wayland=false -Denable-docs=false ', }), From 69ee71cf706079a39526289e94cb85e9c541f894 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 15:52:28 +0200 Subject: [PATCH 0042/2365] Remove duplicate checksum block in X11 (incorrectly created by inject checksums) --- .../x/X11/X11-20201008-GCCcore-10.2.0.eb | 33 ------------------- 1 file changed, 33 deletions(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb index 3b1816070c..041c9f6a6a 100644 --- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -16,39 +16,6 @@ source_urls = [ XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] -checksums = [ - '9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570', # libXfixes-5.0.3.tar.gz - '581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c', # libXcomposite-0.4.5.tar.gz - '770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf', # libXrender-0.9.10.tar.gz - 'ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8', # libXcursor-1.2.0.tar.gz - '630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019', # libXdamage-1.1.5.tar.gz - '895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41', # libfontenc-1.1.4.tar.gz - '59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e', # libXfont-1.5.4.tar.gz - '74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a', # libXfont2-2.0.4.tar.gz - '3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701', # libXft-2.3.3.tar.gz - 'b51e106c445a49409f3da877aa2f9129839001b24697d75a54e5c60507e9a5e3', # libXi-1.7.10.tar.gz - '64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18', # libXinerama-1.1.4.tar.gz - '3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e', # libXrandr-1.5.2.tar.gz - '5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a', # libXres-1.2.0.tar.gz - 'a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2', # libXtst-1.2.3.tar.gz - 'c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1', # libXv-1.0.11.tar.gz - '024c9ec4f001f037eeca501ee724c7e51cf287eb69ced8c6126e16e7fa9864b5', # libXvMC-1.0.12.tar.gz - '715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69', # libXxf86dga-1.1.5.tar.gz - '5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99', # libXxf86vm-1.1.4.tar.gz - '4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925', # libdmx-1.1.4.tar.gz - '2a92adda3992aa7cbad758ef0b8dfeaedebb49338b772c64ddf369d78c1c51d3', # libxkbfile-1.1.0.tar.gz - '7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c', # libxshmfence-1.3.tar.gz - '0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7', # xcb-util-0.4.0.tar.gz - 'cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42', # xcb-util-image-0.4.0.tar.gz - '0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96', # xcb-util-keysyms-0.4.0.tar.gz - '55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5', # xcb-util-renderutil-0.3.9.tar.gz - '038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334', # xcb-util-wm-0.4.1.tar.gz - 'a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8', # xcb-util-cursor-0.1.3.tar.gz - '4424ffaafdf9f09dea69a317709353c4e2b19f69b2405effadce0bac3bdebdff', # xkeyboard-config-2.28.tar.gz - 'e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc', # printproto-1.0.5.tar.gz - 'f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c', # libXp-1.0.3.tar.gz - '27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265', # xbitmaps-1.1.2.tar.gz -] builddependencies = [ ('binutils', '2.35'), From e13ed75869cbe556a6acdea511f4f3c3f7e10e24 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 17:03:11 +0200 Subject: [PATCH 0043/2365] adding easyconfigs: Szip-2.1.1-GCCcore-10.2.0.eb, pigz-2.4-GCCcore-10.2.0.eb, gzip-1.10-GCCcore-10.2.0.eb, lz4-1.9.2-GCCcore-10.2.0.eb, zstd-1.4.5-GCCcore-10.2.0.eb --- .../g/gzip/gzip-1.10-GCCcore-10.2.0.eb | 24 ++++++++ .../l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb | 30 ++++++++++ .../p/pigz/pigz-2.4-GCCcore-10.2.0.eb | 55 +++++++++++++++++++ .../s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb | 29 ++++++++++ .../z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb | 41 ++++++++++++++ 5 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a046e06c02 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.10' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c91f74430bf7bc20402e1f657d0b252cb80aa66ba333a25704512af346633c68'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b30c960112 --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.2' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['658ba6191fa44c92280d4aa2c271b0f4fbc0e34d249578dd05e50e76d0e5efcc'] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a660349126 --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-10.2.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# +# 2.4.0: +# Jonas Demeulemeester +# The Francis Crick Institute +## +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.4' + +homepage = 'https://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://zlib.net/pigz/', + 'https://zlib.net/pigz/fossils/', +] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + 'a4f816222a7b4269bd232680590b579ccc72591f1bb5adafcd7208ca77e14f73', # pigz-2.4.tar.gz + '8de19216a69b6402942f73177c566791f0c7fa4649376029d30d0c537d2195c1', # pigz-2.4_makefile.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..88e067c36e --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..af251418ce --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.4.5' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['734d1f565c42f691f8420c8d06783ad818060fc390dee43ae0a89f86d0a4f8c2'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('XZ', '5.2.5'), + ('lz4', '1.9.2'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From c6620c99b76c1d5527bb7707df61deec9e199562 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 17:17:01 +0200 Subject: [PATCH 0044/2365] Add more compression libs --- .../l/LZO/LZO-2.10-GCCcore-10.2.0.eb | 36 +++++++++++++++++ .../z/Zip/Zip-3.0-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2898f75e50 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.35')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..16af667205 --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' From 21c2ad6478acd9943fff0545d0c28e5acafce371 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 14:18:42 +0200 Subject: [PATCH 0045/2365] adding easyconfigs: re2c-2.0.3-GCCcore-10.2.0.eb, PCRE2-10.35-GCCcore-10.2.0.eb, double-conversion-3.1.5-GCCcore-10.2.0.eb, PCRE-8.44-GCCcore-10.2.0.eb, DBus-1.13.18-GCCcore-10.2.0.eb, libGLU-9.0.1-GCCcore-10.2.0.eb, GLib-2.66.1-GCCcore-10.2.0.eb, NASM-2.15.05-GCCcore-10.2.0.eb, libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb, snappy-1.1.8-GCCcore-10.2.0.eb, NSPR-4.29-GCCcore-10.2.0.eb, NSS-3.57-GCCcore-10.2.0.eb, JasPer-2.0.14-GCCcore-10.2.0.eb --- .../d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb | 42 +++++++++++++++ .../double-conversion-3.1.5-GCCcore-10.2.0.eb | 38 ++++++++++++++ .../g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb | 52 +++++++++++++++++++ .../l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb | 27 ++++++++++ .../libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb | 42 +++++++++++++++ .../n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb | 37 +++++++++++++ .../n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb | 28 ++++++++++ .../n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 49 +++++++++++++++++ .../p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb | 45 ++++++++++++++++ .../p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb | 28 ++++++++++ .../r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb | 25 +++++++++ .../s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb | 29 +++++++++++ 12 files changed, 442 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0073dcb0f0 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.13.18' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7588649b56dd257c6a5f85a8c45aa2dfdf9e99f4de3983710f452081ca43eca6'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('expat', '2.2.9'), +] + +configopts = '--without-systemdsystemunitdir' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..23fc1b1e9f --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.1.5' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a63ecb93182134ba4293fd5f22d6e08ca417caafa244afaa751cbfddf6415b13'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +separate_build_dir = True + +build_type = 'Release' + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', + '-DBUILD_SHARED_LIBS=ON' +] + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f45c527ed4 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.66.1' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['a269ffe69fbcc3a21ff1acb1b6146b2a5723499d6e2de33ae16ccb6d2438ef60'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.8.6'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libffi', '3.3'), + ('gettext', '0.21'), + ('libxml2', '2.9.10'), + ('PCRE', '8.44'), + ('util-linux', '2.36'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..84bcd5868f --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.1' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.gz'] +checksums = ['f6f484cfcd51e489afe88031afdea1e173aa652697e4c19ddbcb8260579a10f7'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ +# ('Mesa', '20.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5ab669488d --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.0.5' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['33dd8547efd5543639e890efbf2ef52d5a21df81faf41bb940657af916a23406'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('NASM', '2.15.05'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..16ff10f655 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.15.05' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['34fd26c70a277a9fdd54cb5ecf389badedaf48047b269d1008fbc819b24e80bc'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a796b4e421 --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.29' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://archive.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['22286bdb8059d74632cc7c2865c139e63953ecfb33bf4362ab58827e86e92582'] + +builddependencies = [('binutils', '2.35')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0f2b08e1b5 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.57' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + '%(name)s-%(version)s_fix_kremlin_ppc64le.patch', +] +checksums = [ + '75348b3b3229362486c57a880db917da1f96ef4eb639dc9cc2ff17d72268459c', # nss-3.51.tar.gz + '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + '2fc7bd556737d34a62c06f86899863b7071b71943ffb4facfb413a087b8bee2e', # NSS-3.51_fix_kremlin_ppc64le.patch +] + +builddependencies = [('binutils', '2.35')] +dependencies = [ + ('NSPR', '4.29'), + ('zlib', '1.2.11'), +] + +# building in parallel fails +parallel = 1 + +# fix for not being able to find header files +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['lib/libnss.a'], + 'dirs': ['bin', 'include/dbm', 'include/nss'], +} + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1dec4bf1fa --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.44' + +homepage = 'https://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.pcre.org/pub/pcre/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aecafd4af3bd0f3935721af77b889d9024b2e01d96b58471bd91a3063fb47728'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +configopts = """\ + --enable-utf\ + --enable-unicode-properties\ + --enable-pcre16\ + --enable-pcre32\ +""" + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..af6d2eaca8 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.35' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.sourceforge.net/pcre'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8fdcef8c8f4cd735169dd0225fd010487970c1bcadd49e9b90e26c7250a33dc9'] + +builddependencies = [('binutils', '2.35')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dba73c221f --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '2.0.3' + +homepage = 'https://re2c.org/' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['b2bc1eb8aaaa21ff2fcd26507b7e6e72c5e3d887e58aa515c2155fb17d744278'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/re2c'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4397a7c987 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.8' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['16b677f07832a612b0836178db7f374e414f94657c138e6993cbfc5dcc58651f'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = ['', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [''] +} + +moduleclass = 'lib' From e9476673327ec98e0cb75b19f741ffe6540d0b81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 18 Oct 2020 14:33:07 +0200 Subject: [PATCH 0046/2365] update to OpenBLAS 0.3.11 as foss/2020b component --- easybuild/easyconfigs/f/foss/foss-2020b.eb | 2 +- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/foss/foss-2020b.eb b/easybuild/easyconfigs/f/foss/foss-2020b.eb index f423f25efa..ba9f8d9d17 100644 --- a/easybuild/easyconfigs/f/foss/foss-2020b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2020b.eb @@ -19,7 +19,7 @@ local_comp_mpi_tc = ('gompi', version) dependencies = [ ('GCC', local_gccver), ('OpenMPI', '4.0.5', '', ('GCC', local_gccver)), - ('OpenBLAS', '0.3.10', '', ('GCC', local_gccver)), + ('OpenBLAS', '0.3.11', '', ('GCC', local_gccver)), ('FFTW', '3.3.8', '', local_comp_mpi_tc), ('ScaLAPACK', '2.1.0', '', local_comp_mpi_tc), ] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb index af6cec3942..9d606926ff 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb @@ -16,6 +16,6 @@ checksums = [ 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch ] -dependencies = [('OpenBLAS', '0.3.10')] +dependencies = [('OpenBLAS', '0.3.11')] moduleclass = 'numlib' From 17cd8e172424c040c43cda8f17dbe736bfdf8763 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 14:41:59 +0200 Subject: [PATCH 0047/2365] Fix checksum in libjpeg-turbo --- .../l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb index 5ab669488d..1214eaa1d2 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['33dd8547efd5543639e890efbf2ef52d5a21df81faf41bb940657af916a23406'] +checksums = ['16f8f6f2715b3a38ab562a84357c793dd56ae9899ce130563c72cd93d8357b5d'] builddependencies = [ ('CMake', '3.18.4'), From 36ed5721b28d2b42180cd40d556ceb3355a58ae4 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 15:02:28 +0200 Subject: [PATCH 0048/2365] Remove incomplete easyconfig --- .../l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb deleted file mode 100644 index 84bcd5868f..0000000000 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libGLU' -version = '9.0.1' - -homepage = 'https://mesa.freedesktop.org/archive/glu/' -description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://mesa.freedesktop.org/archive/glu/'] -sources = ['glu-%(version)s.tar.gz'] -checksums = ['f6f484cfcd51e489afe88031afdea1e173aa652697e4c19ddbcb8260579a10f7'] - -builddependencies = [('binutils', '2.35')] - -dependencies = [ -# ('Mesa', '20.0.2'), -] - -sanity_check_paths = { - 'files': ['lib/libGLU.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' From 38bf8f818ce8fdec9e2c2e2136ff643ddee1b6bd Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 15:16:56 +0200 Subject: [PATCH 0049/2365] Drop seemingly outdated patch from NSS --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 0f2b08e1b5..a0e6062edb 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -13,7 +13,6 @@ source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_ sources = [SOURCELOWER_TAR_GZ] patches = [ 'NSS-3.39_pkgconfig.patch', - '%(name)s-%(version)s_fix_kremlin_ppc64le.patch', ] checksums = [ '75348b3b3229362486c57a880db917da1f96ef4eb639dc9cc2ff17d72268459c', # nss-3.51.tar.gz From f2b4742b291f2c20190400d18c264bd0ecfa20c4 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 15:25:01 +0200 Subject: [PATCH 0050/2365] Update checksums in NSS 3.57 --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index a0e6062edb..528d124955 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -15,9 +15,8 @@ patches = [ 'NSS-3.39_pkgconfig.patch', ] checksums = [ - '75348b3b3229362486c57a880db917da1f96ef4eb639dc9cc2ff17d72268459c', # nss-3.51.tar.gz + '55a86c01be860381d64bb4e5b94eb198df9b0f098a8af0e58c014df398bdc382', # nss-3.57.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch - '2fc7bd556737d34a62c06f86899863b7071b71943ffb4facfb413a087b8bee2e', # NSS-3.51_fix_kremlin_ppc64le.patch ] builddependencies = [('binutils', '2.35')] From fe89413a8188649fbd9d74a903d99670a2d762ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 18 Oct 2020 17:33:29 +0200 Subject: [PATCH 0051/2365] Update easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb index 16ff10f655..27a05a06c8 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['34fd26c70a277a9fdd54cb5ecf389badedaf48047b269d1008fbc819b24e80bc'] +checksums = ['3c4b8339e5ab54b1bcb2316101f8985a5da50a3f9e504d43fa6f35668bee2fd0'] builddependencies = [ ('binutils', '2.35'), From a51be18324f7fde2d7d69a24899afe2589d52d58 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 18:02:44 +0200 Subject: [PATCH 0052/2365] adding easyconfigs: git-2.28.0-GCCcore-10.2.0-nodocs.eb --- .../g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb diff --git a/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb new file mode 100644 index 0000000000..d47acd98a7 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.28.0' +versionsuffix = '-nodocs' + +homepage = 'https://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7d84f5d6f48e95b467a04a8aa1d474e0d21abc7877998af945568d2634fea46a'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +dependencies = [ + ('cURL', '7.72.0'), + ('expat', '2.2.9'), + ('gettext', '0.21'), + ('Perl', '5.32.0'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' From a6e1329bcf380da20c0c5f391b51ee5039354633 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 18 Oct 2020 19:19:11 +0200 Subject: [PATCH 0053/2365] Update easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb index 0073dcb0f0..83b477ea36 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb @@ -18,7 +18,7 @@ toolchainopts = {'pic': True} source_urls = ['https://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['7588649b56dd257c6a5f85a8c45aa2dfdf9e99f4de3983710f452081ca43eca6'] +checksums = ['8078f5c25e34ab907ce06905d969dc8ef0ccbec367e1e1707c7ecf8460f4254e'] builddependencies = [ ('binutils', '2.35'), From 5fd9dfa62b4f511a9039f13cebde9f69ccacc086 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 19:59:15 +0200 Subject: [PATCH 0054/2365] Include comment on NSS test suite --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 528d124955..0635704817 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -34,6 +34,8 @@ buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] From 520bba4f0f81bc1083c50f9aa3f2782ef740ec7f Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 20:23:19 +0200 Subject: [PATCH 0055/2365] Fix checksum --- easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb index d47acd98a7..0ca0d915f4 100644 --- a/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/git/git/archive'] sources = ['v%(version)s.tar.gz'] -checksums = ['7d84f5d6f48e95b467a04a8aa1d474e0d21abc7877998af945568d2634fea46a'] +checksums = ['02016d16dbce553699db5c9c04f6d13a3f50727c652061b7eb97a828d045e534'] builddependencies = [ ('binutils', '2.35'), From bb3a417ac5303d757fadbf938ab452d6968e8d51 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 22:43:34 +0200 Subject: [PATCH 0056/2365] adding easyconfigs: LLVM-11.0.0-GCCcore-10.2.0.eb --- .../l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..88f9f8de51 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +name = 'LLVM' +version = '11.0.0' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['913f68c898dfb4a03b397c5e11c6a2f39d0f22ed7665c9cefa87a34423a72469'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +moduleclass = 'compiler' From 6de8d6fac39444a232e80de2898027f8fe564d6e Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 23:12:37 +0200 Subject: [PATCH 0057/2365] adding easyconfigs: APR-1.7.0-GCCcore-10.2.0.eb, APR-util-1.6.1-GCCcore-10.2.0.eb, utf8proc-2.5.0-GCCcore-10.2.0.eb, SCons-4.0.1-GCCcore-10.2.0.eb, Serf-1.3.9-GCCcore-10.2.0.eb, Subversion-1.14.0-GCCcore-10.2.0.eb --- .../APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb | 32 ++++++++++++ .../a/APR/APR-1.7.0-GCCcore-10.2.0.eb | 22 +++++++++ .../s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb | 35 +++++++++++++ .../s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb | 39 +++++++++++++++ .../Subversion-1.14.0-GCCcore-10.2.0.eb | 49 +++++++++++++++++++ .../utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb | 30 ++++++++++++ 6 files changed, 207 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4934bcbe29 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.1' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('APR', '1.7.0'), + ('SQLite', '3.33.0'), + ('expat', '2.2.9'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c3a8371d34 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.0' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6a8b8a9de3 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '4.0.1' + +homepage = 'https://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['SCons-3.0.4_fix-pip-install.patch'] +checksums = [ + '722ed104b5c624ecdc89bd4e02b094d2b14d99d47b5d0501961e47f579a2007c', # scons-4.0.1.tar.gz + 'c632a50184edbb0dc032943fd717e832577d4ad407eb7743e5331eddb842a69f', # SCons-3.0.4_fix-pip-install.patch +] + +builddependencies = [('binutils', '2.35')] + +multi_deps = {'Python': ['3.8.6', '2.7.18']} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': [], +} + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..710686c4a7 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'SCons' +name = 'Serf' +version = '1.3.9' + +homepage = 'https://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '2.7.18'), # Serfs build scripts are python 2 only + ('SCons', '4.0.1'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it is nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fac1a9e08c --- /dev/null +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'Subversion' +version = '1.14.0' + +homepage = 'https://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://apache.belnet.be/%(namelower)s', + 'http://www.eu.apache.org/dist/%(namelower)s', + 'http://www.us.apache.org/dist/%(namelower)s', + 'https://archive.apache.org/dist/%(namelower)s', +] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Subversion-1.12.0-no_swig.patch'] +checksums = [ + '6ba8e218f9f97a83a799e58a3c6da1221d034b18d9d8cbbcb6ec52ab11722102', # subversion-1.14.0.tar.bz2 + '539ea2118f958d152d78438c81649eb727ff0b2e8491295702ee98e1f922041f', # Subversion-1.12.0-no_swig.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('SQLite', '3.33.0'), + ('zlib', '1.2.11'), + ('lz4', '1.9.2'), + ('utf8proc', '2.5.0'), + ('Serf', '1.3.9'), +] + +preconfigopts = './autogen.sh && ' + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-lz4=$EBROOTLZ4 --with-serf=$EBROOTSERF" + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..28be3ea21d --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.5.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d4e8dfc898cfd062493cb7f42d95d70ccdd3a4cd4d90bec0c71b47cca688f1be'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 2fde0448ae1e1e1825622521efe739141d8e8ca7 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 19 Oct 2020 00:44:56 +0200 Subject: [PATCH 0058/2365] Drop python2 --- .../easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb | 6 ++---- easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb | 8 ++++++-- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb index 6a8b8a9de3..ed589a49fb 100644 --- a/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb @@ -10,22 +10,20 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['SCons-3.0.4_fix-pip-install.patch'] checksums = [ '722ed104b5c624ecdc89bd4e02b094d2b14d99d47b5d0501961e47f579a2007c', # scons-4.0.1.tar.gz - 'c632a50184edbb0dc032943fd717e832577d4ad407eb7743e5331eddb842a69f', # SCons-3.0.4_fix-pip-install.patch ] builddependencies = [('binutils', '2.35')] -multi_deps = {'Python': ['3.8.6', '2.7.18']} +dependencies = [('Python', '3.8.6')] download_dep_fail = True use_pip = True sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'files': ['bin/scons', 'bin/sconsign'], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb index 710686c4a7..d58e446520 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb @@ -10,11 +10,15 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://archive.apache.org/dist/%(namelower)s'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc'] +patches =['Serf-%(version)s_python3_scons.patch'] +checksums = [ + '549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc', # serf-1.3.9.tar.bz2 + 'db401893bfb464ddcf369b543cacb9a165a21f8ff9bf1a819e4b61550bb9d3d0', # Serf-1.3.9_python3_scons.patch +] builddependencies = [ ('binutils', '2.35'), - ('Python', '2.7.18'), # Serfs build scripts are python 2 only + ('Python', '3.8.6'), ('SCons', '4.0.1'), ] From 4a38c08a572e5b491c1e09de9da3ead457ab0b51 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 19 Oct 2020 00:46:45 +0200 Subject: [PATCH 0059/2365] adding easyconfigs: libGLU-9.0.1-GCCcore-10.2.0.eb, libdrm-2.4.102-GCCcore-10.2.0.eb, libglvnd-1.2.0-GCCcore-10.2.0.eb, libunwind-1.4.0-GCCcore-10.2.0.eb, Mako-1.1.3-GCCcore-10.2.0.eb, Mesa-20.2.1-GCCcore-10.2.0.eb --- .../l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb | 27 +++++++ .../l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb | 22 ++++++ .../libunwind-1.4.0-GCCcore-10.2.0.eb | 36 +++++++++ .../m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb | 27 +++++++ .../m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb | 73 +++++++++++++++++++ 5 files changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cea272ad1b --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.1' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.gz'] +checksums = ['f6f484cfcd51e489afe88031afdea1e173aa652697e4c19ddbcb8260579a10f7'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Mesa', '20.2.1'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2aae368ccb --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +name = 'libdrm' +version = '2.4.102' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['8bcbf9336c28e393d76c1f16d7e79e394a7fce8a2e929d52d3ad7ad8525ba05b'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] +dependencies = [('X11', '20201008')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '--disable-manpages' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c0a7684fce --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.4.0' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['libunwind-1.3.1_fix_ppc64_fpreg_t.patch'] +checksums = [ + 'df59c931bd4d7ebfd83ee481c943edf015138089b8e50abed8d9c57ba9338435', # libunwind-1.4.0.tar.gz + '61a507eec7ece286b06be698c742f0016d8c605eaeedf34f451cf1d0e510ec86', # libunwind-1.3.1_fix_ppc64_fpreg_t.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('XZ', '5.2.5'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7ac3876f78 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.1.3' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8195c8c1400ceb53496064314c6736719c6f25e7479cd24c77be3d9361cddc27'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +builddependencies = [('binutils', '2.35')] +multi_deps = {'Python': ['3.8.6', '2.7.18']} + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..218127da18 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,73 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers are enabled based on system architecture: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# Default renderer is llvmpipe. SWR can be enabled by setting the environment +# variable GALLIUM_DRIVER=swr + +name = 'Mesa' +version = '20.2.1' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +patches = ['%(name)s-20.0.2-match-swrast-loosely.patch'] +checksums = [ + 'd1a46d9a3f291bc0e0374600bdcb59844fa3eafaa50398e472a36fc65fd0244a', # mesa-20.2.1.tar.xz + 'e86abc2b9a9ad3e2fc604ad5d9bfe15a62e842e9900365fe7061849ea7438d90', # Mesa-20.0.2-match-swrast-loosely.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('pkg-config', '0.29.2'), + ('Mako', '1.1.3'), + ('libxml2', '2.9.10'), + ('expat', '2.2.9'), + ('gettext', '0.21'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('zstd', '1.4.5'), + ('libdrm', '2.4.102'), + ('libglvnd', '1.2.0'), + ('libunwind', '1.4.0'), + ('LLVM', '11.0.0'), + ('X11', '20201008'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=gallium -Ddri-drivers='' -Dvulkan-drivers='' " +configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast,swr -Dswr-arches=avx,avx2,skx,knl" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +# Tells libglvnd where to find EGL libraries +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} + +moduleclass = 'vis' From 6cab7a5232c48757fa9844b4ae0b9015045deba6 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 19 Oct 2020 01:35:15 +0200 Subject: [PATCH 0060/2365] fix style --- easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb index d58e446520..80f595ab28 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://archive.apache.org/dist/%(namelower)s'] sources = [SOURCELOWER_TAR_BZ2] -patches =['Serf-%(version)s_python3_scons.patch'] +patches = ['Serf-%(version)s_python3_scons.patch'] checksums = [ '549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc', # serf-1.3.9.tar.bz2 'db401893bfb464ddcf369b543cacb9a165a21f8ff9bf1a819e4b61550bb9d3d0', # Serf-1.3.9_python3_scons.patch From 3c43e3c74aba26f026cdbdf78be60f2e6fb35c1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 19 Oct 2020 12:13:02 +0200 Subject: [PATCH 0061/2365] add CMake build dep for ScaLAPACK 2.1.0 built with gompi/2020b --- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb index 9d606926ff..7d4d9145e8 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb @@ -16,6 +16,8 @@ checksums = [ 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch ] +builddependencies = [('CMake', '3.18.4')] + dependencies = [('OpenBLAS', '0.3.11')] moduleclass = 'numlib' From 62a9882fc59989d5130be52cbad91705cdc391b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 19 Oct 2020 22:05:39 +0200 Subject: [PATCH 0062/2365] {devel,lib,system,tools}[GCCcore/10.2.0] OpenPGM v5.2.122, ZeroMQ v4.3.3, IPython v7.18.1, JupyterLab v2.2.8 ... w/ Python 3.8.6 (#11526) * adding easyconfigs: OpenPGM-5.2.122-GCCcore-10.2.0.eb, ZeroMQ-4.3.3-GCCcore-10.2.0.eb, IPython-7.18.1-GCCcore-10.2.0.eb, libsodium-1.0.18-GCCcore-10.2.0.eb * Add jupyterlab, fix deps and checksums * Add missing checksum to jupyterlab * Revert OpenPGM back to python 2.7.18 build dep. * Use pip for updated terminado * Include JUPYTERLAB_DIR env variable Co-authored-by: c3-micke --- .../IPython/IPython-7.18.1-GCCcore-10.2.0.eb | 144 ++++++++++++++++++ .../JupyterLab-2.2.8-GCCcore-10.2.0.eb | 48 ++++++ .../libsodium-1.0.18-GCCcore-10.2.0.eb | 33 ++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb | 37 +++++ .../z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb | 38 +++++ 5 files changed, 300 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a4b5534503 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb @@ -0,0 +1,144 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '7.18.1' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('ZeroMQ', '4.3.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['a331e78086001931de9424940699691ad49dfb457cea31f5471eae7b78222d5e'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '3.0.7', { + 'checksums': ['822f4605f28f7d2ba6b0b09a31e25e140871e96364d1d377667b547bb3bf4489'], + }), + ('traitlets', '5.0.4', { + 'checksums': ['86c9351f94f95de9db8a04ad8e892da299a088a64fd283f9f6f18770ae5eae1b'], + }), + ('parso', '0.7.1', { + 'checksums': ['caba44724b994a8a5e086460bb212abc5a8bc46951bf4a9a1210745953622eb9'], + }), + ('jedi', '0.17.2', { + 'checksums': ['86ed7d9b750603e4ba582ea8edc678657fb4007894a12bcf6f4bb97892f31d20'], + }), + ('testpath', '0.4.4', { + 'use_pip': False, + 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], + }), + ('Send2Trash', '1.5.0', { + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('bleach', '3.2.1', { + 'checksums': ['52b5919b81842b1854196eaae5ca29679a2f2e378905c346d3ca8227c2c66080'], + }), + ('pandocfilters', '1.4.2', { + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('pyzmq', '19.0.2', { + 'modulename': 'zmq', + 'checksums': ['296540a065c8c21b26d63e3cea2d1d57902373b16e4256afe46422691903a438'], + }), + ('entrypoints', '0.3', { + 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('jupyter_core', '4.6.3', { + 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], + }), + ('nbformat', '5.0.7', { + 'checksums': ['54d4d6354835a936bad7e8182dcd003ca3dc0cedfee5a306090e04854343b340'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('nest_asyncio', '1.4.1', { + 'checksums': ['b86c3193abda5b2eeccf8c79894bc71c680369a178f4b068514ac00720b14e01'], + }), + ('nbclient', '0.5.0', { + 'checksums': ['8ad52d27ba144fca1402db014857e53c5a864a2f407be66ca9d74c3a56d6591d'], + }), + ('nbconvert', '6.0.7', { + 'checksums': ['cbbc13a86dfbd4d1b5dee106539de0795b4db156c894c2c5dc382062bbc29002'], + }), + ('tornado', '6.0.4', { + 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], + }), + ('terminado', '0.9.1', { + 'checksums': ['3da72a155b807b01c9e8a5babd214e052a0a45a975751da3521a1c3381ce6d76'], + }), + ('jupyter_client', '6.1.7', { + 'checksums': ['49e390b36fe4b4226724704ea28d9fb903f1a3601b6882ce3105221cd09377a1'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('ipykernel', '5.3.4', { + 'checksums': ['9b2652af1607986a1b231c62302d070bc0534f564c393a5d9d130db9abbbe89d'], + }), + ('prometheus_client', '0.8.0', { + 'checksums': ['c6e6b706833a6bd1fd51711299edee907857be10ece535126a158f911ee80915'], + }), + ('ipywidgets', '7.5.1', { + 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('notebook', '6.1.4', { + 'checksums': ['687d01f963ea20360c0b904ee7a37c3d8cda553858c8d6e33fd0afd13e89de32'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "iptest", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4633201883 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '2.2.8' + +homepage = "https://jupyter.org/" +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('json5', '0.9.5', { + 'checksums': ['703cfee540790576b56a92e1c6aaa6c4b0d98971dc358ead83812aa4d06bdb96'], + }), + ('jupyterlab_server', '1.2.0', { + 'checksums': ['5431d9dde96659364b7cc877693d5d21e7b80cea7ae3959ecc2b87518e5f5d8c'], + }), + (name, version, { + 'patches': ['%(name)s-1.2.5_set-app-path-for-easybuild.patch'], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': [ + 'c8377bee30504919c1e79949f9fe35443ab7f5c4be622c95307e8108410c8b8c', # jupyterlab-2.2.8.tar.gz + # JupyterLab-1.2.5_set-app-path-for-easybuild.patch + 'a219b1071f37f848f7e79c6800149c0b2386a2b748be43288bc32af8e7dab668', + ], + }), +] + +sanity_check_commands = ["jupyter lab --help"] + +modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a9b32bf628 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d79856789c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '2.7.18'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a9ef2d5ea6 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.3' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9d9285db37ae942ed0780c016da87060497877af45094ff9e1a1ca736e3875a2'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.36'), +] + +configopts = '--with-pic --with-pgm --with-libsodium ' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From 3cf1e0def7b3d89605d8ff1f3797e8652698356f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 20 Oct 2020 09:34:26 +0200 Subject: [PATCH 0063/2365] adding easyconfigs: Pango-1.47.0-GCCcore-10.2.0.eb, at-spi2-atk-2.38.0-GCCcore-10.2.0.eb, HarfBuzz-2.6.7-GCCcore-10.2.0.eb, at-spi2-core-2.38.0-GCCcore-10.2.0.eb, Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb, ATK-2.36.0-GCCcore-10.2.0.eb, GObject-Introspection-1.66.1-GCCcore-10.2.0.eb, cairo-1.16.0-GCCcore-10.2.0.eb, ICU-67.1-GCCcore-10.2.0.eb, LibTIFF-4.1.0-GCCcore-10.2.0.eb, FriBidi-1.0.10-GCCcore-10.2.0.eb, pixman-0.40.0-GCCcore-10.2.0.eb (#11532) Co-authored-by: c3-micke --- .../a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb | 39 ++++++++++++++++ .../at-spi2-atk-2.38.0-GCCcore-10.2.0.eb | 37 +++++++++++++++ .../at-spi2-core-2.38.0-GCCcore-10.2.0.eb | 39 ++++++++++++++++ .../c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ .../FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb | 34 ++++++++++++++ ...ect-Introspection-1.66.1-GCCcore-10.2.0.eb | 43 +++++++++++++++++ .../Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb | 44 ++++++++++++++++++ .../HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb | 35 ++++++++++++++ .../i/ICU/ICU-67.1-GCCcore-10.2.0.eb | 29 ++++++++++++ .../l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 43 +++++++++++++++++ .../p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb | 41 +++++++++++++++++ .../p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb | 29 ++++++++++++ 12 files changed, 459 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/ICU/ICU-67.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..91ba9a2e47 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.36.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['fb76247e369402be23f1f5c65d38a9639c1164d934e40f6a9cf3c9e96b652788'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.66.1'), +] + +dependencies = [ + ('GLib', '2.66.1'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a8e89c3094 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.66.1'), + ('DBus', '1.13.18'), + ('at-spi2-core', '2.38.0'), + ('libxml2', '2.9.10'), + ('ATK', '2.36.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d065df3ef5 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['84e36c3fe66862133f5fe229772b76aa2526e10de5014a3778f2fa46ce550da5'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('GObject-Introspection', '1.66.1'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.66.1'), + ('DBus', '1.13.18'), + ('X11', '20201008'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0449c9cee8 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.16.0' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('pixman', '0.40.0'), + ('expat', '2.2.9'), + ('GLib', '2.66.1'), + ('X11', '20201008'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..40e6ff9157 --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.10' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7f1c687c7831499bcacae5e8675945a39bacbad16ecaa945e9454a32df653c01'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..152dc3bc8e --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.66.1' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['dd44a55ee5f426ea22b6b89624708f9e8d53f5cc94e5485c15c87cb30e06161d'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('cairo', '1.16.0'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('GLib', '2.66.1'), + ('libffi', '3.3'), + ('util-linux', '2.36'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2d4114f968 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.40.0' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['1582595099537ca8ff3b99c6804350b4c058bb8ad67411bbaae024ee7cead4e6'] + +builddependencies = [ + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.66.1'), +] + +dependencies = [ + ('GLib', '2.66.1'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('X11', '20201008'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dgir=true " + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a44e86d5ff --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '2.6.7' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['49e481d06cdff97bf68d99fa26bdf785331f411614485d892ea4c78eb479b218'] + +builddependencies = [ + ('binutils', '2.35'), + ('GObject-Introspection', '1.66.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.66.1'), + ('ICU', '67.1'), + ('cairo', '1.16.0'), + ('freetype', '2.10.3'), +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ICU/ICU-67.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-67.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4b6277c96f --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-67.1-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '67.1' + +homepage = 'https://icu-project.org/' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['94a80cd6f251a53bd2a997f6f1b5ac6653fe791dfab66e1eb0227740fb86d5dc'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..43be2ea49e --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.1.0' + +homepage = 'https://libtiff.maptools.org/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.osgeo.org/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['5d29f32517dadb6dbcd1255ea5bbc93a2b54b94fbf83653b4d65c7d6775b8634'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5') +] + +configopts = " --enable-ld-version-script " + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..815a744fab --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.47.0' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['730db8652fc43188e03218c3374db9d152351f51fc7011b9acae6d0a6c92c367'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('GObject-Introspection', '1.66.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20201008'), + ('GLib', '2.66.1'), + ('cairo', '1.16.0'), + ('HarfBuzz', '2.6.7'), + ('FriBidi', '1.0.10'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..21519920c8 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.40.0' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6d200dec3740d9ec4ec8d1180e25779c00bc749f94278c8b9021f5534db223fc'] + +builddependencies = [ + ('binutils', '2.35'), +] + + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [], +} + +moduleclass = 'vis' From 7ec73cd69c11ff9fc64e7186280dd459b8eda562 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 20 Oct 2020 19:16:09 +0200 Subject: [PATCH 0064/2365] Switch libdrm to MesonNinja --- .../l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb index 2aae368ccb..a9b29e1cd1 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb @@ -1,3 +1,4 @@ +easyblock = 'MesonNinja' name = 'libdrm' version = '2.4.102' @@ -13,10 +14,18 @@ checksums = ['8bcbf9336c28e393d76c1f16d7e79e394a7fce8a2e929d52d3ad7ad8525ba05b'] builddependencies = [ ('binutils', '2.35'), ('pkg-config', '0.29.2'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), ] dependencies = [('X11', '20201008')] # installing manpages requires an extra build dependency (docbook xsl) -configopts = '--disable-manpages' +configopts = '-Dman-pages=false' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + moduleclass = 'lib' From e47aec4412cbbfc4f0243bd5b233738be7215a14 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 21 Oct 2020 11:23:45 +0200 Subject: [PATCH 0065/2365] Include patch for libunwind @ GCC10 --- .../l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb index c0a7684fce..1073232ea5 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb @@ -14,10 +14,14 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['libunwind-1.3.1_fix_ppc64_fpreg_t.patch'] +patches = [ + 'libunwind-1.3.1_fix_ppc64_fpreg_t.patch', + 'libunwind-1.4.0_weak_symbol_fix.patch', +] checksums = [ 'df59c931bd4d7ebfd83ee481c943edf015138089b8e50abed8d9c57ba9338435', # libunwind-1.4.0.tar.gz '61a507eec7ece286b06be698c742f0016d8c605eaeedf34f451cf1d0e510ec86', # libunwind-1.3.1_fix_ppc64_fpreg_t.patch + 'fdaf565dc8de48d564562a7258d04fe23f594af1741c49a3062f9f60cde220c8', # libunwind-1.4.0_weak_symbol_fix.patch ] builddependencies = [('binutils', '2.35')] @@ -26,7 +30,7 @@ dependencies = [ ('XZ', '5.2.5'), ] -preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd -fno-common" && ' sanity_check_paths = { 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], From 6147b023561157794b435c794377f51af00560bd Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 21 Oct 2020 11:38:51 +0200 Subject: [PATCH 0066/2365] Update libglvnd to 1.3.2 --- .../libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..13815c2373 --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libglvnd' +version = '1.3.2' + +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['6332c27f4c792b09a3eb1d7ae18c2d6ff6a0acaf3a746489caf859e659fca2f7'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [('X11', '20201008')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' From 516c86a51bad5af9b4159d0624f8ff08eba9dde0 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 21 Oct 2020 12:56:13 +0200 Subject: [PATCH 0067/2365] Update libglvnd dependency in Mesa --- easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb index 218127da18..a2dbdd6eb6 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb @@ -49,7 +49,7 @@ dependencies = [ ('zlib', '1.2.11'), ('zstd', '1.4.5'), ('libdrm', '2.4.102'), - ('libglvnd', '1.2.0'), + ('libglvnd', '1.3.2'), ('libunwind', '1.4.0'), ('LLVM', '11.0.0'), ('X11', '20201008'), From 7a9a1e6a39c86e9cce589db59eea3949fb10b857 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 21 Oct 2020 14:27:04 +0200 Subject: [PATCH 0068/2365] Switch libglvnd to MesonNinja --- .../easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb index 13815c2373..d0f0184cab 100644 --- a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MesonNinja' name = 'libglvnd' version = '1.3.2' @@ -15,6 +15,8 @@ checksums = ['6332c27f4c792b09a3eb1d7ae18c2d6ff6a0acaf3a746489caf859e659fca2f7'] builddependencies = [ ('binutils', '2.35'), ('pkg-config', '0.29.2'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), ] dependencies = [('X11', '20201008')] From efa161fd041b185c45eb279a375c2f53e2291fec Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 21 Oct 2020 19:58:09 +0100 Subject: [PATCH 0069/2365] libarchive: add XZ builddep --- .../easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb index 56c058b302..8c373a125e 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb @@ -19,6 +19,7 @@ checksums = ['ee1e749213c108cb60d53147f18c31a73d6717d7e3d2481c157e1b34c881ea39'] builddependencies = [ ('binutils', '2.35'), + ('XZ', '5.2.5'), ] sanity_check_paths = { From eb580c5bf3ac45c75e5561d8a096abb28b3c544f Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 00:26:58 +0200 Subject: [PATCH 0070/2365] adding easyconfigs: OpenSSL-1.1.1h-GCCcore-10.2.0.eb --- .../OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b233ee7281 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +name = 'OpenSSL' +version = '1.1.1h' + +homepage = 'https://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.openssl.org/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c9ca8774bd7b03e5784f26ae9e9e6d749c9da2438545077e6b3d755a06595d9'] + +dependencies = [('zlib', '1.2.11')] + +builddependencies = [ + ('Perl', '5.32.0'), + ('binutils', '2.35'), +] + +runtest = 'test' + +moduleclass = 'system' From cf6e47a3984a005d1fb4fa7d852384a10ad4d143 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 00:46:59 +0200 Subject: [PATCH 0071/2365] adding easyconfigs: configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb, nodejs-12.19.0-GCCcore-10.2.0.eb, JupyterHub-1.1.0-GCCcore-10.2.0.eb --- ...gurable-http-proxy-4.2.1-GCCcore-10.2.0.eb | 24 ++++ .../JupyterHub-1.1.0-GCCcore-10.2.0.eb | 113 ++++++++++++++++++ .../n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb | 44 +++++++ 3 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fe1c075add --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'configurable-http-proxy' +version = '4.2.1' + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('nodejs', '12.19.0'), +] + +source_urls = ['https://github.com/jupyterhub/configurable-http-proxy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9f95e6893c2b743112b8e591b411a4c109574389253d95a6b5a69109ede53e23'] + +install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz' + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dbd15fbfce --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,113 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '1.1.0' + +homepage = 'http://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), + ('Mako', '1.1.3'), + ('configurable-http-proxy', '4.2.1'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('certipy', '0.1.3', { + 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], + }), + ('pamela', '1.0.0', { + 'checksums': ['65c9389bef7d1bb0b168813b6be21964df32016923aac7515bdf05366acbab6c'], + }), + ('SQLAlchemy', '1.3.20', { + 'checksums': ['d2f25c7f410338d31666d7ddedfa67570900e248b940d186b48461bd4e5569a1'], + }), + ('alembic', '1.4.3', { + 'checksums': ['5334f32314fb2a56d86b4c4dd1ae34b08c03cae4cb888bc699942104d66bc245'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('pyOpenSSL', '19.1.0', { + 'modulename': 'OpenSSL', + 'checksums': ['9a24494b2602aaf402be5c9e30a0b82d4a5c67528fe8fb475e3f3bc00dd69507'], + }), + ('python-json-logger', '2.0.1', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['f26eea7898db40609563bed0a7ca11af12e2a79858632706d835a0f961b7d398'], + }), + ('ruamel.yaml', '0.16.12', { + 'checksums': ['076cc0bc34f1966d920a49f18b52b6ad559fbe656a0748e3535cf7b3f29ebf9e'], + }), + ('ruamel.yaml.clib', '0.2.2', { + 'modulename': False, + 'checksums': ['2d24bd98af676f4990c4d715bcdc2a60b19c56a3fb3a763164d2d8ca0e806ba7'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('jupyter-telemetry', '0.1.0', { + 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', + 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], + }), + ('jupyterhub', version, { + 'checksums': ['852a70225a03abd631b36a207f3ffdf69326a0db4cef539825fde39ec1b713d7'], + }), + ('batchspawner', '1.0.0', { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ, + 'source_urls': ['https://github.com/jupyterhub/batchspawner/archive/']}], + 'checksums': ['207d816480ecb14b6ac19b027d39fcd5aaa993758a3c242d83cd6d3538063f40'], + }), + ('jupyterhub-systemdspawner', '0.14', { + 'modulename': 'systemdspawner', + 'checksums': ['080dd9cd9292266dad35d1efc7aa1af0ed6993d15eadc79bd959d1ee273d1923'], + }), + ('jupyterhub-simplespawner', '0.1', { + 'modulename': 'simplespawner', + 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], + }), + ('ldap3', '2.8.1', { + 'checksums': ['37d633e20fa360c302b1263c96fe932d40622d0119f1bddcb829b03462eeeeb7'], + }), + ('jupyterhub-ldapauthenticator', '1.3.2', { + 'modulename': 'ldapauthenticator', + 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], + }), + ('PyJWT', '1.7.1', { + 'modulename': 'jwt', + 'checksums': ['8d59a976fb773f3e6a39c85636357c4f0e242707394cadadd9814f5cbaa20e96'], + }), + ('jupyterhub-jwtauthenticator-v2', '2.0.2', { + 'modulename': 'jwtauthenticator', + 'checksums': ['9477a606e34c6ff032ee455ffecaf6e13de5e3bce024a2d720f274b421a390c6'], + }), + ('onetimepass', '1.0.1', { + 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], + }), + ('jupyterhub-nativeauthenticator', '0.0.5', { + 'modulename': 'nativeauthenticator', + 'checksums': ['e71b5c3ed1e3af4e307c7a43dce2fb56d4db161ec4fc59764b422cb696606376'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/jupyterhub'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], +} + +sanity_check_commands = ['jupyterhub --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b54074a104 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '12.19.0' # LTS on 2020-10-19 +local_libversion = '72' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://%(name)s.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['1279e49be60d92cf4c1a48c9d92397db4e9284a100bc47689ce7924686bbddd1'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'dirs': ['lib/node_modules', 'include/node'] +} + +modextrapaths = {'CPATH': 'include/node'} + +moduleclass = 'lang' From e46a553b7f6212ff1fab25967b3c5ad679d0f349 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 01:01:28 +0200 Subject: [PATCH 0072/2365] Fix sanity checks and missing build deps --- .../configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb | 4 ++++ .../j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb | 2 ++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb index fe1c075add..aef22909e6 100644 --- a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb @@ -9,6 +9,10 @@ description = """HTTP proxy for node.js including a REST API for updating the ro toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = { + ('binutils', '2.35'), +} + dependencies = [ ('nodejs', '12.19.0'), ] diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb index dbd15fbfce..2bdae502d7 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -108,6 +108,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], } +sanity_pip_check = True + sanity_check_commands = ['jupyterhub --help'] moduleclass = 'tools' From 0c77e0168b644da9f2f11346e333286170feb5a1 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 01:27:05 +0200 Subject: [PATCH 0073/2365] Add sanity_check_paths to configureable http proxy --- .../configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb index aef22909e6..be9c499a5a 100644 --- a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb @@ -23,6 +23,11 @@ checksums = ['9f95e6893c2b743112b8e591b411a4c109574389253d95a6b5a69109ede53e23'] install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz' +sanity_check_paths = { + 'files': ['bin/configurable-http-proxy'], + 'dirs': [], +} + sanity_check_commands = ['%(name)s --version'] moduleclass = 'tools' From c47c082ce52a17cf3b894d54b7fd62c7806c7961 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 02:12:09 +0200 Subject: [PATCH 0074/2365] adding easyconfigs: GTK+-3.24.23-GCCcore-10.2.0.eb, libepoxy-1.5.4-GCCcore-10.2.0.eb --- .../g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb | 69 +++++++++++++++++++ .../libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb | 36 ++++++++++ 2 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..daf5522a2c --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb @@ -0,0 +1,69 @@ +easyblock = 'Bundle' + +name = 'GTK+' +version = '3.24.23' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), + ('GObject-Introspection', '1.66.1'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('cairo', '1.16.0'), + ('Perl', '5.32.0'), +] + +dependencies = [ + ('ATK', '2.36.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.40.0'), + ('Pango', '1.47.0'), + ('libepoxy', '1.5.4'), + ('X11', '20201008'), + ('FriBidi', '1.0.10'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '3.38.0', { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97'], + }), + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2bf072bd40 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.4' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['c926fcc606901f3e03e371027056fd478da43e01ce2da7ffc48b5a0de0ca107c'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), +] + +configopts = '-Degl=no --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' From 4c6dfca11245ba3e96c1b580e0b288b49e724a23 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 02:16:50 +0200 Subject: [PATCH 0075/2365] Fix https url --- .../easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb index 2bdae502d7..ac2d8ad3bb 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'JupyterHub' version = '1.1.0' -homepage = 'http://jupyter.org' +homepage = 'https://jupyter.org' description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.""" From 2f4d0bd34d2cda33486b1fe121d3957982b21cb3 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 11:00:54 +0200 Subject: [PATCH 0076/2365] Include binutils build dep --- .../j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb index ac2d8ad3bb..941bc4ae31 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -9,6 +9,10 @@ description = """JupyterHub is a multiuser version of the Jupyter (IPython) note toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = { + ('binutils', '2.35'), +} + dependencies = [ ('Python', '3.8.6'), ('IPython', '7.18.1'), From 2cfcf11fee29b2495be3e788616456f5deda446c Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 13:37:10 +0200 Subject: [PATCH 0077/2365] Drop versionsuffix --- .../p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 92 +++++++++++++++++++ 1 file changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8706486679 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -0,0 +1,92 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.1' + +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.35')] +dependencies = [ + ('Python', '3.8.6'), + ('Qt5', '5.15.1'), +] + +default_easyblock = 'PythonPackage' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_sipver = '5.4.0' +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + ('PyQt-builder', '1.5.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + ('PyQt5_sip', '12.8.1', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], + 'easyblock': 'Binary', + 'start_dir': '%(name)s-%(version)s', + 'skipsteps': ['configure', 'build'], + 'install_cmd': local_setup_env + local_pyqt5_sip_install, + }), + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip5 --help", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From fcd954323b833eb3975aab017f06e17c5f769a7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 24 Oct 2020 15:55:52 +0200 Subject: [PATCH 0078/2365] update OpenBLAS component for foss/2020a to version 0.3.12 --- easybuild/easyconfigs/f/foss/foss-2020b.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 28 +++++++++++++++++++ .../ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb | 2 +- 3 files changed, 30 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2020b.eb b/easybuild/easyconfigs/f/foss/foss-2020b.eb index ba9f8d9d17..2b3e59acb6 100644 --- a/easybuild/easyconfigs/f/foss/foss-2020b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2020b.eb @@ -19,7 +19,7 @@ local_comp_mpi_tc = ('gompi', version) dependencies = [ ('GCC', local_gccver), ('OpenMPI', '4.0.5', '', ('GCC', local_gccver)), - ('OpenBLAS', '0.3.11', '', ('GCC', local_gccver)), + ('OpenBLAS', '0.3.12', '', ('GCC', local_gccver)), ('FFTW', '3.3.8', '', local_comp_mpi_tc), ('ScaLAPACK', '2.1.0', '', local_comp_mpi_tc), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb new file mode 100644 index 0000000000..8d522bf013 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -0,0 +1,28 @@ +name = 'OpenBLAS' +version = '0.3.12' + +homepage = 'https://xianyi.github.com/OpenBLAS/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), +] +checksums = [ + '65a7d3a4010a4e3bd5c0baa41a234797cd3a1735449a4a5902129152601dc57b', # v0.3.12.tar.gz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb index 7d4d9145e8..3943b1ff81 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb @@ -18,6 +18,6 @@ checksums = [ builddependencies = [('CMake', '3.18.4')] -dependencies = [('OpenBLAS', '0.3.11')] +dependencies = [('OpenBLAS', '0.3.12')] moduleclass = 'numlib' From 497f4490433c8e0074e6de754e1bb96d665d14a5 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 26 Oct 2020 12:36:13 +0100 Subject: [PATCH 0079/2365] adding easyconfigs: packmol-20.2.2-GCC-10.2.0.eb --- .../p/packmol/packmol-20.2.2-GCC-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/packmol/packmol-20.2.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/p/packmol/packmol-20.2.2-GCC-10.2.0.eb b/easybuild/easyconfigs/p/packmol/packmol-20.2.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..3f8f47c180 --- /dev/null +++ b/easybuild/easyconfigs/p/packmol/packmol-20.2.2-GCC-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'packmol' +version = '20.2.2' + +homepage = 'http://m3g.iqm.unicamp.br/packmol' +description = "Packing Optimization for Molecular Dynamics Simulations" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/m3g/packmol/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['129cc1b7e6b00c1740c5c6f285a2c6207e18f05cdeb71af8107c3fedf48f23de'] + +buildopts = 'FORTRAN="$F90"' + +files_to_copy = [(['packmol'], 'bin'), 'AUTHORS', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/packmol', 'AUTHORS', 'LICENSE'], + 'dirs': [], +} + +moduleclass = 'chem' From b1e8c65750b25138a1721aad3e96bdc7aa7cbae8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Oct 2020 20:12:49 +0100 Subject: [PATCH 0080/2365] update intel/2020.10 to Intel compilers 2020 update 4 --- .../i/iccifort/iccifort-2020.4.304.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb new file mode 100644 index 0000000000..fbd8bc1719 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'iccifort' +version = '2020.4.304' + +homepage = 'https://software.intel.com/en-us/intel-compilers/' +description = "Intel C, C++ & Fortran compilers" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17117/'] +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] +patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] +checksums = [ + # parallel_studio_xe_2020_update3_composer_edition.tgz + 'ac1efeff608a8c3a416e6dfe20364061e8abf62d35fbaacdffe3fc9676fc1aa3', + # iccifort-2020.4.304_no_mpi_rt_dependency.patch + 'c330473fc452214b5fffafc5dc962e99fd369582ff9efeda6548b5895a67abb1', +] + +local_gccver = '10.2.0' + +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.35', '', ('GCCcore', local_gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = [ + 'intel-comp', 'intel-ccomp', 'intel-fcomp', 'intel-icc', 'intel-ifort', + 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)' +] + +dontcreateinstalldir = True + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' From bb02473aff98b8654f0d5f7dcadb28386e1e2e43 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 3 Nov 2020 22:03:33 +0200 Subject: [PATCH 0081/2365] adding easyconfigs: CUDA-11.1.1-GCC-10.2.0.eb, CUDAcore-11.1.1.eb, gcccuda-2020b.eb --- .../c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb | 17 +++++++++++++++++ .../easyconfigs/g/gcccuda/gcccuda-2020b.eb | 19 +++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/gcccuda/gcccuda-2020b.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..d6d90b8133 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' +name = 'CUDA' +version = '11.1.1' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +dependencies = [('CUDAcore', version, '', True)] + +altroot = 'CUDAcore' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2020b.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2020b.eb new file mode 100644 index 0000000000..7b990a8842 --- /dev/null +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2020b.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gcccuda' +version = '2020b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" + +toolchain = SYSTEM + +local_gcc_version = '10.2.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gcc_version), + ('CUDA', '11.1.1', '', ('GCC', local_gcc_version)), +] + +moduleclass = 'toolchain' From 05b65634a18aaa8caccbe9f179ea906ceb270679 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 5 Nov 2020 18:57:35 +0200 Subject: [PATCH 0082/2365] adding easyconfigs: Eigen-3.3.8-GCCcore-10.2.0.eb --- .../e/Eigen/Eigen-3.3.8-GCCcore-10.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..37d76d4f48 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.8-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'Eigen' +version = '3.3.8' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['0215c6593c4ee9f1f7f28238c4e8995584ebf3b556e9dbf933d84feb98d5b9ef'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.35'), # to make CMake compiler health check pass on old systems + ('CMake', '3.18.4'), +] + +moduleclass = 'math' From 77a0ecf23566fb6aadd1e9bc91ad945a34009c3b Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 5 Nov 2020 19:40:24 +0200 Subject: [PATCH 0083/2365] adding easyconfigs: pybind11-2.6.0-GCCcore-10.2.0.eb --- .../pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..60135a6d7f --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +name = 'pybind11' +version = '2.6.0' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Eigen', '3.3.8'), +] +dependencies = [('Python', '3.8.6')] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' From 4a1f6d9eb56d4895f61983f95a64413c3d07b055 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Nov 2020 09:01:39 +0100 Subject: [PATCH 0084/2365] update impi to 2019 update 9 in intel/2020.10 toolchain --- .../impi-2019.9.304-iccifort-2020.4.304.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..d4a9ef76ae --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2019.9.304' + +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] + +dependencies = [ + # needed by libfabric provider MLX introduced in Intel MPI v2019.6, + # https://software.intel.com/en-us/articles/improve-performance-and-stability-with-intel-mpi-library-on-infiniband + ('UCX', '1.9.0'), +] + +dontcreateinstalldir = True + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = True + +modextravars = { + # to enable SLURM integration with srun (site-specific) + # 'I_MPI_PMI_LIBRARY': 'libpmi2.so', +} + +# may be needed if you enable I_MPI_PMI_LIBRARY above +# osdependencies = [('slurm-libpmi')] + +moduleclass = 'mpi' From c414b5cbe49cd685921a7d3d6cb5f1dd08dced56 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Nov 2020 09:04:16 +0100 Subject: [PATCH 0085/2365] rename intel/2020.10 to intel/2020b --- .../easyconfigs/h/HPL/HPL-2.3-intel-2020b.eb | 21 ++++++++++ easybuild/easyconfigs/i/iimpi/iimpi-2020b.eb | 18 +++++++++ .../i/imkl/imkl-2020.4.304-iimpi-2020b.eb | 39 +++++++++++++++++++ easybuild/easyconfigs/i/intel/intel-2020b.eb | 21 ++++++++++ 4 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020b.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2020b.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2020b.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020b.eb new file mode 100644 index 0000000000..49bf61f015 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2020b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2020b.eb new file mode 100644 index 0000000000..656957fc24 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2020b.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2020b' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_compver = '2020.4.304' +dependencies = [ + ('iccifort', local_compver), + ('impi', '2019.9.304', '', ('iccifort', local_compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb new file mode 100644 index 0000000000..9675315f1d --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.4.304' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/intel/intel-2020b.eb b/easybuild/easyconfigs/i/intel/intel-2020b.eb new file mode 100644 index 0000000000..f1e345c4cf --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2020b.eb @@ -0,0 +1,21 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2020b' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_compver = '2020.4.304' +local_gccver = '10.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.35', '', ('GCCcore', local_gccver)), + ('iccifort', local_compver), + ('impi', '2019.9.304', '', ('iccifort', local_compver)), + ('imkl', local_compver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From 8b194569658a700047800cdf930c9ebe8c55be5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Nov 2020 11:45:19 +0100 Subject: [PATCH 0086/2365] add patch for GCCcore 10.2 to fix __has_include regression --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 0cac7b1b4a..462a9b073d 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -28,6 +28,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCC-10.2_fix-has-include-Fortran.patch', ] checksums = [ '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz @@ -37,6 +38,7 @@ checksums = [ '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCC-10.2_fix-has-include-Fortran.patch ] builddependencies = [ From 97015d4d59546c146ddf9eaa8004c33977f7226f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 Nov 2020 13:30:20 +0100 Subject: [PATCH 0087/2365] adding easyconfigs: ImageMagick-7.0.10-35-GCCcore-10.2.0.eb, Ghostscript-9.53.3-GCCcore-10.2.0.eb, LittleCMS-2.11-GCCcore-10.2.0.eb --- .../Ghostscript-9.53.3-GCCcore-10.2.0.eb | 56 +++++++++++++++++++ .../ImageMagick-7.0.10-35-GCCcore-10.2.0.eb | 44 +++++++++++++++ .../LittleCMS-2.11-GCCcore-10.2.0.eb | 26 +++++++++ 3 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6af8079fd4 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.53.3' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6eaf422f26a81854a230b80fd18aaef7e8d94d661485bd2e97e695b9dce7bf7f'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('libjpeg-turbo', '2.0.5'), + ('expat', '2.2.9'), + ('GLib', '2.66.1'), + ('cairo', '1.16.0'), + ('LibTIFF', '4.1.0'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +postinstallcmds = [ + # build and install shared libs + "make so && make soinstall", + # install header files + "mkdir -p %(installdir)s/include/ghostscript", + "install -v -m644 base/*.h %(installdir)s/include/ghostscript", + "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b59eec3649 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.10-35' + +homepage = 'https://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/ImageMagick/ImageMagick/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['fca8e29822ac97b5de755d8809ffccc6585df4c4dde61f93d13ce2bd269982b7'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20201008'), + ('Ghostscript', '9.53.3'), + ('JasPer', '2.0.14'), + ('libjpeg-turbo', '2.0.5'), + ('LibTIFF', '4.1.0'), + ('LittleCMS', '2.11'), +] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', + 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ee895da869 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.11' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['dc49b9c8e4d7cdff376040571a722902b682a795bf92985a85b48854c270772e'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('libjpeg-turbo', '2.0.5')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' From 7f0fddb5ea6b3d658976b8c45c83397b8fdb2b4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 Nov 2020 13:53:46 +0100 Subject: [PATCH 0088/2365] adding easyconfigs: UDUNITS-2.2.26-GCCcore-10.2.0.eb --- .../UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..db193785a1 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.26' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.unidata.ucar.edu/downloads/udunits'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('expat', '2.2.9')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From c300f9dbe488ddc71e2572abe2ab0903414ed090 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 Nov 2020 13:54:11 +0100 Subject: [PATCH 0089/2365] adding easyconfigs: libsndfile-1.0.28-GCCcore-10.2.0.eb --- .../libsndfile-1.0.28-GCCcore-10.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..74a8116b7b --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libsndfile' +version = '1.0.28' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://www.mega-nerd.com/libsndfile/files/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1ff33929f042fa333aed1e8923aa628c3ee9e1eb85512686c55092d1e5a9dfa9'] + +builddependencies = [('binutils', '2.35')] + +configopts = '--enable-octave=no' + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'lib' From c570559568cd922ec99d0b6b0e4c81c40f2b6d84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 Nov 2020 13:54:35 +0100 Subject: [PATCH 0090/2365] adding easyconfigs: GLPK-4.65-GCCcore-10.2.0.eb --- .../g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9a861968d8 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.65' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4281e29b628864dfe48d393a7bedd781e5b475387c20d8b0158f329994721a10'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('GMP', '6.2.0')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' From 8f322eba95842d8fbb5f25fd00e6c168596bd06f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 Nov 2020 13:54:57 +0100 Subject: [PATCH 0091/2365] adding easyconfigs: NLopt-2.6.2-GCCcore-10.2.0.eb --- .../n/NLopt/NLopt-2.6.2-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.6.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9d4bf341cd --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.2-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2019-06-05 John Dey jfdey@fredhutch.org fizwit@github.com - updated for CMake +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.6.2' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cfa5981736dd60d0109c534984c4e13c615314d3584cf1c392a155bfe1a3b17e'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' From ba52db0c85a8e4b3b7be5a54ec8fcea4d4e02401 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 Nov 2020 14:08:31 +0100 Subject: [PATCH 0092/2365] add patch for Ghostscript 9.53.3 to fix compilation on top of freetype 2.10.3 --- .../g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb index 6af8079fd4..e12d5fc6ba 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb @@ -14,7 +14,12 @@ source_urls = [ 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), ] sources = [SOURCELOWER_TAR_GZ] -checksums = ['6eaf422f26a81854a230b80fd18aaef7e8d94d661485bd2e97e695b9dce7bf7f'] +patches = ['Ghostscript-9.53.3_fix-freetype-callback.patch'] +checksums = [ + '6eaf422f26a81854a230b80fd18aaef7e8d94d661485bd2e97e695b9dce7bf7f', # ghostscript-9.53.3.tar.gz + # Ghostscript-9.53.3_fix-freetype-callback.patch + 'c539e6c9e1ddaeee132e12265a6918eb6c4c71aec20e8c0e7b703159c13dc12f', +] dependencies = [ ('zlib', '1.2.11'), From bfb0e498b96a6497cfbf3d8df5c126c2bbdb6bca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 Nov 2020 14:12:57 +0100 Subject: [PATCH 0093/2365] use https URLs in LittleCMS 2.11 easyconfig --- .../easyconfigs/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb index ee895da869..aa4fb28b4c 100644 --- a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'LittleCMS' version = '2.11' -homepage = 'http://www.littlecms.com/' +homepage = 'https://www.littlecms.com/' description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] sources = ['lcms2-%(version)s.tar.gz'] checksums = ['dc49b9c8e4d7cdff376040571a722902b682a795bf92985a85b48854c270772e'] From 1ca21644c6afb07d107c9f772a2d5f50b0652098 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 Nov 2020 16:06:21 +0100 Subject: [PATCH 0094/2365] adding easyconfigs: Xvfb-1.20.9-GCCcore-10.2.0.eb, nettle-3.6-GCCcore-10.2.0.eb --- .../n/nettle/nettle-3.6-GCCcore-10.2.0.eb | 36 ++++++ .../x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb | 110 ++++++++++++++++++ 2 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..76ecdf835b --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.6' + +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d24c0d0f2abffbc8f4f34dcf114b0f131ec3774895f3555922fe2f40f3d5e3f1'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +dependencies = [ + ('GMP', '6.2.0'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5341032753 --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb @@ -0,0 +1,110 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '1.20.9' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('X11', '20201008'), + ('pixman', '0.40.0'), + ('libdrm', '2.4.102'), + ('Mesa', '20.2.1'), + ('nettle', '3.6'), + ('libunwind', '1.4.0'), + ('XZ', '5.2.5'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'source_urls': ['https://www.x.org/archive//individual/font/'], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.1', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['e5b687029e44d0bd3ccd254a4da6a5cbfc40350aa8b43fcca16ef6e9b9bb9f22'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.3.2', { + 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], + }), + ('font-misc-misc', '1.1.2', { + 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.4', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['159fba6b62ef4a3fb16ef7fc4eb4fc26f3888652471ceb604c495783dda020bc'], + }), + ('xkeyboard-config', '2.31', { + 'source_urls': ['https://www.x.org/archive//individual/data/xkeyboard-config/'], + 'checksums': ['5ac6b5b661aeb9d0ea84ad961cbbdd8fdf2503d6e8ca65ca1b1c5d9aea2ddc52'], + 'configopts': '--with-xkb-rules-symlink=xorg', + }), + ('xauth', '1.1', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual//xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + '067c348fe1a86a1924010354c1c7cf1eaa9e43866e48540aa56a465f2a341ddc', # xorg-server-1.20.9.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' From 65a0f66d92c300f1beb11a8e78ef466354873dc8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Nov 2020 11:55:10 +0100 Subject: [PATCH 0095/2365] {data}[gompi/2020b,iimpi/2020b] HDF5 v1.10.7, netCDF v4.7.4, netCDF-Fortran v4.5.3 --- .../Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb | 28 ++++++++++++++ .../h/HDF5/HDF5-1.10.7-gompi-2020b.eb | 21 ++++++++++ .../h/HDF5/HDF5-1.10.7-iimpi-2020b.eb | 21 ++++++++++ .../netCDF-Fortran-4.5.3-gompi-2020b.eb | 25 ++++++++++++ .../netCDF-Fortran-4.5.3-iimpi-2020b.eb | 25 ++++++++++++ .../n/netCDF/netCDF-4.7.4-gompi-2020b.eb | 38 +++++++++++++++++++ .../n/netCDF/netCDF-4.7.4-iimpi-2020b.eb | 38 +++++++++++++++++++ 7 files changed, 196 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpi-2020b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f972f6c1aa --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +name = 'Doxygen' +version = '1.8.20' + +homepage = 'https://www.doxygen.org' +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['e0db6979286fd7ccd3a99af9f97397f2bae50532e4ecb312aa18862f8401ddec'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), + ('pkg-config', '0.29.2'), +] +dependencies = [('libiconv', '1.16')] + +configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompi-2020b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompi-2020b.eb new file mode 100644 index 0000000000..df02939510 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompi-2020b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.7' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpi-2020b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpi-2020b.eb new file mode 100644 index 0000000000..4e1c74a08b --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpi-2020b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.7' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb new file mode 100644 index 0000000000..a4fe7306cb --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb @@ -0,0 +1,25 @@ +name = 'netCDF-Fortran' +version = '4.5.3' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c6da30c2fe7e4e614c1dff4124e857afbd45355c6798353eccfa60c0702b495a'] + +builddependencies = [ + ('M4', '1.4.18'), +] + +dependencies = [('netCDF', '4.7.4')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb new file mode 100644 index 0000000000..47dc0efa8e --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb @@ -0,0 +1,25 @@ +name = 'netCDF-Fortran' +version = '4.5.3' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c6da30c2fe7e4e614c1dff4124e857afbd45355c6798353eccfa60c0702b495a'] + +builddependencies = [ + ('M4', '1.4.18'), +] + +dependencies = [('netCDF', '4.7.4')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020b.eb new file mode 100644 index 0000000000..f7f2694014 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020b.eb @@ -0,0 +1,38 @@ +name = 'netCDF' +version = '4.7.4' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['netCDF-%(version)s_fix-ocdebug.patch'] +checksums = [ + '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b', # v4.7.4.tar.gz + '94c9883005f189a4551947e04191a68199cf4cdcada4b2d313115720fb4690e9', # netCDF-4.7.4_fix-ocdebug.patch +] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('cURL', '7.72.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpi-2020b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpi-2020b.eb new file mode 100644 index 0000000000..10064fa9b0 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpi-2020b.eb @@ -0,0 +1,38 @@ +name = 'netCDF' +version = '4.7.4' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['netCDF-%(version)s_fix-ocdebug.patch'] +checksums = [ + '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b', # v4.7.4.tar.gz + '94c9883005f189a4551947e04191a68199cf4cdcada4b2d313115720fb4690e9', # netCDF-4.7.4_fix-ocdebug.patch +] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('cURL', '7.72.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From 6e9aab0b4ccaf26d70462e25041db33217dabf54 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Nov 2020 12:07:52 +0100 Subject: [PATCH 0096/2365] add missing libiconv easyconfig, required as dep for Doxygen --- .../libiconv/libiconv-1.16-GCCcore-10.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6b87eb86c4 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.16' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e6a1b1b589654277ee790cce3734f07876ac4ccfaecbee8afa0b649cf529cc04'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' From aa5498c63331dd9c157c8bbdf84b28779787b30d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Nov 2020 16:16:46 +0100 Subject: [PATCH 0097/2365] drop versionsuffix for SciPy-bundle 2020.10 with Python 3.8.6 --- .../SciPy-bundle-2020.11-foss-2020b.eb | 49 +++++++++++++++++ .../SciPy-bundle-2020.11-intel-2020b.eb | 55 +++++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb new file mode 100644 index 0000000000..1cf04c9f8f --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2020.11' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), # required by scipy +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +# order is important! +exts_list = [ + ('hypothesis', '5.41.1', { + 'checksums': ['06776c245b5eb25011040f94779fda6bbfa9def72074672af2e79a5e6bce8b38'], + }), + ('numpy', '1.19.4', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512'], + }), + ('scipy', '1.5.4', { + 'checksums': ['4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b'], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('pandas', '1.1.4', { + 'checksums': ['a979d0404b135c63954dea79e6246c45dd45371a88631cdbb4877d844e6de3b6'], + }), + ('mpmath', '1.1.0', { + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb new file mode 100644 index 0000000000..2664d1c89d --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2020.11' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), # required by scipy +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +# order is important! +exts_list = [ + ('hypothesis', '5.41.1', { + 'checksums': ['06776c245b5eb25011040f94779fda6bbfa9def72074672af2e79a5e6bce8b38'], + }), + ('numpy', '1.19.4', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.18.2-mkl.patch'], + 'checksums': [ + '141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512', # numpy-1.19.4.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + ], + }), + ('scipy', '1.5.4', { + 'checksums': ['4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b'], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('pandas', '1.1.4', { + 'checksums': ['a979d0404b135c63954dea79e6246c45dd45371a88631cdbb4877d844e6de3b6'], + # strip out use of -Werror to avoid failing compilation due to Intel compiler warning + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + }), + ('mpmath', '1.1.0', { + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From ee59fea7e8bbc15293558163d2f76fe8a64d6c1b Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 9 Nov 2020 18:39:47 +0100 Subject: [PATCH 0098/2365] Add setting of JUPYTER_PATH --- .../easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb index a4b5534503..0c967ad135 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb @@ -128,9 +128,14 @@ exts_list = [ }), ] +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/IPython', + 'share/jupyter' + ], } sanity_check_commands = [ From efce37b03d448594fd044a18e2e4da0b7f0c7c34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Nov 2020 21:57:13 +0100 Subject: [PATCH 0099/2365] adding easyconfigs: GSL-2.6-GCC-10.2.0.eb, GSL-2.6-iccifort-2020.4.304.eb --- .../easyconfigs/g/GSL/GSL-2.6-GCC-10.2.0.eb | 25 +++++++++++++++++++ .../g/GSL/GSL-2.6-iccifort-2020.4.304.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-10.2.0.eb new file mode 100644 index 0000000000..46c108f2f4 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.6' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.4.304.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..3757a22104 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.4.304.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.6' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' From 8a286288b79c4f11a3170cd6c11102c7bbf0069e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Nov 2020 13:22:16 +0100 Subject: [PATCH 0100/2365] also add extensions required for QIIME2 to Perl 5.32.0 easyconfig --- .../p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 18b17c57ec..9c2b7edb9a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -1743,6 +1743,51 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], }), + ('Business::ISBN', '3.005', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], + 'checksums': ['6530fbae40c56376db4e6686c34af8da3db5c4baad0d104047b1ef3e24fe2e2a'], + }), + ('Business::ISBN::Data', '20191107', { + 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], + 'checksums': ['844c4f64f193d389340b4465a1d5bc34c60f0c8e42e5c69ac8afe3d3bbc5ca0d'], + }), + ('common::sense', '3.75', { + 'source_tmpl': 'common-sense-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], + 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], + }), + ('IO::Compress::Bzip2', '2.096', { + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], + 'checksums': ['9d219fd5df4b490b5d2f847921e3cb1c3392758fa0bae9b05a8992b3620ba572'], + }), + ('JSON::XS', '4.03', { + 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], + 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], + }), + ('List::MoreUtils::XS', '0.430', { + 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], + 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], + }), + ('Authen::NTLM', '1.09', { + 'source_tmpl': 'NTLM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT/'], + 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], + }), + ('Types::Serialiser', '1.0', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], + 'checksums': ['7ad3347849d8a3da6470135018d6af5fd8e58b4057cd568c3813695f2a04730d'], + }), + ('XML::SAX::Expat', '0.51', { + 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN/'], + 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], + }), ] moduleclass = 'lang' From 4ee790113068de68e45625baef756f0e4eda7dff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 09:51:36 +0100 Subject: [PATCH 0101/2365] adding easyconfigs: R-4.0.3-foss-2020b.eb --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 2735 +++++++++++++++++ 1 file changed, 2735 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb new file mode 100644 index 0000000000..4733702683 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -0,0 +1,2735 @@ +name = 'R' +version = "4.0.3" + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.9'), +] +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('PCRE2', '10.35'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.5'), # for plottting in R + ('LibTIFF', '4.1.0'), + ('Java', '11', '', True), + ('Tk', '8.6.10'), # for tcltk + ('cURL', '7.72.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.0'), # for igraph + ('NLopt', '2.6.2'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '67.1'), # for rJava & gdsfmt + ('HDF5', '1.10.7'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.10-35'), # for animation + ('GLPK', '4.65'), # for Rglpk + ('nodejs', '12.19.0'), # for V8 (required by rstan) + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1e'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 23 July 2020 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9', { + 'checksums': ['b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.5', { + 'checksums': ['b8462c643bcc6fe3b0e9caee9e0cd76c5f7f0e34ee2e7397f93c4c43885c5c04'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '4.0.4', { + 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], + }), + ('bnlearn', '4.6.1', { + 'checksums': ['e4544465af3330e53e4777079c448585a8a97be2d3862a5264169007c20daeaf'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.15', { + 'checksums': ['65f964aa768d0703ceb7a199adc5e79ca79a6d29d7bc053a262eb533697686c0'], + }), + ('formatR', '1.7', { + 'checksums': ['a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb'], + }), + ('gtools', '3.8.2', { + 'checksums': ['503ba60a41f3c61b8129c25de62c74dab29761d2e661d4addd106e2e02f1dcde'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('highr', '0.8', { + 'checksums': ['4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.9', { + 'checksums': ['2ccf97d2940a09539dc051c7a9a1aee90ef04b34e9bc6c0b64b4435fb3c2fa80'], + }), + ('xfun', '0.19', { + 'checksums': ['3b027bade119637478eb25733fc6702ad8de48aa199e044e4b3cbd40e78bde97'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-1', { + 'checksums': ['748141d56531a39dc4d37cf0a5165a40b653a04c507e916854053ed77119e0e6'], + }), + ('NLP', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '5.4.6', { + 'checksums': ['d4ffcf36bf709ad42dccb2387263f67ca32012b0707f0ef6eda32730b5c286fc'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('segmented', '1.3-0', { + 'checksums': ['a58fe9503570d89b2521237ba5c2be274ea40f0a3d854fc68c4422891cb536a9'], + }), + ('som', '0.3-5.1', { + 'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'], + }), + ('SuppDists', '1.1-9.5', { + 'checksums': ['680b67145c07d44e200275e08e48602fe19cd99fb106c05422b3f4a244c071c4'], + }), + ('stabledist', '0.7-1', { + 'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'], + }), + ('survivalROC', '1.0.3', { + 'checksums': 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['b064cde7d63ce93ec9969c8c4463c1e327758b6f8ea7765217d77f9ba9d590bf'], + }), + ('KODAMA', '1.5', { + 'checksums': ['8ecf53732c1be2bd1e111b3c6de65b66caf28360306e683fe945dc76d4c267dd'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-2', { + 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + }), + ('dtw', '1.22-3', { + 'checksums': ['df7cf9adf613422ddb22a160597eb5f5475ab6c67c0d790092edb7f72ba98f00'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.2', { + 'checksums': ['b03a775df279a71f259470335decf033b0b9e34b7ee5726681b302ae4e11ff0e'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-1', { + 'checksums': ['546e700a39c4ad1dbecf06ba8724e4cf73cb500009027c28762511d52bb7cee6'], + }), + ('rappdirs', '0.3.1', { + 'checksums': ['2fd891ec16d28862f65bb57e4a78f77a597930abb59380e757afd8b6c6d3264a'], + }), + ('reticulate', '1.18', { + 'checksums': ['b33f855a58f446eefbe38df8a1a4865390f5d4ebd64b2c72266baaee64628513'], + }), + ('hdf5r', '1.3.3', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['a0f83cbf21563e81dbd1a1bd8379623ed0c9c4df4e094c75013abfd7a5271545'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('pulsar', '0.3.7', { + 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], + }), + ('bayesm', '3.1-4', { + 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('energy', '1.7-7', { + 'checksums': ['67b88fb33ee6e7bec2e4fe356a4efd36f70c3cf9b0ebe2f6d9da9ec96de9968f'], + }), + ('compositions', '2.0-0', { + 'checksums': ['19cb515e5e61348c1f3672c8d00e8c3491c84774716729e62559e0948c255d77'], + }), + ('clustree', '0.4.3', { + 'checksums': ['5ff3afc3fb3e1d20d033328935084de574250d29545c0a5b69180fe4846fbe53'], + }), + ('plotly', '4.9.2.1', { + 'checksums': ['f45eae325ab7e7924b0be098bad866ce003d657cf63e137104401c2dd4401db8'], + }), + ('tweedie', '2.3.2', { + 'checksums': ['9a6226e64e3d56eb7eb2a408f8b825c2ad6ee0ea203a9220e85e7789514adb81'], + }), + ('RcppGSL', '0.3.8', { + 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], + }), + ('mvabund', '4.1.3', { + 'checksums': ['4b98049026fcc5a262163f6801d5b98b8543267cf7b0edac8382d5311b81a8fc'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.2.2', { + 'checksums': ['5efa9ecc957407cf130f093bd5cce376e753ac6399ec78d7a313cdec3ea899a4'], + }), + ('grpreg', '3.3.0', { + 'checksums': ['d7c93c62659bd0f0d944cc1470f13443ffdebfeac5ef21ffb604ff6acbeb455b'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('ergm', '3.11.0', { + 'checksums': ['4e5506b44badc2343be3657acbf2bca51b47d7c187ff499d5a5e70a9811fe9f2'], + }), + ('networkDynamic', '0.10.1', { + 'checksums': ['22eed8d9dea8d70877c1619eb2bc3f1ac5142ce3db6fd6eb3e0879ca56b76ca0'], + }), + ('tergm', '3.7.0', { + 'checksums': ['afd2b160bda691127f8fc57c4caff61f688cc03e71e622f8e833b2a26dc635df'], + }), + ('ergm.count', '3.4.0', { + 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], + }), + ('tsna', '0.3.1', { + 'checksums': ['bba4b5e04ba647784581a2137f653f60b4c83cfd726c399556054c5a6d2cbd95'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.4-9', { + 'checksums': ['2c45c188c753f566eb9b0429ca4e5af779309dadbaa689752cc63f77788b53bb'], + }), + ('shinythemes', '1.1.2', { + 'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.13', { + 'checksums': ['a9429e5325368cd3ed30ccaaa8147a960ee7970e83bc80eb42bc56cfeddaf6f8'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.32.0.1', { + 'checksums': ['86161b81e4aecf0243b17cabcd1f887cf4b9104918d91c804810be603d50ab66'], + }), + ('mlegp', '3.1.8', { + 'checksums': ['eac1df085a608451828575028ca05b78dc6b5035da14cabc141bfee5ef986de9'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.5.1', { + 'checksums': ['7204200631039f5f00dc0dd36ea21bf979b33c99c1561d54914129cfadbf7d9d'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.2.0', { + 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.5', { + 'checksums': ['9c41ca817104ab076bfd62cccac7d024658ebf4a11dcd91654f0588868aa8d74'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0-1', { + 'checksums': ['9fc1f7432a40d8911393701ca33e2ad64356c3bd12128f01dd216399b16e3d93'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.16', { + 'checksums': ['d216a46d65e2b7f5dae2eb06ff44bee16262f1d29605e3267456191b39143575'], + }), + ('BMA', '3.18.12', { + 'checksums': ['cbabb77d92b09a11a986ad03950322e78dff743f82ff67fda51d32e44135dd79'], + }), + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-57', { + 'checksums': ['6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17'], + }), + ('bdsmatrix', '1.3-4', { + 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], + }), + ('fftwtools', '0.9-9', { + 'checksums': ['a9273b7e495d228d740ab4525467e4bbefe8614bd2d97e7234017f1305f51441'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.19.3', { + 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.4', { + 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.8', { + 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '3.0', { + 'checksums': ['ada4e1f8cbb08ba8ff16275ec5f9a453857e0cab63b70d42753989ab4c716b7b'], + }), + ('bbmle', '1.0.23.1', { + 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.49', { + 'checksums': ['738a616840eff67d911abee2b9eaeddaae7bddb749796ff4e5c17386fb812234'], + }), + ('tictoc', '1.0', { + 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], + }), + ('ISOcodes', '2020.03.16', { + 'checksums': ['160eb4ea23be53305e4e728002c8f5d3852d89155f538deccb734e7c8ad4e1c3'], + }), + ('stopwords', '2.0', { + 'checksums': ['5cca60ce9f44406486e0dca2e36cec2488096c3558b45fc3bd0e7b6d1500af94'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0', { + 'checksums': ['01fb9c87f7cf094aaad3b7098378134f2e503286224351e91d08c00b6ee19857'], + }), + ('topicmodels', '0.2-11', { + 'checksums': ['9c26b4d967be6ec26834a39f04aa92b059ea9503eb70c700e1c0a7a43637b74a'], + }), + ('tidytext', '0.2.6', { + 'checksums': ['494c1e274e58d975193c74f05eab49d021d7ec86490d479f6376847b969ab276'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-11', { + 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.3.1', { + 'checksums': ['d98de21b71d9d9386131ae5ba4da051362c3ad39e0305af4f33d830f299ae08b'], + }), + ('RcppParallel', '5.0.2', { + 'checksums': ['8ca200908c6365aafb2063be1789f0894969adc03c0f523c6cc45434b8236f81'], + }), + ('StanHeaders', '2.21.0-6', { + 'checksums': ['a0282a054d0e6ab310ec7edcffa953b77c7e4a858d9ac7028aab1b4fb4ce8cf3'], + }), + ('V8', '3.4.0', { + 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + }), + ('rstan', '2.21.2', { + 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.0', { + 'checksums': ['6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.6.0', { + 'checksums': ['ebb28e20c7e28809194a2a027bc83303b17be1e3db32f49325727c9279df9c5b'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.4.0', { + 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.0.1', { + 'checksums': ['02bcc43ca778a0f981fd7f36c0b15b0d1eb8ed87d3db0b8bfd33b708881aa972'], + }), + ('leiden', '0.3.4', { + 'checksums': ['c2c233a43b251e464655f7ef579d96a1f07961588d7761a16ae19cd482464932'], + }), + ('future.apply', '1.6.0', { + 'checksums': ['ba1adfd6d97decf9c66146101eaf02cf246edf17cd096aea8bd9f6ed24f36efd'], + }), + ('sctransform', '0.3.1', { + 'checksums': ['8a772dec0030b4e326f1dad62c3bc6a03fbf53f48897be44953332fa1b8a162d'], + }), + ('packrat', '0.5.0', { + 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], + }), + ('shinyjs', '2.0.0', { + 'checksums': ['c2cdd9fab41f6b46bb41b288cd9b3fb3a7fe9627b664e3a58a0cb5dd4c19f8ff'], + }), + ('colourpicker', '1.1.0', { + 'checksums': ['2dfbb6262d187d3b17357ff9c22670ced3621feda5b2a2a500558478e4d551e2'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), + ('findpython', '1.0.5', { + 'checksums': ['3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145'], + }), + ('argparse', '2.0.3', { + 'checksums': ['d26139c610ea0adf8d6632699cd34c4595ae3e7963bfc7a00cb3b7504f2059b0'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), + ('qqman', '0.1.4', { + 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], + }), + ('rstantools', '2.1.1', { + 'checksums': ['c95b15de8ec577eeb24bb5206e7b685d882f88b5e6902efda924b7217f463d2d'], + }), + ('bayesplot', '1.7.2', { + 'checksums': ['94f1fbf137f0ce4fd5029c6c3239ba0c890223ae9aa9bb816ed5052cdd221e2b'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.16', { + 'checksums': ['3f728c6a5153dca28f69b9355ae9d18c5f7e70d12495c0c047eef673c1053116'], + }), + ('shinystan', '2.5.0', { + 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'], + }), + ('optimx', '2020-4.2', { + 'checksums': ['6381c25c322287fc98ab1b2965d3f68c9a92c587c76aca1d33fd6428b2167101'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('projpred', '2.0.2', { + 'checksums': ['af0a9fb53f706090fe81b6381b27b0b6bd3f7ae1e1e44b0ada6f40972b09a55b'], + }), + ('brms', '2.14.4', { + 'checksums': ['3295f775de69a181f09140e224df836c4c82010a2a04fc0d2d80d8fa208cfc57'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.0', { + 'checksums': ['b423df43e9c4bb8ffafe2de88b93fdcf3a90f964f136580ea1b849a83dba7400'], + }), + ('mcmcse', '1.4-1', { + 'checksums': ['6b181f56d60ddf55c9c08a2468ef9ffe3ec8a1b16cfa9a7742c3872597f85d17'], + }), + ('copCAR', '2.0-3', { + 'checksums': ['e626380d3f11ca6c756381f2423ef3661efb52667147114253416cc6151a71b8'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.5.3', { + 'checksums': ['86090718f13bb0fb2b84fd18ea7d485ec7b55e991db4b27fbdaa3b11e969583c'], + }), + ('drugCombo', '1.1.1', { + 'checksums': ['9fdc3a7cf63552c32f1c7573258fc4ceacdaf5c475fe79aa4ca8c9226b9f8a38'], + }), + ('betareg', '3.1-3', { + 'checksums': ['cc19387ec516492d11cf59cdfa07e1733950a2af8196c1e155bc95939bc76246'], + }), + ('unmarked', '1.0.1', { + 'checksums': ['a3bb9bdc7a4a79ea38482df3f8cbb6e9082332a0d894eeb4b3dc816344cec0e4'], + }), + ('maxlike', '0.1-8', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-16', { + 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.2', { + 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], + }), + ('ENMeval', '0.3.1', { + 'checksums': ['e7f20c1b4d7ede82a3aca86e3ce3fc4ae46337f812dfc171b499c2558b0183d0'], + }), + ('plotmo', '3.6.0', { + 'checksums': ['c05afcc442f9542868beea5c3c40fb93b049f9b61c42725b2a1e2bc750c241e3'], + }), + ('earth', '5.3.0', { + 'checksums': ['05ace806271a74b3ddf8718a93237fe2a8550a8659ebd87f8079c0bda5e02437'], + }), + ('mda', '0.5-2', { + 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], + }), + ('biomod2', '3.4.6', { + 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], + }), + ('poLCA', '1.4.1', { + 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], + }), + ('PermAlgo', '1.1', { + 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.12', { + 'checksums': ['9acdf912f0e7a68a5b6a7946d5ebb0c2007b3d6cd2e39075eddae2b586354e89'], + }), + ('data.tree', '1.0.0', { + 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('gsl', '2.1-6', { + 'checksums': ['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5', { + 'checksums': ['d526b99d17c1dfd5e399f4af1bc09c8a267add80d3b0a454790728420f0e8fd7'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-18', { + 'patches': ['dbarts-0.9-18_fix-simd-on-non-x86.patch'], + 'checksums': [ + 'fd99f99d1a24c16596767246618cf240ebd8d86fa82b0e5ce65b737b9afb4ac4', # dbarts_0.9-18.tar.gz + # dbarts-0.9-18_fix-simd-on-non-x86.patch + '80a7e84c691d418da4e90a38db1caebed31d01771e4e7f64d24676ee8d84c104', + ], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.4.0', { + 'checksums': ['49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + ('memoise', '1.1.0', { + 'checksums': ['b276f9452a26aeb79e12dd7227fcc8712832781a42f92d70e86040da0573980c'], + }), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.2', { + 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], + }), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), + ('assertive.base', '0.0-7', { + 'checksums': ['f02d4eca849f512500abb266a2a751d1fa2cf064f7142e5161a77c20b7f643f7'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '2.1', { + 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], + }), + ('lmom', '2.8', { + 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], + }), + ('gld', '2.6.2', { + 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], + }), + ('DescTools', '0.99.38', { + 'checksums': ['bd8edce64a8f9e295611959295b85cf8d7bbf915093158016169bd334e0e1104'], + }), +] + +moduleclass = 'lang' From 565c4ae0859112b8280747e0b01844c7069524a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 09:54:49 +0100 Subject: [PATCH 0102/2365] fix date when extensions were last updated in R 4.0.3 easyconfig --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 4733702683..21d752462c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -72,7 +72,7 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 23 July 2020 +# packages updated on 10 Nov 2020 exts_list = [ 'base', 'datasets', From 13410d10cf9e1b9b62cef871eeb7d20dc5d80ac8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 09:57:00 +0100 Subject: [PATCH 0103/2365] adding easyconfigs: FFTW-3.3.8-intel-2020b.eb --- .../f/FFTW/FFTW-3.3.8-intel-2020b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2020b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2020b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2020b.eb new file mode 100644 index 0000000000..00efb3ab98 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2020b.eb @@ -0,0 +1,30 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +patches = ['FFTW-%(version)s_fix-icc-no-gcc.patch'] +checksums = [ + '6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303', # fftw-3.3.8.tar.gz + '1b3319b98a2ca4ead68290b3229385c0573e22749a5a2ffb49486a0bbb37dc1e', # FFTW-3.3.8_fix-icc-no-gcc.patch +] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails on AMD systems when configuring with --enable-avx-128-fma, +# because Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' From 9a4717c532217fab746d2a92115e4b2f631cf706 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 10:11:25 +0100 Subject: [PATCH 0104/2365] adding easyconfigs: libxc-4.3.4-GCC-10.2.0.eb, libxc-4.3.4-iccifort-2020.4.304.eb --- .../l/libxc/libxc-4.3.4-GCC-10.2.0.eb | 51 +++++++++++++++++ .../libxc/libxc-4.3.4-iccifort-2020.4.304.eb | 57 +++++++++++++++++++ 2 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..1bd1ee4c45 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '4.3.4' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'libxc-%(version)s_lm-fix.patch', + 'libxc-%(version)s_fix-CMakeLists.patch', + 'libxc-%(version)s_fix-timeout.patch', +] +checksums = [ + 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch + '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch + 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Perl', '5.32.0'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info', 'bin/xc-threshold'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..a07e6e4dbc --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb @@ -0,0 +1,57 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '4.3.4' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'libxc-%(version)s_rename-F03.patch', + 'libxc-%(version)s_lm-fix.patch', + 'libxc-%(version)s_fix-CMakeLists.patch', + 'libxc-%(version)s_fix-timeout.patch', +] +checksums = [ + 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + 'e494be3ca2026998f2dd7c6b03a4e662f204fd3d963271e588f9f0d5739e76b5', # libxc-4.3.4_rename-F03.patch + 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch + '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch + 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Perl', '5.32.0'), +] + +separate_build_dir = True + +# rename *.F03 source file since Intel Fortran compiler doesn't like that extension +# also requires patch file to rename file in CMakeLists.txt and src/Makefile.in +preconfigopts = "mv ../libxc-%(version)s/src/libxc_master.F03 ../libxc-%(version)s/src/libxc_master_F03.F90 && " + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info', 'bin/xc-threshold'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' From 327fa0d085297f9833af5ff8abd4c04dd022d895 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 10:12:30 +0100 Subject: [PATCH 0105/2365] adding easyconfigs: libxsmm-1.16.1-GCC-10.2.0.eb, libxsmm-1.16.1-iccifort-2020.4.304.eb --- .../l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb | 27 +++++++++++++++++++ .../libxsmm-1.16.1-iccifort-2020.4.304.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..cc99b62c39 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.16.1' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['93dc7a3ec40401988729ddb2c6ea2294911261f7e6cd979cf061b5c3691d729d'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..fba1cdf479 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.16.1' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['93dc7a3ec40401988729ddb2c6ea2294911261f7e6cd979cf061b5c3691d729d'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' From e49247575a2bcb622ce72ba41d294ec137b3e02d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 10:16:43 +0100 Subject: [PATCH 0106/2365] adding easyconfigs: CP2K-7.1-foss-2020b.eb --- .../easyconfigs/c/CP2K/CP2K-7.1-foss-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b.eb new file mode 100644 index 0000000000..742f3d1372 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b.eb @@ -0,0 +1,34 @@ +name = 'CP2K' +version = '7.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ccd711a09a426145440e666310dd01cc5772ab103493c4ae6a3470898cd0addb'] + +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '4.3.4'), + ('libxsmm', '1.16.1'), + ('FFTW', '3.3.8'), + ('PLUMED', '2.6.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.1'), +] + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' From 44215e1a62610971e59ddd6d39b5fbba67109e9c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 10:28:21 +0100 Subject: [PATCH 0107/2365] adding easyconfigs: CP2K-7.1-intel-2020b.eb --- .../c/CP2K/CP2K-7.1-intel-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-7.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-7.1-intel-2020b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-intel-2020b.eb new file mode 100644 index 0000000000..ee964e56ae --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-intel-2020b.eb @@ -0,0 +1,34 @@ +name = 'CP2K' +version = '7.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ccd711a09a426145440e666310dd01cc5772ab103493c4ae6a3470898cd0addb'] + +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '4.3.4'), + ('libxsmm', '1.16.1'), + ('FFTW', '3.3.8'), + ('PLUMED', '2.6.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.1'), +] + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' From cdf715aece6de01a4bda9638ba9fe65e8f13c12a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 10:35:31 +0100 Subject: [PATCH 0108/2365] {vis}[GCCcore/10.2.0] FFmpeg v4.3.1 --- .../f/FFmpeg/FFmpeg-4.3.1-GCCcore-10.2.0.eb | 44 +++++++++++++++++++ .../l/LAME/LAME-3.100-GCCcore-10.2.0.eb | 42 ++++++++++++++++++ .../x/x264/x264-20201026-GCCcore-10.2.0.eb | 34 ++++++++++++++ .../x/x265/x265-3.3-GCCcore-10.2.0.eb | 41 +++++++++++++++++ .../y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb | 35 +++++++++++++++ 5 files changed, 196 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/x265/x265-3.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..edbc0620c2 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.1-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '4.3.1' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ffmpeg.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f4a4ac63946b6eee3bbdde523e298fca6019d048d6e1db0d1439a62cea65f0d9'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2') +] + +dependencies = [ + ('NASM', '2.15.05'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('x264', '20201026'), + ('LAME', '3.100'), + ('x265', '3.3'), + ('X11', '20201008'), + ('freetype', '2.10.3'), + ('fontconfig', '2.13.92'), + ('FriBidi', '1.0.10'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ecd79e6d2f --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +dependencies = [('ncurses', '6.2')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ab66b16bf1 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +local_commit = '4121277b' +version = '20201026' + +homepage = 'https://www.videolan.org/developers/x264.html' + +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://code.videolan.org/videolan/x264/-/archive/%s/' % local_commit] +sources = [{'download_filename': 'x264-%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['4dba5ab9e744f85d8a37ccdcc9467d27c5409c7e4f7e397580b5921be09b4d1e'] + +builddependencies = [ + ('binutils', '2.35'), + ('NASM', '2.15.05'), +] + +configopts = " --enable-shared --enable-static" + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', + 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1a0bb416da --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.3-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.3' + +homepage = 'https://x265.org/' + +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://bitbucket.org/multicoreware/x265_git/downloads/', + 'https://download.videolan.org/pub/videolan/x265/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = [( + # checksum for new source tarball (from https://bitbucket.org/multicoreware/x265_git/downloads) + 'c6d744a87eda55560da715f56f878640554ddc06e2d0fcbd822fa330affc22cc', + # checksum for original source tarball (from https://bitbucket.org/multicoreware/x265/downloads) + 'f26e148ed1f4dfb33fd1eb3ff5e60e08078d1b2017e88bcbb045b3fb58300b9c', +)] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Yasm', '1.3.0'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..30cc501dda --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: # https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' + +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.tortall.net/projects/yasm/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' From da8bbd170cbe1b10b9f69bbd599e5fd967015636 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 10:51:35 +0100 Subject: [PATCH 0109/2365] adding easyconfigs: METIS-5.1.0-GCCcore-10.2.0.eb --- .../m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7c20746615 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +# We use 32bit for indices and 64bit for content +patches = ['%(name)s-%(version)s-use-doubles.patch'] + +checksums = [ + '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2', # source + '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67', # patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' From b18ab89afa95edee457bed5dca121c8f1ff609c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 11:00:01 +0100 Subject: [PATCH 0110/2365] bump to SCOTCH 6.1.0 --- .../s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb | 19 +++++++++++++++++++ .../s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb new file mode 100644 index 0000000000..4963e9ab5b --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb @@ -0,0 +1,19 @@ +name = 'SCOTCH' +version = '6.1.0' + +homepage = 'https://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://gforge.inria.fr/frs/download.php/file/38352/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['a3bc3fa3b243fcb52f8d68de4272562a0328afb18a96f535724d284e36730485'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb new file mode 100644 index 0000000000..2bded2513c --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb @@ -0,0 +1,19 @@ +name = 'SCOTCH' +version = '6.1.0' + +homepage = 'https://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://gforge.inria.fr/frs/download.php/file/38352/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['a3bc3fa3b243fcb52f8d68de4272562a0328afb18a96f535724d284e36730485'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' From 4c435e46e93c8b785c36b8965e6d81bf845ec966 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 11:41:47 +0100 Subject: [PATCH 0111/2365] adding easyconfigs: OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb, OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb --- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb | 25 +++++++++++++++++++ .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb new file mode 100644 index 0000000000..b13a760b9d --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.6.3' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb new file mode 100644 index 0000000000..169f912486 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.6.3' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 24c424060dcb204a9f0b5dd4ad3bfb91bd1896d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 11:47:12 +0100 Subject: [PATCH 0112/2365] {geo}[foss/2020b,intel/2020b] WRF v3.9.1.1 --- .../t/time/time-1.9-GCCcore-10.2.0.eb | 27 +++++++++++ .../w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb | 48 +++++++++++++++++++ .../w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb | 48 +++++++++++++++++++ 3 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/t/time/time-1.9-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c8fda7a1c7 --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.35')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb new file mode 100644 index 0000000000..88c16adb95 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb @@ -0,0 +1,48 @@ +name = 'WRF' +version = '3.9.1.1' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.mmm.ucar.edu/weather-research-and-forecasting-model' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = [ + 'https://www2.mmm.ucar.edu/wrf/src/', + 'https://www.mmm.ucar.edu/wrf/src/', +] +sources = ['%(name)sV%(version)s.TAR.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', + 'WRF-%(version)s_GCC-10-allow-argument-mismatch.patch', + 'WRF_libtirpc.patch', +] +checksums = [ + 'e2c503c1b5adc2d3409b39d37df29d60188ff1de8c870eca15197a86d3538299', # WRFV3.9.1.1.TAR.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + # WRF-3.9.1.1_netCDF-Fortran_separate_path.patch + '49ae0eb4c5bacd3b932be14ccb9ac2d28cbd70828b633d9f13860c92d92b1eb7', +] + +# csh is used by WRF install scripts +builddependencies = [ + ('tcsh', '6.22.02'), + ('time', '1.9'), +] + +dependencies = [ + ('libtirpc', '1.2.6'), + ('JasPer', '2.0.14'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb new file mode 100644 index 0000000000..0ac579d561 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb @@ -0,0 +1,48 @@ +name = 'WRF' +version = '3.9.1.1' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.mmm.ucar.edu/weather-research-and-forecasting-model' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = [ + 'https://www2.mmm.ucar.edu/wrf/src/', + 'https://www.mmm.ucar.edu/wrf/src/', +] +sources = ['%(name)sV%(version)s.TAR.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', + 'WRF-%(version)s_GCC-10-allow-argument-mismatch.patch', + 'WRF_libtirpc.patch', +] +checksums = [ + 'e2c503c1b5adc2d3409b39d37df29d60188ff1de8c870eca15197a86d3538299', # WRFV3.9.1.1.TAR.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + # WRF-3.9.1.1_netCDF-Fortran_separate_path.patch + '49ae0eb4c5bacd3b932be14ccb9ac2d28cbd70828b633d9f13860c92d92b1eb7', +] + +# csh is used by WRF install scripts +builddependencies = [ + ('tcsh', '6.22.02'), + ('time', '1.9'), +] + +dependencies = [ + ('libtirpc', '1.2.6'), + ('JasPer', '2.0.14'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' From 2509e0938523e8651496c274225ec37f65032049 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 20:32:15 +0100 Subject: [PATCH 0113/2365] use correct libtirpc patch in WRF 3.9.1.1 easyconfigs + add missing checksums --- easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb | 5 ++++- easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb index 88c16adb95..54909c4e81 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb @@ -20,13 +20,16 @@ patches = [ 'WRF_parallel_build_fix.patch', 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', 'WRF-%(version)s_GCC-10-allow-argument-mismatch.patch', - 'WRF_libtirpc.patch', + 'WRF-3.9.1.1_libtirpc.patch', ] checksums = [ 'e2c503c1b5adc2d3409b39d37df29d60188ff1de8c870eca15197a86d3538299', # WRFV3.9.1.1.TAR.gz 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch # WRF-3.9.1.1_netCDF-Fortran_separate_path.patch '49ae0eb4c5bacd3b932be14ccb9ac2d28cbd70828b633d9f13860c92d92b1eb7', + # WRF-3.9.1.1_GCC-10-allow-argument-mismatch.patch + '3cc8a43838c7d821d02a7c64acbc08b730691af5ab6bc5f6ba0afd6356c4af01', + '9a8547d6c68b0f318f74063b690c5c8cfcd3437ebebe837dbd1d4a2dc1ad2427', # WRF-3.9.1.1_libtirpc.patch ] # csh is used by WRF install scripts diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb index 0ac579d561..9f9491846b 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb @@ -20,13 +20,16 @@ patches = [ 'WRF_parallel_build_fix.patch', 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', 'WRF-%(version)s_GCC-10-allow-argument-mismatch.patch', - 'WRF_libtirpc.patch', + 'WRF-3.9.1.1_libtirpc.patch', ] checksums = [ 'e2c503c1b5adc2d3409b39d37df29d60188ff1de8c870eca15197a86d3538299', # WRFV3.9.1.1.TAR.gz 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch # WRF-3.9.1.1_netCDF-Fortran_separate_path.patch '49ae0eb4c5bacd3b932be14ccb9ac2d28cbd70828b633d9f13860c92d92b1eb7', + # WRF-3.9.1.1_GCC-10-allow-argument-mismatch.patch + '3cc8a43838c7d821d02a7c64acbc08b730691af5ab6bc5f6ba0afd6356c4af01', + '9a8547d6c68b0f318f74063b690c5c8cfcd3437ebebe837dbd1d4a2dc1ad2427', # WRF-3.9.1.1_libtirpc.patch ] # csh is used by WRF install scripts From 1625eb8ee884d4dc300e55926f704bdc83be1cdb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Nov 2020 20:50:46 +0100 Subject: [PATCH 0114/2365] use Python 2 build dep for nodejs 12.19.0 --- easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb index b54074a104..34e7ea3828 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb @@ -18,7 +18,7 @@ checksums = ['1279e49be60d92cf4c1a48c9d92397db4e9284a100bc47689ce7924686bbddd1'] builddependencies = [ ('binutils', '2.35'), - ('Python', '3.8.6'), + ('Python', '2.7.18'), ] configopts = [ From 05df600a59cede0c93fd636b73e6265ef2fc02b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Nov 2020 12:25:10 +0100 Subject: [PATCH 0115/2365] move Boost 1.74.0 to compiler-only toolchain --- .../b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 26 ++++++++++++++++++ .../Boost/Boost-1.74.0-iccifort-2020.4.304.eb | 27 +++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..fe7439b16c --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -0,0 +1,26 @@ +name = 'Boost' +version = '1.74.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, enable threading support +boost_mpi = False +boost_multi_thread = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..1391b652d5 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb @@ -0,0 +1,27 @@ +name = 'Boost' +version = '1.74.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} +# add C++ compiler option as workaround for "error: no instance of constructor .* matches the argument list" errors +toolchainopts = {'pic': True, 'extra_cxxflags': '-DBOOST_ASIO_USE_TS_EXECUTOR_AS_DEFAULT=1'} + +source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, enable threading support +boost_mpi = False +boost_multi_thread = True + +moduleclass = 'devel' From f15c2fe3561d06f2d75e2b0e02620ee858e91bd7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Nov 2020 15:12:45 +0100 Subject: [PATCH 0116/2365] only include hypothesis as build dep in SciPy-bundle 2020.11 easyconfigs (test dep for numpy) --- .../hypothesis-5.41.2-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ .../SciPy-bundle-2020.11-foss-2020b.eb | 5 ++-- .../SciPy-bundle-2020.11-intel-2020b.eb | 5 ++-- 3 files changed, 31 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3ca1fb9593 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '5.41.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f8c281355aaba1da696e40f1488c2bb47c42660424f5750daea45a85e2d047b3'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb index 1cf04c9f8f..4f0a9bfb11 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb @@ -9,6 +9,8 @@ description = "Bundle of Python packages for scientific software" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'lowopt': True} +builddependencies = [('hypothesis', '5.41.2')] + dependencies = [ ('Python', '3.8.6'), ('pybind11', '2.6.0'), # required by scipy @@ -20,9 +22,6 @@ exts_default_options = {'source_urls': [PYPI_SOURCE]} # order is important! exts_list = [ - ('hypothesis', '5.41.1', { - 'checksums': ['06776c245b5eb25011040f94779fda6bbfa9def72074672af2e79a5e6bce8b38'], - }), ('numpy', '1.19.4', { 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512'], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb index 2664d1c89d..ab163750ce 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb @@ -9,6 +9,8 @@ description = "Bundle of Python packages for scientific software" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'pic': True, 'lowopt': True} +builddependencies = [('hypothesis', '5.41.2')] + dependencies = [ ('Python', '3.8.6'), ('pybind11', '2.6.0'), # required by scipy @@ -20,9 +22,6 @@ exts_default_options = {'source_urls': [PYPI_SOURCE]} # order is important! exts_list = [ - ('hypothesis', '5.41.1', { - 'checksums': ['06776c245b5eb25011040f94779fda6bbfa9def72074672af2e79a5e6bce8b38'], - }), ('numpy', '1.19.4', { 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': ['numpy-1.18.2-mkl.patch'], From 36ba769557233a20bf8a70f6acfcd214fcb5e89c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Nov 2020 15:15:49 +0100 Subject: [PATCH 0117/2365] remove versionsuffix for hypothesis 5.41.2 --- .../easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb index 3ca1fb9593..b5e6c59197 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb @@ -3,7 +3,6 @@ easyblock = 'PythonPackage' name = 'hypothesis' version = '5.41.2' -versionsuffix = '-Python-%(pyver)s' homepage = "https://github.com/HypothesisWorks/hypothesis" description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized From 67b01df984f90c07f1d2283aac6d7185520f0427 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 13 Nov 2020 01:21:37 +0200 Subject: [PATCH 0118/2365] adding easyconfigs: Check-0.15.2-GCCcore-10.2.0.eb, GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb, UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb, OpenMPI-4.0.5-gcccuda-2020b.eb, gompic-2020b.eb, FFTW-3.3.8-gompic-2020b.eb, ScaLAPACK-2.1.0-gompic-2020b.eb, fosscuda-2020b.eb --- .../c/Check/Check-0.15.2-GCCcore-10.2.0.eb | 37 ++++++++++++ .../f/FFTW/FFTW-3.3.8-gompic-2020b.eb | 17 ++++++ .../easyconfigs/f/fosscuda/fosscuda-2020b.eb | 29 ++++++++++ .../GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb | 58 +++++++++++++++++++ .../easyconfigs/g/gompic/gompic-2020b.eb | 21 +++++++ .../o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb | 32 ++++++++++ .../ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb | 17 ++++++ .../UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb | 55 ++++++++++++++++++ 8 files changed, 266 insertions(+) create mode 100644 easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2020b.eb create mode 100644 easybuild/easyconfigs/f/fosscuda/fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb create mode 100644 easybuild/easyconfigs/g/gompic/gompic-2020b.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb diff --git a/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..730f400e97 --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Check' +version = '0.15.2' + +homepage = 'https://libcheck.github.io/check/' +description = """ +Check is a unit testing framework for C. It features a simple interface for +defining unit tests, putting little in the way of the developer. Tests are +run in a separate address space, so both assertion failures and code errors +that cause segmentation faults or other signals can be caught. Test results +are reportable in the following: Subunit, TAP, XML, and a generic logging +format.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'libcheck' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['998d355294bb94072f40584272cf4424571c396c631620ce463f6ea97aa67d2e'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-build-docs" + +sanity_check_paths = { + 'files': ['bin/checkmk', 'lib/libcheck.a', 'lib/libcheck.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2020b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2020b.eb new file mode 100644 index 0000000000..d536144165 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2020b.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompic', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2020b.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2020b.eb new file mode 100644 index 0000000000..89c986f17f --- /dev/null +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'Toolchain' + +name = 'fosscuda' +version = '2020b' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '10.2.0' + +# toolchain used to build fosscuda dependencies +local_comp_mpi_tc = ('gompic', version) + +# compiler toolchain dependencies +# We need GCC, CUDA and OpenMPI as explicit dependencies instead of +# gompic toolchain because of toolchain preperation functions. +dependencies = [ + ('GCC', local_gccver), # part of gompic + ('CUDA', '11.1.1', '', ('GCC', local_gccver)), # part of gompic + ('OpenMPI', '4.0.5', '', ('gcccuda', version)), # part of gompic + ('OpenBLAS', '0.3.12', '', ('GCC', local_gccver)), + ('FFTW', '3.3.8', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.1.0', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb new file mode 100644 index 0000000000..37db8b0407 --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.1' +local_cudaversion = '11.1.1' +versionsuffix = '-CUDA-%s' % local_cudaversion + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['cecc7dcc071107f77396f5553c9109790b6d2298ae29eb2dbbdd52b2a213e4ea'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CUDAcore', local_cudaversion, '', True), + ('Check', '0.15.2'), +] + +# This easyconfig only installs the library and binaries of GDRCopy. Please +# keep in mind that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] + +local_envopts = "PREFIX=%(installdir)s CUDA=$EBROOTCUDACORE" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib exes %s" % local_envopts +installopts = local_envopts + +sanity_check_paths = { + 'files': ['bin/copybw', 'bin/copylat', 'bin/sanity', 'lib/libgdrapi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2020b.eb b/easybuild/easyconfigs/g/gompic/gompic-2020b.eb new file mode 100644 index 0000000000..b5d2a9fd20 --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-2020b.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '2020b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, + including OpenMPI for MPI support with CUDA features enabled.""" + +toolchain = SYSTEM + +local_gccver = '10.2.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # part of gcccuda + ('CUDA', '11.1.1', '', ('GCC', local_gccver)), # part of gcccuda + ('OpenMPI', '4.0.5', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb new file mode 100644 index 0000000000..b83f21c664 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -0,0 +1,32 @@ +name = 'OpenMPI' +version = '4.0.5' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'gcccuda', 'version': '2020b'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('libevent', '2.1.12'), + ('UCX', '1.9.0', '-CUDA-11.1.1'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb new file mode 100644 index 0000000000..c7a884c36d --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb @@ -0,0 +1,17 @@ +name = 'ScaLAPACK' +version = '2.1.0' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompic', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +checksums = ['61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6'] + +dependencies = [('OpenBLAS', '0.3.12')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb new file mode 100644 index 0000000000..25e219e43e --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -0,0 +1,55 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.9.0' +local_cudaversion = '11.1.1' +versionsuffix = '-CUDA-%s' % local_cudaversion + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['a7a2c8841dc0d5444088a4373dc9b9cc68dbffcd917c1eba92ca8ed8e5e635fb'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +dependencies = [ + ('numactl', '2.0.13'), + ('CUDAcore', local_cudaversion, '', True), + ('GDRCopy', '2.1', versionsuffix), +] + +# CUDA_CFLAGS set by EB toolchain but also used differently in UCX makefiles +# unset LIBS from EB toolchain to avoid unconditional linking to libcudart: +# it only needs to be linked by the CUDA run-time plugins +preconfigopts = 'autoreconf && unset CUDA_CFLAGS && unset LIBS && ' +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' +configopts += '--with-cuda=$EBROOTCUDACORE --with-gdrcopy=$EBROOTGDRCOPY ' + +prebuildopts = 'unset CUDA_CFLAGS && unset LIBS && ' +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From e7cd2ba58ebda34479d9805beaab11a56ec7bb91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Nov 2020 16:21:20 +0100 Subject: [PATCH 0119/2365] adding easyconfigs: netCDF-C++4-4.3.1-gompi-2020b.eb --- .../netCDF-C++4-4.3.1-gompi-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020b.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020b.eb new file mode 100644 index 0000000000..7afed09346 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.7.4')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' From 0585f5c8dee3f552d0888abc24007174044bbe8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 Nov 2020 16:45:18 +0100 Subject: [PATCH 0120/2365] Update easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb Co-authored-by: Alex Domingo --- .../easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb index 25e219e43e..0f4274fa67 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -26,7 +26,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -osdependencies = [OS_PKG_OPENSSL_DEV] +osdependencies = [OS_PKG_IBVERBS_DEV] dependencies = [ ('numactl', '2.0.13'), From c876f076e454c525841ff9f11d13ea58eca8eb69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 Nov 2020 16:45:25 +0100 Subject: [PATCH 0121/2365] Update easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb Co-authored-by: Alex Domingo --- .../g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb index 37db8b0407..5e4e8fe1c8 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', True), # needed by GDRCopy binaries, which are tools for testing ('Check', '0.15.2'), ] From b0c72eb71b294e9a9c35ec8c18c7a785eff38e56 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Sun, 15 Nov 2020 02:52:47 +0000 Subject: [PATCH 0122/2365] GCCcore-10.2.0: enable NVPTX offload Requires https://github.com/easybuilders/easybuild-easyblocks/pull/2235 --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 462a9b073d..8cb648bbd1 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -17,6 +17,8 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'ftp://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools ] sources = [ 'gcc-%(version)s.tar.gz', @@ -24,6 +26,8 @@ sources = [ 'mpfr-4.1.0.tar.bz2', 'mpc-1.1.0.tar.gz', 'isl-0.22.1.tar.bz2', + 'newlib-3.3.0.tar.gz', + '5f6f343.tar.gz', # nvptx-tools ] patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', @@ -36,6 +40,8 @@ checksums = [ 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 + '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66', # newlib-3.3.0.tar.gz + 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # 5f6f343.tar.gz '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCC-10.2_fix-has-include-Fortran.patch @@ -49,5 +55,6 @@ builddependencies = [ languages = ['c', 'c++', 'fortran'] withisl = True +withnvptx = True moduleclass = 'compiler' From 6eb1b3d47bfa1bd061d3b3bd0672f3bad5fd44b5 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 15 Nov 2020 17:49:08 +0200 Subject: [PATCH 0123/2365] fix configure step for ucx --- .../u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb index 0f4274fa67..48c65be294 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -34,10 +34,7 @@ dependencies = [ ('GDRCopy', '2.1', versionsuffix), ] -# CUDA_CFLAGS set by EB toolchain but also used differently in UCX makefiles -# unset LIBS from EB toolchain to avoid unconditional linking to libcudart: -# it only needs to be linked by the CUDA run-time plugins -preconfigopts = 'autoreconf && unset CUDA_CFLAGS && unset LIBS && ' +configure_cmd = "contrib/configure-release" configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' configopts += '--without-java --disable-doxygen-doc ' configopts += '--with-cuda=$EBROOTCUDACORE --with-gdrcopy=$EBROOTGDRCOPY ' From 79f3fcf71d8d09df7533a397b198588e6ce6aad9 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 16 Nov 2020 04:40:21 +0200 Subject: [PATCH 0124/2365] rebase gompic-2020b scalapack on gompi-2020b --- .../s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb index c7a884c36d..802ecd11e9 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb @@ -10,7 +10,13 @@ toolchainopts = {'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] -checksums = ['61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6'] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6', # scalapack-2.1.0.tgz + 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch +] + +builddependencies = [('CMake', '3.18.4')] dependencies = [('OpenBLAS', '0.3.12')] From 9b6639f2a2252afdca322f9d1bf2680c13a98639 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Nov 2020 16:02:38 +0100 Subject: [PATCH 0125/2365] add numexpr and Bottleneck to SciPy-bundle 2020.11 (recommended deps for pandas), fixes #11363 --- .../s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb | 6 ++++++ .../s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb index 4f0a9bfb11..4e8b17e249 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb @@ -32,6 +32,12 @@ exts_list = [ ('mpi4py', '3.0.3', { 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], }), + ('numexpr', '2.7.1', { + 'checksums': ['b0d239d9827e1bcee08344fd05835823bc60aff97232e35a928214d03ff802b1'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), ('pandas', '1.1.4', { 'checksums': ['a979d0404b135c63954dea79e6246c45dd45371a88631cdbb4877d844e6de3b6'], }), diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb index ab163750ce..f8aaa020b3 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb @@ -36,6 +36,12 @@ exts_list = [ ('mpi4py', '3.0.3', { 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], }), + ('numexpr', '2.7.1', { + 'checksums': ['b0d239d9827e1bcee08344fd05835823bc60aff97232e35a928214d03ff802b1'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), ('pandas', '1.1.4', { 'checksums': ['a979d0404b135c63954dea79e6246c45dd45371a88631cdbb4877d844e6de3b6'], # strip out use of -Werror to avoid failing compilation due to Intel compiler warning From 2d808de7ae9540363abaea403a13351cd5955127 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 16 Nov 2020 21:16:11 +0200 Subject: [PATCH 0126/2365] adding easyconfigs: CUDA-11.1.1-iccifort-2020.4.304.eb, iccifortcuda-2020b.eb, impi-2019.9.304-iccifortcuda-2020b.eb, iimpic-2020b.eb, imkl-2020.4.304-iimpic-2020b.eb, intelcuda-2020b.eb --- .../c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb | 17 ++++++++ .../i/iccifortcuda/iccifortcuda-2020b.eb | 18 +++++++++ .../easyconfigs/i/iimpic/iimpic-2020b.eb | 19 +++++++++ .../i/imkl/imkl-2020.4.304-iimpic-2020b.eb | 39 ++++++++++++++++++ .../impi-2019.9.304-iccifortcuda-2020b.eb | 40 +++++++++++++++++++ .../i/intelcuda/intelcuda-2020b.eb | 20 ++++++++++ 6 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2020b.eb create mode 100644 easybuild/easyconfigs/i/iimpic/iimpic-2020b.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb create mode 100644 easybuild/easyconfigs/i/intelcuda/intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..c9848f3232 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' +name = 'CUDA' +version = '11.1.1' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +dependencies = [('CUDAcore', version, '', True)] + +altroot = 'CUDAcore' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2020b.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2020b.eb new file mode 100644 index 0000000000..ffe511679a --- /dev/null +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2020b.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'iccifortcuda' +version = '2020b' + +homepage = '(none)' +description = "Intel C, C++ & Fortran compilers with CUDA toolkit" + +toolchain = SYSTEM + +local_compver = '2020.4.304' + +dependencies = [ + ('iccifort', local_compver), + ('CUDA', '11.1.1', '', ('iccifort', local_compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2020b.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2020b.eb new file mode 100644 index 0000000000..bb2d747fe5 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2020b.eb @@ -0,0 +1,19 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ +easyblock = "Toolchain" + +name = 'iimpic' +version = '2020b' + +homepage = '(none)' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA.""" + +toolchain = SYSTEM + +local_compver = '2020.4.304' +dependencies = [ + ('iccifort', local_compver), + ('CUDA', '11.1.1', '', ('iccifort', local_compver)), + ('impi', '2019.9.304', '', ('iccifortcuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb new file mode 100644 index 0000000000..e26a6afff2 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.4.304' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpic', 'version': '2020b'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb new file mode 100644 index 0000000000..3305cf60a8 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2019.9.304' + +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'iccifortcuda', 'version': '2020b'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] + +dependencies = [ + # needed by libfabric provider MLX introduced in Intel MPI v2019.6, + # https://software.intel.com/en-us/articles/improve-performance-and-stability-with-intel-mpi-library-on-infiniband + ('UCX', '1.9.0'), +] + +dontcreateinstalldir = True + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = True + +modextravars = { + # to enable SLURM integration with srun (site-specific) + # 'I_MPI_PMI_LIBRARY': 'libpmi2.so', + + # set this if mpirun gives you a floating point exception (SIGFPE), see + # https://software.intel.com/en-us/forums/intel-clusters-and-hpc-technology/topic/852307 + # 'I_MPI_HYDRA_TOPOLIB': 'ipl', +} + +# may be needed if you enable I_MPI_PMI_LIBRARY above +# osdependencies = [('slurm-libpmi')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2020b.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2020b.eb new file mode 100644 index 0000000000..c9456eab5c --- /dev/null +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2020b.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'intelcuda' +version = '2020b' + +homepage = '(none)' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, + Intel MPI & Intel MKL, with CUDA toolkit""" + +toolchain = SYSTEM + +local_compver = '2020.4.304' +dependencies = [ + ('iccifort', local_compver), + ('CUDA', '11.1.1', '', ('iccifort', local_compver)), + ('impi', '2019.9.304', '', ('iccifortcuda', version)), + ('imkl', local_compver, '', ('iimpic', version)), +] + +moduleclass = 'toolchain' From 73027dcc440f46a91a793ab85fe5376f6bbd6fb3 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 17 Nov 2020 20:06:51 +0000 Subject: [PATCH 0127/2365] Better source urls/filenames as suggested by @boegel --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 8cb648bbd1..494e8f85cb 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -17,7 +17,7 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies 'http://isl.gforge.inria.fr/', # original HTTP source for ISL - 'ftp://sourceware.org/pub/newlib/', # for newlib + 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools ] sources = [ @@ -27,7 +27,7 @@ sources = [ 'mpc-1.1.0.tar.gz', 'isl-0.22.1.tar.bz2', 'newlib-3.3.0.tar.gz', - '5f6f343.tar.gz', # nvptx-tools + {'download_filename': '5f6f343.tar.gz', 'filename': 'nvptx-tools-20180301.tar.gz'}, ] patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', @@ -41,7 +41,7 @@ checksums = [ '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66', # newlib-3.3.0.tar.gz - 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # 5f6f343.tar.gz + 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # nvptx-tools-20180301.tar.gz '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCC-10.2_fix-has-include-Fortran.patch From 37f9bd372ad50bd92a3b085c921ca94f1b36dc13 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 18 Nov 2020 00:26:38 +0000 Subject: [PATCH 0128/2365] at least two spaces before inline comment --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 494e8f85cb..ead740a862 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -17,8 +17,8 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies 'http://isl.gforge.inria.fr/', # original HTTP source for ISL - 'https://sourceware.org/pub/newlib/', # for newlib - 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools ] sources = [ 'gcc-%(version)s.tar.gz', From f1a8c42ccc06f6164cee7045a9811478f824fbdc Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 20 Nov 2020 15:18:41 +0200 Subject: [PATCH 0129/2365] Downgrade to Qt 5.14.2 --- .../q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f3c5d73a63 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb @@ -0,0 +1,72 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.14.2' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +patches = [ + 'Qt5-5.13.1_fix-avx2.patch', + 'Qt5-5.13.1_fix-qmake-libdir.patch', + 'Qt5-5.14.1_fix-OF-Gentoo.patch', +] +checksums = [ + 'c6fcd53c744df89e7d3223c02838a33309bd1c291fcb6f9341505fe99f7f19fa', # qt-everywhere-src-5.14.2.tar.xz + '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch + '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch + '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), + # deps for QtWebEngine + ('Bison', '3.7.1'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.10.1'), + ('Python', '3.8.6'), + ('re2c', '2.0.3') +] + +dependencies = [ + ('double-conversion', '3.1.5'), + ('GLib', '2.66.1'), + ('PCRE2', '10.35'), + ('libpng', '1.6.37'), + # deps for QtWebEngine + ('X11', '20201008'), + ('fontconfig', '2.13.92'), + ('DBus', '1.13.18'), + ('libevent', '2.1.12'), + ('libGLU', '9.0.1'), + ('libjpeg-turbo', '2.0.5'), + ('NSS', '3.57'), + ('snappy', '1.1.8'), + ('JasPer', '2.0.14'), + ('bzip2', '1.0.8'), + # OS dependency should be preferred if the os version is more recent then this version, + # it is nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), # Qt5 > 5.15.0 requires OpenSSL 1.1.1 +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +# qtwayland fails to build on (some) Centos 7 systems +configopts = '-skip qtgamepad -skip qtwayland' + +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' From 02bf89a68ef73eead613e375f7ebecb885bea0dd Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 21 Nov 2020 05:10:04 +0200 Subject: [PATCH 0130/2365] Include additional patch --- easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb index f3c5d73a63..b99b7bfdf2 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb @@ -19,12 +19,14 @@ patches = [ 'Qt5-5.13.1_fix-avx2.patch', 'Qt5-5.13.1_fix-qmake-libdir.patch', 'Qt5-5.14.1_fix-OF-Gentoo.patch', + 'Qt5-5.14.2_fix-missing-stdint.patch', ] checksums = [ 'c6fcd53c744df89e7d3223c02838a33309bd1c291fcb6f9341505fe99f7f19fa', # qt-everywhere-src-5.14.2.tar.xz '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch + '48f8819034084335fbf89a297f29dff1b10fdb7bc5f1dbbd6a7c03f5edaafa21', # Qt5-5.14.2_fix-missing-stdint.patch ] builddependencies = [ From cdaee5909f36b0d7d602db6e903b9fd417f8344e Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 23 Nov 2020 12:48:05 +0200 Subject: [PATCH 0131/2365] Include yet another missing header in patch --- easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb index b99b7bfdf2..909d8a6ba3 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb @@ -26,7 +26,7 @@ checksums = [ '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch - '48f8819034084335fbf89a297f29dff1b10fdb7bc5f1dbbd6a7c03f5edaafa21', # Qt5-5.14.2_fix-missing-stdint.patch + '465e4dc69adb2be9dd2954fc6c9a347191d9d937c6d5e004938873772537e33f', # Qt5-5.14.2_fix-missing-stdint.patch ] builddependencies = [ From b3de58f1d2a39c94a5b638b404854dee1acc0677 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 28 Nov 2020 17:59:47 +0200 Subject: [PATCH 0132/2365] Yet more patches for GCC 10 --- easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb index 909d8a6ba3..7a16ddabda 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb @@ -20,13 +20,15 @@ patches = [ 'Qt5-5.13.1_fix-qmake-libdir.patch', 'Qt5-5.14.1_fix-OF-Gentoo.patch', 'Qt5-5.14.2_fix-missing-stdint.patch', + 'Qt5-5.14.2_fix-webengine-bison.patch', ] checksums = [ 'c6fcd53c744df89e7d3223c02838a33309bd1c291fcb6f9341505fe99f7f19fa', # qt-everywhere-src-5.14.2.tar.xz '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch - '465e4dc69adb2be9dd2954fc6c9a347191d9d937c6d5e004938873772537e33f', # Qt5-5.14.2_fix-missing-stdint.patch + '648e2a92d5ea139543db5d01a80aa33d4721e52bb59c785490b64497b0ede4ab', # Qt5-5.14.2_fix-missing-stdint.patch + '6ace4735e35dee95d6b6c7eea3a7c46c264589a319d745310282ee724f632861', # Qt5-5.14.2_fix-webengine-bison.patch ] builddependencies = [ From a19753e4a97cb46e4fb8a8df4372f44ea928ee12 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 28 Nov 2020 18:12:32 +0200 Subject: [PATCH 0133/2365] Drop back to Qt 5.14.2 --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index 8706486679..2fc24f0a12 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ toolchainopts = {'cstd': 'c++11'} builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '3.8.6'), - ('Qt5', '5.15.1'), + ('Qt5', '5.14.2'), ] default_easyblock = 'PythonPackage' From 753ea7c83171cb3f75bdf39859721e1f4df04d80 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 28 Nov 2020 21:54:20 +0200 Subject: [PATCH 0134/2365] QtWebEngine is the worst thing ever, reverting dep to python 2 --- easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb index 7a16ddabda..9a0f8bec84 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb @@ -39,7 +39,7 @@ builddependencies = [ ('flex', '2.6.4'), ('gperf', '3.1'), ('Ninja', '1.10.1'), - ('Python', '3.8.6'), + ('Python', '2.7.18'), ('re2c', '2.0.3') ] From 5066af771ea9faa50dee2a98707d7bf278ef9814 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Nov 2020 21:56:24 +0100 Subject: [PATCH 0135/2365] disable broken numpy test in SciPy-bundle 2020.11 easyconfig using intel/2020b (fixes #11789) --- .../s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb index f8aaa020b3..9d3c3bddbc 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb @@ -24,10 +24,15 @@ exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ ('numpy', '1.19.4', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'patches': ['numpy-1.18.2-mkl.patch'], + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.19.4_disable-broken-test.patch', + ], 'checksums': [ '141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512', # numpy-1.19.4.zip 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + # numpy-1.19.4_disable-broken-test.patch + '9cc8bbd106ecba603254536101f53fdc200e81d43ca4800b5a84be9b645e9320', ], }), ('scipy', '1.5.4', { From 58051bd47bcbf66a20035662f6fbb2997c1ab360 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 3 Dec 2020 02:59:42 +0200 Subject: [PATCH 0136/2365] adding easyconfigs: giflib-5.2.1-GCCcore-10.2.0.eb --- .../g/giflib/giflib-5.2.1-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0a9b9da5c1 --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' From da3a4b221d35b610b0ace3e0c7cab3d5f3fb10ed Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 3 Dec 2020 03:03:35 +0200 Subject: [PATCH 0137/2365] adding easyconfigs: JsonCpp-1.9.4-GCCcore-10.2.0.eb --- .../j/JsonCpp/JsonCpp-1.9.4-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dccb8a613b --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.4' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['e34a628a8142643b976c7233ef381457efad79468c67cb1ae0b83a33d7493999'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.so'], + 'dirs': [], +} + +moduleclass = 'lib' From c64865eebac98a401d65bc0b7388d9088ac46eb3 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 3 Dec 2020 03:05:01 +0200 Subject: [PATCH 0138/2365] adding easyconfigs: LMDB-0.9.24-GCCcore-10.2.0.eb --- .../l/LMDB/LMDB-0.9.24-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMDB/LMDB-0.9.24-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.24-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.24-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..155ad1c68c --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.24-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.24' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['44602436c52c29d4f301f55f6fd8115f945469b868348e3cddaf91ab2473ea26'] + +builddependencies = [('binutils', '2.35')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'], 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From d99458be081a461d301f309daa24a06d4c977823 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 3 Dec 2020 03:08:35 +0200 Subject: [PATCH 0139/2365] adding easyconfigs: nsync-1.24.0-GCCcore-10.2.0.eb --- .../n/nsync/nsync-1.24.0-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0f9cc830a4 --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.24.0' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/nsync/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['47a6eb2a295be5121a1904a6a775722338a20dc02ee3eec4169ed2c3f203617a'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Ninja', '1.10.1'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' From 746f81d212d35336e7cf10f16086a3aaac1eca75 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 3 Dec 2020 03:15:01 +0200 Subject: [PATCH 0140/2365] adding easyconfigs: SWIG-4.0.2-GCCcore-10.2.0.eb --- .../s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..90a44c127b --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +name = 'SWIG' +version = '4.0.2' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d53be9730d8d58a16bf0cbd1f8ac0c0c3e1090573168bfa151b01eb47fa906fc'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('zlib', '1.2.11'), + ('PCRE', '8.44'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' From 2608339676f2b66296c57f52cea9c7c4ef94e8e7 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 3 Dec 2020 04:21:42 +0200 Subject: [PATCH 0141/2365] Drop versionsuffix --- .../p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ccc0793115 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '8.0.1' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.1.0'), + ('freetype', '2.10.3') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From e44c40eaffe266131bab4b84761ef3e34de24e14 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 3 Dec 2020 20:07:03 +0200 Subject: [PATCH 0142/2365] adding easyconfigs: MPFR-4.1.0-GCCcore-10.2.0.eb --- .../m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..07cac7df6c --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '4.1.0' + +homepage = 'https://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('GMP', '6.2.0'), +] + +runtest = 'check' + +# copy libmpfr.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a src/.libs/libmpfr.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' From 352ab8d2ae8c94e7f331003b61ed3fd5d7fd804e Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 3 Dec 2020 20:23:11 +0200 Subject: [PATCH 0143/2365] adding easyconfigs: PyYAML-5.3.1-GCCcore-10.2.0.eb, libyaml-0.2.5-GCCcore-10.2.0.eb --- .../l/libyaml/libyaml-0.2.5-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ .../p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb | 27 ++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ca89e6e47b --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.5' + +homepage = 'https://pyyaml.org/wiki/LibYAML' + +description = """LibYAML is a YAML parser and emitter written in C.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://pyyaml.org/download/libyaml/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.%s" % SHLIB_EXT], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0375b33263 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '5.3.1' + +homepage = "https://github.com/yaml/pyyaml" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e9f45bd5b92c7974e59bcd2dcc8631a6b6cc380a904725fce7bc08872e691615'] + +builddependencies = [('binutils', '2.35')] + +multi_deps = {'Python': ['3.8.6', '2.7.18']} + +dependencies = [('libyaml', '0.2.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'yaml'} + +moduleclass = 'lib' From dea2321dc8250ae577694a8d4cc61a8c17b4e0c0 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 3 Dec 2020 20:38:31 +0200 Subject: [PATCH 0144/2365] Fix checksum --- easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb index 0375b33263..ded1c9a677 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['e9f45bd5b92c7974e59bcd2dcc8631a6b6cc380a904725fce7bc08872e691615'] +checksums = ['b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d'] builddependencies = [('binutils', '2.35')] From 6287ad9c32a5d9f4aaf795f439d5314fb82dd6a7 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 3 Dec 2020 21:36:15 +0200 Subject: [PATCH 0145/2365] adding easyconfigs: protobuf-python-3.14.0-foss-2020b.eb, protobuf-3.14.0-GCCcore-10.2.0.eb --- .../protobuf-3.14.0-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.14.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.14.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.14.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..83617c750d --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.14.0-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '3.14.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d0f5f605d0d656007ce6c8b5a82df3037e1d8fe8b121ed42e536f569dec16113'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +srcdir = 'cmake' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 68e08d2d364285fb9478ae7d9fd7b0208798f165 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 4 Dec 2020 02:25:51 +0200 Subject: [PATCH 0146/2365] adding easyconfigs: SciPy-bundle-2020.03-intelcuda-2020a-Python-3.8.2.eb, SciPy-bundle-2020.11-fosscuda-2020b.eb, SciPy-bundle-2020.11-intelcuda-2020b.eb --- .../SciPy-bundle-2020.11-fosscuda-2020b.eb | 54 +++++++++++++++ .../SciPy-bundle-2020.11-intelcuda-2020b.eb | 65 +++++++++++++++++++ 2 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb new file mode 100644 index 0000000000..3b06eb52b6 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2020.11' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [('hypothesis', '5.41.2')] + +dependencies = [ + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), # required by scipy +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +# order is important! +exts_list = [ + ('numpy', '1.19.4', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512'], + }), + ('scipy', '1.5.4', { + 'checksums': ['4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b'], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('numexpr', '2.7.1', { + 'checksums': ['b0d239d9827e1bcee08344fd05835823bc60aff97232e35a928214d03ff802b1'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '1.1.4', { + 'checksums': ['a979d0404b135c63954dea79e6246c45dd45371a88631cdbb4877d844e6de3b6'], + }), + ('mpmath', '1.1.0', { + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb new file mode 100644 index 0000000000..d254373f04 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2020.11' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [('hypothesis', '5.41.2')] + +dependencies = [ + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), # required by scipy +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +# order is important! +exts_list = [ + ('numpy', '1.19.4', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.19.4_disable-broken-test.patch', + ], + 'checksums': [ + '141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512', # numpy-1.19.4.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + # numpy-1.19.4_disable-broken-test.patch + '9cc8bbd106ecba603254536101f53fdc200e81d43ca4800b5a84be9b645e9320', + ], + }), + ('scipy', '1.5.4', { + 'checksums': ['4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b'], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('numexpr', '2.7.1', { + 'checksums': ['b0d239d9827e1bcee08344fd05835823bc60aff97232e35a928214d03ff802b1'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '1.1.4', { + 'checksums': ['a979d0404b135c63954dea79e6246c45dd45371a88631cdbb4877d844e6de3b6'], + # strip out use of -Werror to avoid failing compilation due to Intel compiler warning + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + }), + ('mpmath', '1.1.0', { + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 725dbb4bec4410625b17b6423c820dafdfcd997a Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 4 Dec 2020 04:10:53 +0200 Subject: [PATCH 0147/2365] Add pyhon versionsuffix, add download_dep_fail --- .../pkgconfig-1.5.1-GCCcore-10.2.0-python.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb new file mode 100644 index 0000000000..de70590971 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.1' +versionsuffix = '-python' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('pkg-config', '0.29.2'), +] + +# Due to poetry doing the actual build of pkgconfig we need use_pip=False +use_pip = False +download_dep_fail = True + +moduleclass = 'devel' From 29a635a416afcf3ba214d5332eec1009fa41df08 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Dec 2020 15:03:32 +0100 Subject: [PATCH 0148/2365] fix version for (commented out) OpenSSL dep --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 21d752462c..208a7b4dcf 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -48,7 +48,7 @@ dependencies = [ # OS dependency should be preferred if the os version is more recent then # this version, it's nice to have an up to date openssl for security # reasons - # ('OpenSSL', '1.1.1e'), + # ('OpenSSL', '1.1.1h'), ] osdependencies = [OS_PKG_OPENSSL_DEV] From 20b5743bd696739d9be821d5b5184486e6a4453c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Dec 2020 15:16:13 +0100 Subject: [PATCH 0149/2365] include blavaan + required packages as extensions in R 4.0.3 easyconfig --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 208a7b4dcf..264f099c23 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2730,6 +2730,18 @@ exts_list = [ ('DescTools', '0.99.38', { 'checksums': ['bd8edce64a8f9e295611959295b85cf8d7bbf915093158016169bd334e0e1104'], }), + ('RcppParallel', '5.0.2', { + 'checksums': ['8ca200908c6365aafb2063be1789f0894969adc03c0f523c6cc45434b8236f81'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.3-12', { + 'checksums': ['9a44a21343e1dcced0c65c3117edc5ab2412513c258f1422fd39852e4d9cd706'], + }), ] moduleclass = 'lang' From 8cc0e63e3df5b00501af2064fbfbfd777affe8dd Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 5 Dec 2020 18:52:13 +0200 Subject: [PATCH 0150/2365] adding easyconfigs: HDF5-1.10.7-gompic-2020b.eb, HDF5-1.10.7-iimpic-2020b.eb --- .../h/HDF5/HDF5-1.10.7-gompic-2020b.eb | 21 +++++++++++++++++++ .../h/HDF5/HDF5-1.10.7-iimpic-2020b.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompic-2020b.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpic-2020b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompic-2020b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompic-2020b.eb new file mode 100644 index 0000000000..351bed5f26 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-gompic-2020b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.7' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompic', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpic-2020b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpic-2020b.eb new file mode 100644 index 0000000000..e0191b8fb7 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iimpic-2020b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.7' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpic', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From 5961365f8b856771a2b661b4179012d4092ef5b1 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 5 Dec 2020 21:52:35 +0200 Subject: [PATCH 0151/2365] adding easyconfigs: h5py-3.1.0-foss-2020b.eb, h5py-3.1.0-fosscuda-2020b.eb, h5py-3.1.0-intel-2020b.eb, h5py-3.1.0-intelcuda-2020b.eb --- .../h/h5py/h5py-3.1.0-foss-2020b.eb | 32 +++++++++++++++++++ .../h/h5py/h5py-3.1.0-fosscuda-2020b.eb | 32 +++++++++++++++++++ .../h/h5py/h5py-3.1.0-intel-2020b.eb | 32 +++++++++++++++++++ .../h/h5py/h5py-3.1.0-intelcuda-2020b.eb | 32 +++++++++++++++++++ 4 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb new file mode 100644 index 0000000000..a14cc3f059 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.1.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2'] + +builddependencies = [('pkgconfig', '1.5.1', '-python')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..dd5d5e8161 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.1.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2'] + +builddependencies = [('pkgconfig', '1.5.1', '-python')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb new file mode 100644 index 0000000000..8da1824847 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.1.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2'] + +builddependencies = [('pkgconfig', '1.5.1', '-python')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb new file mode 100644 index 0000000000..1bc2912405 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.1.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2'] + +builddependencies = [('pkgconfig', '1.5.1', '-python')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' + +moduleclass = 'data' From 7c0f786da3127b14b0f6b89790a5a38390b3e58b Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 5 Dec 2020 23:16:39 +0200 Subject: [PATCH 0152/2365] adding easyconfigs: libidn-1.36-GCCcore-10.2.0.eb, wget-1.20.3-GCCcore-10.2.0.eb --- .../l/libidn/libidn-1.36-GCCcore-10.2.0.eb | 22 +++++++++ .../w/wget/wget-1.20.3-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.36-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.36-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.36-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6a64b05a39 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.36-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.36' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['14b67108344d81ba844631640df77c9071d9fb0659b080326ff5424e86b14038'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..16e7bb29ad --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.20.3' + +homepage = 'https://www.gnu.org/software/wget' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31cccfc6630528db1c8e3a06f6decf2a370060b982841cfab2b8677400a5092e'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('PCRE', '8.44'), + ('libidn', '1.36'), + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.6.14'), +] + +# make sure pkg-config picks up system packages (OpenSSL & co) +preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +configopts = '--with-ssl=openssl ' + +osdependencies = [OS_PKG_OPENSSL_DEV] +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'devel' From b520a52ba2aa6b2d78c32ea0701dccb96ff49143 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 6 Dec 2020 21:07:09 +0200 Subject: [PATCH 0153/2365] adding easyconfigs: hypothesis-5.41.5-GCCcore-10.2.0.eb --- .../hypothesis-5.41.5-GCCcore-10.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6a08263f91 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '5.41.5' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['a74e127a865fde12b853cc00f5f52a3a1601d2a1c311b3ffc8de92a4c06778f7'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 9f7495ea22efffea9eff40ff346b1a4ee0707254 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 6 Dec 2020 22:43:56 +0200 Subject: [PATCH 0154/2365] Drop protobuf-python to gcccore --- .../protobuf-python-3.14.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3a704fdfd3 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.14.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = [{'download_filename': 'protobuf-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['1d63eb389347293d8915fb47bee0951c7b5dab522a4a60118b9a18f33e21f8ce'] + +dependencies = [ + ('Python', '3.8.6'), + ('protobuf', version) +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' From 8a48865006a07701892515e6e5033d6cc9e1b7c8 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 7 Dec 2020 00:57:42 +0200 Subject: [PATCH 0155/2365] Add missing binutils build dep --- .../p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb index 3a704fdfd3..8d37e9a2d1 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb @@ -12,6 +12,8 @@ source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] sources = [{'download_filename': 'protobuf-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] checksums = ['1d63eb389347293d8915fb47bee0951c7b5dab522a4a60118b9a18f33e21f8ce'] +builddependencies = [('binutils', '2.35')] + dependencies = [ ('Python', '3.8.6'), ('protobuf', version) From bdcd6d8563187713cd18c61b24b4cf12ccb41eeb Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 7 Dec 2020 03:07:40 +0200 Subject: [PATCH 0156/2365] adding easyconfigs: scikit-learn-0.23.2-foss-2020b.eb, scikit-learn-0.23.2-fosscuda-2020b.eb, scikit-learn-0.23.2-intel-2020b.eb, scikit-learn-0.23.2-intelcuda-2020b.eb --- .../scikit-learn-0.23.2-foss-2020b.eb | 28 +++++++++++++++++++ .../scikit-learn-0.23.2-fosscuda-2020b.eb | 28 +++++++++++++++++++ .../scikit-learn-0.23.2-intel-2020b.eb | 28 +++++++++++++++++++ .../scikit-learn-0.23.2-intelcuda-2020b.eb | 28 +++++++++++++++++++ 4 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb new file mode 100644 index 0000000000..7fab0ef313 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.23.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11') +] + +use_pip = True +sanity_pip_check = True + +modulename = 'sklearn' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..f39ecbe453 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.23.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11') +] + +use_pip = True +sanity_pip_check = True + +modulename = 'sklearn' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb new file mode 100644 index 0000000000..c588294783 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.23.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11') +] + +use_pip = True +sanity_pip_check = True + +modulename = 'sklearn' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb new file mode 100644 index 0000000000..4284375f56 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.23.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11') +] + +use_pip = True +sanity_pip_check = True + +modulename = 'sklearn' + +moduleclass = 'data' From 30c22b57ba7f0659388c9dc15ebab435bd24b7d5 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 7 Dec 2020 03:51:55 +0200 Subject: [PATCH 0157/2365] adding easyconfigs: matplotlib-3.3.3-foss-2020b.eb, matplotlib-3.3.3-fosscuda-2020b.eb, matplotlib-3.3.3-intel-2020b.eb, matplotlib-3.3.3-intelcuda-2020b.eb --- .../matplotlib/matplotlib-3.3.3-foss-2020b.eb | 56 +++++++++++++++++++ .../matplotlib-3.3.3-fosscuda-2020b.eb | 56 +++++++++++++++++++ .../matplotlib-3.3.3-intel-2020b.eb | 56 +++++++++++++++++++ .../matplotlib-3.3.3-intelcuda-2020b.eb | 56 +++++++++++++++++++ 4 files changed, 224 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb new file mode 100644 index 0000000000..fc861d5299 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.3.3' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..bf918e4c83 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.3.3' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb new file mode 100644 index 0000000000..4ccf19ae6c --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.3.3' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb new file mode 100644 index 0000000000..f3fd380030 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.3.3' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From 3029445ff27b9652e3b0774027f5a169fc85da92 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 7 Dec 2020 18:23:23 +0200 Subject: [PATCH 0158/2365] Fix modulename variable --- .../s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb | 2 +- .../s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb | 2 +- .../s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb | 2 +- .../s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb index 7fab0ef313..04df12fb64 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb @@ -23,6 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -modulename = 'sklearn' +options = {'modulename': 'sklearn'} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb index f39ecbe453..7ed52a034d 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb @@ -23,6 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -modulename = 'sklearn' +options = {'modulename': 'sklearn'} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb index c588294783..99a2858d94 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb @@ -23,6 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -modulename = 'sklearn' +options = {'modulename': 'sklearn'} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb index 4284375f56..8de6ecd21b 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb @@ -23,6 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -modulename = 'sklearn' +options = {'modulename': 'sklearn'} moduleclass = 'data' From 0fe424ef7eac8675bfff0ec63403a25722abb04a Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 7 Dec 2020 19:29:53 +0200 Subject: [PATCH 0159/2365] Add new Pillow dep --- .../easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb | 1 + .../easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb | 1 + .../easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb | 1 + .../easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb index fc861d5299..ed77f16aee 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb @@ -20,6 +20,7 @@ dependencies = [ ('libpng', '1.6.37'), ('freetype', '2.10.3'), ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), ] use_pip = True diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb index bf918e4c83..8fb868afac 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb @@ -20,6 +20,7 @@ dependencies = [ ('libpng', '1.6.37'), ('freetype', '2.10.3'), ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), ] use_pip = True diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb index 4ccf19ae6c..d05fd348d9 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb @@ -20,6 +20,7 @@ dependencies = [ ('libpng', '1.6.37'), ('freetype', '2.10.3'), ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), ] use_pip = True diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb index f3fd380030..f20755abf9 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb @@ -20,6 +20,7 @@ dependencies = [ ('libpng', '1.6.37'), ('freetype', '2.10.3'), ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), ] use_pip = True From 733fd1a024f2ed17da21e744f0e476625df56c03 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 7 Dec 2020 19:35:47 +0200 Subject: [PATCH 0160/2365] Add download_dep_fail --- .../easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb | 1 + .../s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb | 1 + .../s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb | 1 + .../s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb index 04df12fb64..daedc9ec68 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb @@ -21,6 +21,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True options = {'modulename': 'sklearn'} diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb index 7ed52a034d..f4d14cdcf2 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb @@ -21,6 +21,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True options = {'modulename': 'sklearn'} diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb index 99a2858d94..043cb44f29 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb @@ -21,6 +21,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True options = {'modulename': 'sklearn'} diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb index 8de6ecd21b..76e425daff 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb @@ -21,6 +21,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True options = {'modulename': 'sklearn'} From 76a64c2b3d78b9014386d402c857eedb8be55157 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 8 Dec 2020 01:18:07 +0200 Subject: [PATCH 0161/2365] adding easyconfigs: tbb-2020.3-GCCcore-10.2.0.eb --- .../t/tbb/tbb-2020.3-GCCcore-10.2.0.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3b9ad904fe --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb @@ -0,0 +1,18 @@ +name = 'tbb' +version = '2020.3' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ebc4f6aa47972daed1f7bf71d100ae5bf6931c2e3144cf299c8cc7d041dca2f3'] + +builddependencies = [ + ('binutils', '2.35') +] + +moduleclass = 'lib' From fff4e8c8cf45acda108dbcfe00d7c01bd29d9f49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Dec 2020 13:38:57 +0100 Subject: [PATCH 0162/2365] don't add include/node to $CPATH in nodejs easyconfigs (because nodejs installations include OpenSSL header files) + tweak V8 easyconfigs accordingly --- easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb index 34e7ea3828..56583356f9 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb @@ -39,6 +39,4 @@ sanity_check_paths = { 'dirs': ['lib/node_modules', 'include/node'] } -modextrapaths = {'CPATH': 'include/node'} - moduleclass = 'lang' From 450fb359b2007c8713ee3f5e025f915d5f164d8f Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 11 Dec 2020 13:50:14 +0200 Subject: [PATCH 0163/2365] Move magma back to fosscuda --- .../m/magma/magma-2.5.4-fosscuda-2020b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.5.4-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.4-fosscuda-2020b.eb b/easybuild/easyconfigs/m/magma/magma-2.5.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..086ba038c0 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.5.4-fosscuda-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'magma' +version = '2.5.4' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['7734fb417ae0c367b418dea15096aef2e278a423e527c615aab47f0683683b67'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +# Override with --cuda-compute-capabilities +local_ccc = '%(cuda_sm_space_sep)s' or 'sm_35 sm_50 sm_60 sm_70 sm_75 sm_80' +# make sure both static and shared libs are built +configopts = [ + '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%s" ' % (local_shared, local_ccc) for local_shared in ('ON', 'OFF') +] + +sanity_check_paths = { + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From 14603c77838ff327e6f5fbd102965863372f87aa Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 11 Dec 2020 16:08:53 +0100 Subject: [PATCH 0164/2365] update version to 3.4.0 --- .../a/ack/ack-3.4.0-GCCcore-10.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/ack/ack-3.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/ack/ack-3.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/ack/ack-3.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e73c3d3f5f --- /dev/null +++ b/easybuild/easyconfigs/a/ack/ack-3.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PerlModule' + +name = 'ack' +version = '3.4.0' + +homepage = 'https://beyondgrep.com' +description = "ack is a tool like grep, optimized for programmers" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['6ecfd6b9b9e129a1dee42f800283fb8d9fece925abc0ca6fa136d029989a6b50'] + +builddependencies = [('binutils', '2.35')] +dependencies = [('Perl', '5.32.0')] + +options = {'modulename': 'App::Ack'} + +sanity_check_paths = { + 'files': ['bin/ack', 'lib/perl5/site_perl/%(perlver)s/App/Ack.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/App/Ack'], +} + +moduleclass = 'bio' From 5df741d3f84ed86a9ef9b78e9429410394472c21 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 11 Dec 2020 18:54:32 +0000 Subject: [PATCH 0165/2365] change moduleclass - merge sprint, so I'll apply the change --- easybuild/easyconfigs/a/ack/ack-3.4.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ack/ack-3.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/ack/ack-3.4.0-GCCcore-10.2.0.eb index e73c3d3f5f..d532200154 100644 --- a/easybuild/easyconfigs/a/ack/ack-3.4.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/ack/ack-3.4.0-GCCcore-10.2.0.eb @@ -22,4 +22,4 @@ sanity_check_paths = { 'dirs': ['lib/perl5/site_perl/%(perlver)s/App/Ack'], } -moduleclass = 'bio' +moduleclass = 'tools' From eda5f15680666c8963767d321973cd0c471a97b2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 13 Dec 2020 03:38:13 +0200 Subject: [PATCH 0166/2365] adding easyconfigs: libpci-3.7.0-GCCcore-10.2.0.eb, libpci-3.7.0-GCCcore-6.4.0.eb and patches: libpci-3.7.0_fix-install-lib-symlinks.patch --- .../l/libpci/libpci-3.7.0-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpci/libpci-3.7.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libpci/libpci-3.7.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libpci/libpci-3.7.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..acbdbf0ad9 --- /dev/null +++ b/easybuild/easyconfigs/l/libpci/libpci-3.7.0-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libpci' +version = '3.7.0' + +homepage = 'https://github.com/pciutils/pciutils' +description = "Library for portable access to PCI bus configuration registers from PCI Utils." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pciutils/pciutils/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-install-lib-symlinks.patch'] +checksums = [ + 'ea768aa0187ba349391c6c157445ecc2b42e7d671fc1ce8c53ff5ef513f1e2ab', # v3.7.0.tar.gz + '4f078fcfe76b79d82a7b428afcfe866aab94c9e4bd52d0bf41c57a4ef47d124c', # libpci-3.7.0_fix-install-lib-symlinks.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +skipsteps = ['configure'] + +buildopts = "PREFIX=%(installdir)s SHARED=yes ZLIB=yes" + +# only install the library and header files +install_cmd = "make install-lib" +installopts = buildopts + +sanity_check_paths = { + 'files': ['lib/libpci.%s' % SHLIB_EXT], + 'dirs': ['include/pci', 'lib/pkgconfig'], +} + +moduleclass = 'system' From 409689396258fa28a73019d4035396d743bb93e1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 15 Dec 2020 17:09:58 +0200 Subject: [PATCH 0167/2365] fix sources of GDRCopy --- .../g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb index 5e4e8fe1c8..ecc2aa7e0a 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] +sources = ['v%(version)s.tar.gz'] checksums = ['cecc7dcc071107f77396f5553c9109790b6d2298ae29eb2dbbdd52b2a213e4ea'] builddependencies = [ From 2538a9a958b9e274fceaa56db1815e762978d57b Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 15 Dec 2020 18:17:53 +0100 Subject: [PATCH 0168/2365] adding easyconfigs: MPICH-3.3.2-GCC-10.2.0.eb --- .../m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..ba802ba558 --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb @@ -0,0 +1,16 @@ +name = 'MPICH' +version = '3.3.2' + +homepage = 'https://www.mpich.org/' +description = """MPICH is a high-performance and widely portable implementation +of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.mpich.org/static/tarballs/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4bfaf8837a54771d3e4922c84071ef80ffebddbb6971a006038d91ee7ef959b9'] + +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" ' + +moduleclass = 'mpi' From 10884aa943f48e77440d8fc7539145317c1fa642 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 15 Dec 2020 21:23:20 +0200 Subject: [PATCH 0169/2365] adding easyconfigs: ASE-3.20.1-foss-2020b.eb, ASE-3.20.1-intel-2020b.eb, GPAW-20.10.0-foss-2020b.eb, GPAW-20.10.0-intel-2020b.eb, spglib-python-1.16.0-foss-2020b.eb, spglib-python-1.16.0-intel-2020b.eb, libvdwxc-0.4.0-foss-2020b.eb --- .../a/ASE/ASE-3.20.1-foss-2020b.eb | 63 +++++++++++++++++ .../a/ASE/ASE-3.20.1-intel-2020b.eb | 67 +++++++++++++++++++ .../g/GPAW/GPAW-20.10.0-foss-2020b.eb | 49 ++++++++++++++ .../g/GPAW/GPAW-20.10.0-intel-2020b.eb | 51 ++++++++++++++ .../l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb | 27 ++++++++ .../spglib-python-1.16.0-foss-2020b.eb | 32 +++++++++ .../spglib-python-1.16.0-intel-2020b.eb | 35 ++++++++++ 7 files changed, 324 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb new file mode 100644 index 0000000000..400f57a2b3 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.20.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.3.3'), + ('spglib-python', '1.16.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('itsdangerous', '1.1.0', { + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Flask', '1.1.2', { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('ase', version, { + 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb new file mode 100644 index 0000000000..9e25633298 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.20.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.3.3'), + ('spglib-python', '1.16.0'), +] + +use_pip = True +sanity_pip_check = True + +# required because we're building Python packages (MarkupSafe, +# ase-ext) using Intel compilers on top of Python built with GCC. +check_ldshared = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('itsdangerous', '1.1.0', { + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Flask', '1.1.2', { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('ase', version, { + 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb new file mode 100644 index 0000000000..8fdc6c36cb --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '20.10.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), + ('GPAW-20.10.0-test-mpi.patch', 1), +] +checksums = [ + '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', '3.20.1'), + ('libxc', '4.3.4'), + ('libvdwxc', '0.4.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb new file mode 100644 index 0000000000..177107614f --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -0,0 +1,51 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '20.10.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), + ('GPAW-20.10.0-test-mpi.patch', 1), +] +checksums = [ + '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', '3.20.1'), + ('libxc', '4.3.4'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC. +check_ldshared = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb new file mode 100644 index 0000000000..9dee6b6ef2 --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.org' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb new file mode 100644 index 0000000000..1ba7ab46b3 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['94d056e48e7e6fe2e6fe4161471e774ac03221a6225fd83d551d3184220c1edf'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb new file mode 100644 index 0000000000..e5decd25a0 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['94d056e48e7e6fe2e6fe4161471e774ac03221a6225fd83d551d3184220c1edf'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_pip_check = True + +moduleclass = 'chem' From 3402af465262f5ac9025a00da8f9c59fb800796b Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 16 Dec 2020 18:08:37 +0200 Subject: [PATCH 0170/2365] adding easyconfigs: pytest-xdist-2.1.0-GCCcore-10.2.0.eb --- .../pytest-xdist-2.1.0-GCCcore-10.2.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..45f4f4e036 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'pytest-xdist' +version = '2.1.0' + +homepage = 'https://github.com/pytest-dev/pytest-xdist' +description = """xdist: pytest distributed testing plugin + +The pytest-xdist plugin extends pytest with some unique test execution modes: + + * test run parallelization: if you have multiple CPUs or hosts you + can use those for a combined test run. This allows to speed up + development or to use special resources of remote machines. + + * --looponfail: run your tests repeatedly in a subprocess. After + each run pytest waits until a file in your project changes and + then re-runs the previously failing tests. This is repeated + until all tests pass after which again a full run is + performed. + + * Multi-Platform coverage: you can specify different Python + interpreters or different platforms and run tests in parallel on + all of them. + +Before running tests remotely, pytest efficiently “rsyncs” your +program source code to the remote place. All test results are reported +back and displayed to your local terminal. You may specify different +Python versions and interpreters.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('apipkg', '1.5', { + 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], + }), + ('execnet', '1.7.1', { + 'checksums': ['cacb9df31c9680ec5f95553976c4da484d407e85e41c83cb812aa014f0eddc50'], + }), + ('pytest-forked', '1.3.0', { + 'checksums': ['6aa9ac7e00ad1a539c41bec6d21011332de671e938c7637378ec9710204e37ca'], + }), + (name, version, { + 'checksums': ['82d938f1a24186520e2d9d3a64ef7d9ac7ecdf1a0659e095d18e596b8cbd0672'], + 'modulename': 'xdist', + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 41221d87d2efd35670084298039f1b84332c57e8 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 16 Dec 2020 18:37:47 +0200 Subject: [PATCH 0171/2365] Add binutils as a build dependency --- .../p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb index 45f4f4e036..596b4a4cb3 100644 --- a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb @@ -29,6 +29,8 @@ Python versions and interpreters.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] + dependencies = [ ('Python', '3.8.6'), ] From dbe4902c8ca3d299200e97b40eca487058166668 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Thu, 17 Dec 2020 09:57:49 +0200 Subject: [PATCH 0172/2365] adding easyconfigs: Wannier90-3.1.0-foss-2020b.eb, Wannier90-3.1.0-intel-2020b.eb --- .../w/Wannier90/Wannier90-3.1.0-foss-2020b.eb | 35 +++++++++++++++++++ .../Wannier90/Wannier90-3.1.0-intel-2020b.eb | 32 +++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2020b.eb new file mode 100644 index 0000000000..bad8326376 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +# The -fallow-argument-mismatch allows MPI communication calls to be +# called with arrays of different types at different places in the +# code. This otherwise cause an error in GCC 10.X +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2020b.eb new file mode 100644 index 0000000000..ada3e6966d --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From 5795160de52edd7b609f9e7b088c885a0f1ff25b Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 17 Dec 2020 19:49:32 +0200 Subject: [PATCH 0173/2365] Rebase on patched magma 2.5.4 --- .../m/magma/magma-2.5.4-fosscuda-2020b.eb | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.4-fosscuda-2020b.eb b/easybuild/easyconfigs/m/magma/magma-2.5.4-fosscuda-2020b.eb index 086ba038c0..daaf3b0b03 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.5.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.5.4-fosscuda-2020b.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = "CMakeMake" name = 'magma' version = '2.5.4' @@ -12,17 +12,21 @@ toolchainopts = {'pic': True, 'openmp': True} source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/'] sources = [SOURCE_TAR_GZ] -checksums = ['7734fb417ae0c367b418dea15096aef2e278a423e527c615aab47f0683683b67'] +patches = ['magma-2.5.4_allow-all-sms.patch'] +checksums = [ + '7734fb417ae0c367b418dea15096aef2e278a423e527c615aab47f0683683b67', # magma-2.5.4.tar.gz + '4e47ecc080ff761866f179c9b383b8930e4daa2fcee1c2a48db585fc50531561', # magma-2.5.4_allow-all-sms.patch +] builddependencies = [ ('CMake', '3.18.4'), ] -# Override with --cuda-compute-capabilities -local_ccc = '%(cuda_sm_space_sep)s' or 'sm_35 sm_50 sm_60 sm_70 sm_75 sm_80' +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0'] # make sure both static and shared libs are built configopts = [ - '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%s" ' % (local_shared, local_ccc) for local_shared in ('ON', 'OFF') + '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') ] sanity_check_paths = { From 64bfcc44995e8b452dc020f18817957c6ea9c20b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Dec 2020 20:08:02 +0100 Subject: [PATCH 0174/2365] move down Libint to GCC/iccifort toolchain --- .../Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb | 49 +++++++++++++++++++ ...t-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb | 44 +++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb new file mode 100644 index 0000000000..3c7b8ecba4 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb @@ -0,0 +1,49 @@ +name = 'Libint' +version = '2.6.0' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch', + 'Libint-2.6.0_remove-test-eri.patch', +] +checksums = [ + '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz + # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch + 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', + # Libint-2.6.0_remove-test-eri.patch + 'e47868901250078adeb35b80ab866ba8063ad9756881d1b557cb925334df653b', +] + +builddependencies = [ + ('Autotools', '20200321'), + ('GMP', '6.2.0'), + ('Boost', '1.74.0'), + ('Eigen', '3.3.8'), + ('Python', '2.7.18'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb new file mode 100644 index 0000000000..01567f5450 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb @@ -0,0 +1,44 @@ +name = 'Libint' +version = '2.6.0' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch'] +checksums = [ + '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz + # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch + 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', +] + +builddependencies = [ + ('Autotools', '20200321'), + ('GMP', '6.2.0'), + ('Boost', '1.74.0'), + ('Eigen', '3.3.8'), + ('Python', '2.7.18'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' From c5cd60491f6010990c6a3aa446a6c276eb69cc7e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Dec 2020 20:08:02 +0100 Subject: [PATCH 0175/2365] move down Libint 2.6.0 to GCC/iccifort toolchain for 2020b generation of easyconfigs --- .../Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb | 49 +++++++++++++++++++ ...t-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb | 44 +++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb new file mode 100644 index 0000000000..3c7b8ecba4 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb @@ -0,0 +1,49 @@ +name = 'Libint' +version = '2.6.0' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch', + 'Libint-2.6.0_remove-test-eri.patch', +] +checksums = [ + '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz + # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch + 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', + # Libint-2.6.0_remove-test-eri.patch + 'e47868901250078adeb35b80ab866ba8063ad9756881d1b557cb925334df653b', +] + +builddependencies = [ + ('Autotools', '20200321'), + ('GMP', '6.2.0'), + ('Boost', '1.74.0'), + ('Eigen', '3.3.8'), + ('Python', '2.7.18'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb new file mode 100644 index 0000000000..01567f5450 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb @@ -0,0 +1,44 @@ +name = 'Libint' +version = '2.6.0' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch'] +checksums = [ + '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz + # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch + 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', +] + +builddependencies = [ + ('Autotools', '20200321'), + ('GMP', '6.2.0'), + ('Boost', '1.74.0'), + ('Eigen', '3.3.8'), + ('Python', '2.7.18'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' From 65ef0ea5017500765f2c9fba9fc485abc6c2f768 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Dec 2020 13:16:20 +0100 Subject: [PATCH 0176/2365] drop '-Python*' versionsuffix for PLUMED with 2020b toolchain --- .../p/PLUMED/PLUMED-2.6.2-foss-2020b.eb | 58 +++++++++++++++++++ .../p/PLUMED/PLUMED-2.6.2-intel-2020b.eb | 58 +++++++++++++++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb new file mode 100644 index 0000000000..3fb97d9ba7 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -0,0 +1,58 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.6.2' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['1ab3153db2010406852b30201ed94112e25eca4c4c8c4b41a29c22a7a3303f96'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb new file mode 100644 index 0000000000..16200c8e59 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb @@ -0,0 +1,58 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.6.2' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['1ab3153db2010406852b30201ed94112e25eca4c4c8c4b41a29c22a7a3303f96'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From 21a664bff1be9afdc3343f4156c31c1df3942215 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Dec 2020 09:58:28 +0100 Subject: [PATCH 0177/2365] {bio}[gompi/2020b] Salmon v1.4.0 --- .../jemalloc/jemalloc-5.2.1-GCCcore-10.2.0.eb | 37 +++++++++++ .../s/Salmon/Salmon-1.4.0-gompi-2020b.eb | 61 +++++++++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-1.4.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8e43deb719 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.2.1' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ed51b0b37098af4ca6ed31c22324635263f8ad6471889e0592a9c0dba9136aea'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.4.0-gompi-2020b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.4.0-gompi-2020b.eb new file mode 100644 index 0000000000..51ca3848e2 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.4.0-gompi-2020b.eb @@ -0,0 +1,61 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GLPv2 +# +# Notes:: +## +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# Thanks to people like Simon Brandord, Mikael Oehmann and Kenneth Hoste +# for their help with the ICE + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '1.4.0' + +homepage = 'https://github.com/COMBINE-lab/salmon' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'COMBINE-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6d3e25387450710f0aa779a1e9aaa9b4dec842324ff8551d66962d7c7606e71d'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), + ('jemalloc', '5.2.1'), +] + +dependencies = [ + ('Boost', '1.74.0'), + ('tbb', '2020.3'), +] + +# Disable link-time optimizations (-flto) because it triggers a segfault/internal compiler error (ICE) with GCC 9.3.0 +# This problem might be solved with a newer version of either GCC or Salmon. +configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC -DNO_IPO=1' + +# need to unset the $LD_PRELOAD set be jemalloc to avoid hanging 'make test' +# since jemalloc is statically linked in Salmon (and hence only a build dep), +# this only affects the tests +pretestopts = "unset LD_PRELOAD && " +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'] + ['lib/lib%s.a' % x for x in ['graphdump', 'ntcard', 'salmon_core', 'twopaco']], + 'dirs': [], +} + +sanity_check_commands = ["salmon --help"] + +moduleclass = 'bio' From c1c49d194e1fb76cb38bb2e730734594eb0c5776 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Dec 2020 10:23:33 +0100 Subject: [PATCH 0178/2365] add path to v8.h to $CPATH when installing V8 extension in R 4.0.3 --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 264f099c23..2318c3d945 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2387,6 +2387,7 @@ exts_list = [ }), ('V8', '3.4.0', { 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', }), ('rstan', '2.21.2', { From c1086ff4dcb36b394d79c248f69b18694d03d7b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Dec 2020 22:15:26 +0100 Subject: [PATCH 0179/2365] add additional extensions to R v4.0.3 easyconfig --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 2318c3d945..62902ac0d0 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2731,6 +2731,36 @@ exts_list = [ ('DescTools', '0.99.38', { 'checksums': ['bd8edce64a8f9e295611959295b85cf8d7bbf915093158016169bd334e0e1104'], }), + ('orthopolynom', '1.0-5', { + 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], + }), + ('gaussquad', '1.0-2', { + 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.0', { + 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], + }), + ('tableone', '0.12.0', { + 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], + }), + ('jstable', '1.0.1', { + 'checksums': ['2e4cfce264a2353e4655d0faafc93969222d67a21c0c9cc61a2454abd99c5cdc'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.2', { + 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], + }), + ('sensemakr', '0.1.3', { + 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], + }), ('RcppParallel', '5.0.2', { 'checksums': ['8ca200908c6365aafb2063be1789f0894969adc03c0f523c6cc45434b8236f81'], }), From 406919457b166042896a9995840db1c7c17aacb7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Dec 2020 14:43:34 +0100 Subject: [PATCH 0180/2365] adding easyconfigs: FIGARO-1.1.2-intel-2020b.eb --- .../f/FIGARO/FIGARO-1.1.2-intel-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIGARO/FIGARO-1.1.2-intel-2020b.eb diff --git a/easybuild/easyconfigs/f/FIGARO/FIGARO-1.1.2-intel-2020b.eb b/easybuild/easyconfigs/f/FIGARO/FIGARO-1.1.2-intel-2020b.eb new file mode 100644 index 0000000000..e372c08053 --- /dev/null +++ b/easybuild/easyconfigs/f/FIGARO/FIGARO-1.1.2-intel-2020b.eb @@ -0,0 +1,43 @@ +easyblock = 'Tarball' + +name = 'FIGARO' +version = '1.1.2' + +homepage = 'https://github.com/Zymo-Research/figaro' +description = "FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters." + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://github.com/Zymo-Research/figaro/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b80d8258574ae9c6ba402e8e8de5eebb1fa1f71a3d81c1cc2d9c0f6729b9a3ec'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +fix_python_shebang_for = ['figaro.py'] + +postinstallcmds = [ + "chmod a+x %(installdir)s/figaro.py", + "cd %(installdir)s && ln -s figaro.py figaro", +] + +sanity_check_paths = { + 'files': ['figaro'], + 'dirs': [], +} + +sanity_check_commands = [ + "figaro --help", + "python -c 'import figaro'", +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +moduleclass = 'bio' From 77b753fe1337aabdfd646a61a6cfaf235039eb1f Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 22 Dec 2020 14:54:28 +0000 Subject: [PATCH 0181/2365] adding easyconfigs: ELPA-2020.11.001-foss-2020b.eb, ELPA-2020.11.001-intel-2020b.eb --- .../e/ELPA/ELPA-2020.11.001-foss-2020b.eb | 33 +++++++++++++++++++ .../e/ELPA/ELPA-2020.11.001-intel-2020b.eb | 28 ++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb new file mode 100644 index 0000000000..ae57cde8dc --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2020.11.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['15591f142eeaa98ab3201d27ca9ac328e21beabf0803b011a04183fcaf6efdde'] + +builddependencies = [ + ('Autotools', '20200321'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.8.6'), +] + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb new file mode 100644 index 0000000000..43fe81a27f --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2020.11.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['15591f142eeaa98ab3201d27ca9ac328e21beabf0803b011a04183fcaf6efdde'] + +builddependencies = [ + ('Autotools', '20200321'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.8.6'), +] + +moduleclass = 'math' From 5b99950619ee02c9ed29bca347262c8658438d59 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Dec 2020 15:56:16 +0100 Subject: [PATCH 0182/2365] use dependency on Flask in easyconfigs ASE-3.20.1-foss-2020b.eb and ASE-3.20.1-intel-2020b.eb --- .../a/ASE/ASE-3.20.1-foss-2020b.eb | 23 ++------- .../a/ASE/ASE-3.20.1-intel-2020b.eb | 23 ++------- .../f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb | 48 +++++++++++++++++++ 3 files changed, 54 insertions(+), 40 deletions(-) create mode 100644 easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb index 400f57a2b3..d78de78cef 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb @@ -15,9 +15,10 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Tkinter', '%(pyver)s'), + ('Flask', '1.1.2'), ('matplotlib', '3.3.3'), - ('spglib-python', '1.16.0'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional ] use_pip = True @@ -26,24 +27,6 @@ sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ - ('MarkupSafe', '1.1.1', { - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('Jinja2', '2.11.2', { - 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], - }), - ('Werkzeug', '1.0.1', { - 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('itsdangerous', '1.1.0', { - 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], - }), - ('Flask', '1.1.2', { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), ('ase', version, { 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], }), diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb index 9e25633298..82de3ea825 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb @@ -15,9 +15,10 @@ toolchain = {'name': 'intel', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Tkinter', '%(pyver)s'), + ('Flask', '1.1.2'), ('matplotlib', '3.3.3'), - ('spglib-python', '1.16.0'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional ] use_pip = True @@ -30,24 +31,6 @@ check_ldshared = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ - ('MarkupSafe', '1.1.1', { - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('Jinja2', '2.11.2', { - 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], - }), - ('Werkzeug', '1.0.1', { - 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('itsdangerous', '1.1.0', { - 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], - }), - ('Flask', '1.1.2', { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), ('ase', version, { 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], }), diff --git a/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d9084f7f06 --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '1.1.2' + +homepage = 'https://www.palletsprojects.com/p/flask/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), +] + +builddependencies = [('binutils', '2.35')] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +exts_list = [ + ('itsdangerous', '1.1.0', { + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + (name, version, { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('Flask-Cors', '3.0.9', { + 'checksums': ['6bcfc100288c5d1bcb1dbb854babd59beee622ffd321e444b05f24d6d58466b8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/flask'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['flask --version'] + +moduleclass = 'lib' From e8bf04707d6505a48e3582d11ad335c141c1750b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Dec 2020 15:56:53 +0100 Subject: [PATCH 0183/2365] remove default sanity checks in spglib-python-1.16.0-foss-2020b.eb and spglib-python-1.16.0-intel-2020b.eb --- .../spglib-python/spglib-python-1.16.0-foss-2020b.eb | 11 +++-------- .../spglib-python/spglib-python-1.16.0-intel-2020b.eb | 11 +++-------- 2 files changed, 6 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb index 1ba7ab46b3..460c5ccc1f 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb @@ -4,7 +4,7 @@ name = 'spglib-python' version = '1.16.0' homepage = 'https://pypi.python.org/pypi/spglib' -description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." toolchain = {'name': 'foss', 'version': '2020b'} @@ -20,13 +20,8 @@ dependencies = [ download_dep_fail = True use_pip = True -options = {'modulename': 'spglib'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - sanity_pip_check = True +options = {'modulename': 'spglib'} + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb index e5decd25a0..bc1f8c26b1 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb @@ -4,7 +4,7 @@ name = 'spglib-python' version = '1.16.0' homepage = 'https://pypi.python.org/pypi/spglib' -description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." toolchain = {'name': 'intel', 'version': '2020b'} @@ -23,13 +23,8 @@ check_ldshared = True download_dep_fail = True use_pip = True -options = {'modulename': 'spglib'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - sanity_pip_check = True +options = {'modulename': 'spglib'} + moduleclass = 'chem' From 8ab28b550244cd0bca6ee94b491cd7f83aa8f83c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Dec 2020 15:57:21 +0100 Subject: [PATCH 0184/2365] add comment about libvdwxc to GPAW-20.10.0-intel-2020b.eb --- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb index 177107614f..e34fb5f250 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -24,6 +24,7 @@ checksums = [ '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] +# libvdwxc is not a dependency of the intel build, as it is incompatible with the Intel MKL. dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), From e18da9f9493542e704896f260e70ebbc0ae5a03e Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 22 Dec 2020 12:15:53 -0800 Subject: [PATCH 0185/2365] libgit2 GCCcore-10.2.0 --- .../l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cfe5ecaa90 --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.1.0' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'libgit2' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['41a6d5d740fd608674c7db8685685f45535323e73e784062cf000a633d420d1e'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('PCRE', '8.44'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], + 'dirs': [] +} + +moduleclass = 'devel' From 90771fb961bf7532c0d797040aeec2d1b8592b66 Mon Sep 17 00:00:00 2001 From: John Dey Date: Tue, 22 Dec 2020 12:29:20 -0800 Subject: [PATCH 0186/2365] Update easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb index cfe5ecaa90..3706959da0 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('PCRE', '8.44'), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [OS_PKG_OPENSSL_DEV] sanity_check_paths = { 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], From ced39d702791b8bf7eff6fa44530be971f0fd0bf Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 22 Dec 2020 12:32:50 -0800 Subject: [PATCH 0187/2365] fix deps --- easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb index 3706959da0..3826f08432 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb @@ -23,6 +23,8 @@ builddependencies = [ dependencies = [ ('PCRE', '8.44'), + # ('OpenSSL', '1.1.1h') + # OS dependency should be preferred if the os version is more recent than this version ] osdependencies = [OS_PKG_OPENSSL_DEV] From 0e61f6b6bfca96068a5bdacf57a0cdbba9709ad3 Mon Sep 17 00:00:00 2001 From: John Dey Date: Thu, 31 Dec 2020 07:13:49 -0800 Subject: [PATCH 0188/2365] Rename PyClone-2020.9b2-GCCcore-10.2.0-Python-3.8.6.eb to PyClone-2020.9b2-GCCcore-10.2.0.eb change file name --- .../PyClone-2020.9b2-GCCcore-10.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..487d7a6529 --- /dev/null +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +# +easyblock = 'Bundle' + +name = 'PyClone' +version = '2020.9b2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gitlab.com/ltgiv/pyclone' +description = """PyClone is a Python package that wraps rclone and provides a threaded interface for + an installation at the host or container level.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True +} + +exts_list = [ + ('Logbook', '1.5.3', { + 'checksums': ['66f454ada0f56eae43066f604a222b09893f98c1adc18df169710761b8f32fe8'], + }), + ('arrow', '0.17.0', { + 'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'], + }), + (name, version, { + 'checksums': ['e294e875fdd9131526ba9974ad478f213c6d982d273b4b385346e3147e672bc0'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' From fd1f1782b9c9830a1c6aa8f3a01c3009136951ec Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 31 Dec 2020 07:16:30 -0800 Subject: [PATCH 0189/2365] PyClone resolve conversation --- .../p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index 487d7a6529..167d9f78d0 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -4,11 +4,10 @@ # # Fred Hutchinson Cancer Research Center - Seattle Washington - US # -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'PyClone' version = '2020.9b2' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://gitlab.com/ltgiv/pyclone' description = """PyClone is a Python package that wraps rclone and provides a threaded interface for @@ -16,6 +15,8 @@ description = """PyClone is a Python package that wraps rclone and provides a th toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] + dependencies = [ ('Python', '3.8.6'), ] @@ -38,11 +39,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' From 4d56e252fd57604aa907119457fe3da82eb20dbb Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 31 Dec 2020 07:18:24 -0800 Subject: [PATCH 0190/2365] PyClone resolve conversation --- .../easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index 167d9f78d0..58d1a9a962 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -21,7 +21,6 @@ dependencies = [ ('Python', '3.8.6'), ] -exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_urls': [PYPI_SOURCE], 'use_pip': True From 36439f90c87bf42f8655cb4913e5e232e55dde68 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 1 Jan 2021 13:32:58 -0800 Subject: [PATCH 0191/2365] update libwebp --- .../l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..06e2a0c516 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.1.0' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['98a052268cc4d5ece27f76572a7f50293f439c17a98e67c4ea0c7ed6f50ef043'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('giflib', '5.2.1'), +] + +configopts = "--enable-libwebpmux" + +sanity_check_paths = { + 'files': ['include/webp/%s' % f for f in ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h']] + + ['lib/lib%s.a' % l for l in ['webp', 'webpdemux', 'webpmux']] + + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['webp', 'webpdemux', 'webpmux']], + 'dirs': ['lib/'] +} + +moduleclass = 'lib' From 0ebf225d555dde7448e1eb13e4167a2193678701 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 Jan 2021 14:09:59 +0100 Subject: [PATCH 0192/2365] enable sanity_pip_check in PyClone easyconfig --- .../easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index 58d1a9a962..b4d46a0f4f 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -38,4 +38,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'tools' From 552049c34b82d4e6d7d6d1f8c75497f8a5b3926e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 Jan 2021 20:56:09 +0100 Subject: [PATCH 0193/2365] adding easyconfigs: OpenMPI-4.1.0-GCC-10.2.0.eb --- .../o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..b4d152df08 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -0,0 +1,37 @@ +name = 'OpenMPI' +version = '4.1.0' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('libevent', '2.1.12'), + ('UCX', '1.9.0'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), +] + +# replace -march=skylake-avx512 option with equivalent -m* flags, +# to avoid problems when building on systems which don't support AVX-512; +# cfr. https://github.com/open-mpi/ompi/issues/8306 +preconfigopts = "sed -i 's/-march=skylake-avx512/-mavx512f -mavx512bw -mavx512vl -mavx512dq/g' configure && " + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 8737c6faf6d07542fd71b44646a8cb3e4e55d5b7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 4 Jan 2021 10:48:24 +0800 Subject: [PATCH 0194/2365] adding easyconfigs: fftlib-20170628-gompi-2020b.eb --- .../f/fftlib/fftlib-20170628-gompi-2020b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb diff --git a/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb b/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb new file mode 100644 index 0000000000..04614a3523 --- /dev/null +++ b/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'fftlib' +version = '20170628' +_commit = '44c5fa0' + +homepage = 'https://github.com/flwende/fftlib' +description = """A library that intercepts FFTW calls and adds features on top of it. + In particular, it enables FFT plan reuse when there are multiple calls for the same geometry.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/flwende/fftlib/archive/'] +sources = [{'filename': '%s.zip' % _commit, 'extract_cmd': 'unzip %s'}] +checksums = ['f73dffeaf5c2e6972a5bc67d11ec28390f9eda281a7cb47edc1ee2fe394ed057'] + +dependencies = [('FFTW', '3.3.8')] + +_options = "-DFFTLIB_THREADSAFE " # use this when multiple threads access fftlib +# _options += "-DFFTLIB_USE_MKL " # use symbols from MKL's fft library +# _options += "-DFFTLIB_BYPASS " # bypass fftlib's internal logic +# _options += "-DFFTLIB_OWN_LOCK " # use fftlib's reader/writer lock +# _options += "-DFFTLIB_UNSAFE_OPT " # activate unsafe optimizations in fftlib +# _options += "-DFFTLIB_DEBUG " # print debug messages (infos and warnings) +# _options += "-DFFTLIB_WARNINGS_ONLY " # print warnings only +# _options += "-DFFTLIB_COMPOSED_FFT " # split 3d FFT computation into 2d+1d FFT + +start_dir = 'src' + +parallel = False + +build_cmd = "$CXX $CXXFLAGS -I../include -I$EBROOTFFTW/include %s -c fftlib.cpp -o fftlib.o" % _options + +files_to_copy = [(['fftlib.o'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/fftlib.o'], + 'dirs': ["."] +} + +# this should be prepended to $LIBFFT(_MT) when building applications in order to intercept their FFT calls +modextravars = {'FFTLIB': "%(installdir)s/lib/fftlib.o -lgomp -lstdc++ -ldl"} + +moduleclass = 'lib' From 933c3cb669034921332ef79833d81924ad60f57f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 4 Jan 2021 16:18:59 +0800 Subject: [PATCH 0195/2365] adding easyconfigs: QuantumESPRESSO-6.6-foss-2020b.eb --- .../QuantumESPRESSO-6.6-foss-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb new file mode 100644 index 0000000000..02147ccb84 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb @@ -0,0 +1,43 @@ +name = 'QuantumESPRESSO' +version = '6.6' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', + 'https://github.com/dceresoli/qe-gipaw/archive/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + 'de6996b9f1bf480bcd0166d24e918f5ff3c8fdb710f59f781bc9d33819280eb5', # qe-6.6-ReleasePack.tgz + '277fbe3bd10cb8f64e0f351a0c2fff1f68fb3ccdeb18107900803f4566661459', # qe-gipaw-6.6.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('ELPA', '2020.11.001'), + ('libxc', '4.3.4'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From 6713fbbebb6b2c7271bcd840e43cc3246f23c789 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 4 Jan 2021 20:24:16 +0800 Subject: [PATCH 0196/2365] rename file on download, rename local variables --- .../f/fftlib/fftlib-20170628-gompi-2020b.eb | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb b/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb index 04614a3523..2a62a4bc71 100644 --- a/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb +++ b/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'fftlib' version = '20170628' -_commit = '44c5fa0' +local_commit = '44c5fa0' homepage = 'https://github.com/flwende/fftlib' description = """A library that intercepts FFTW calls and adds features on top of it. @@ -12,25 +12,25 @@ toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'openmp': True, 'cstd': 'c++11'} source_urls = ['https://github.com/flwende/fftlib/archive/'] -sources = [{'filename': '%s.zip' % _commit, 'extract_cmd': 'unzip %s'}] +sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_ZIP}] checksums = ['f73dffeaf5c2e6972a5bc67d11ec28390f9eda281a7cb47edc1ee2fe394ed057'] dependencies = [('FFTW', '3.3.8')] -_options = "-DFFTLIB_THREADSAFE " # use this when multiple threads access fftlib -# _options += "-DFFTLIB_USE_MKL " # use symbols from MKL's fft library -# _options += "-DFFTLIB_BYPASS " # bypass fftlib's internal logic -# _options += "-DFFTLIB_OWN_LOCK " # use fftlib's reader/writer lock -# _options += "-DFFTLIB_UNSAFE_OPT " # activate unsafe optimizations in fftlib -# _options += "-DFFTLIB_DEBUG " # print debug messages (infos and warnings) -# _options += "-DFFTLIB_WARNINGS_ONLY " # print warnings only -# _options += "-DFFTLIB_COMPOSED_FFT " # split 3d FFT computation into 2d+1d FFT +local_options = "-DFFTLIB_THREADSAFE " # use this when multiple threads access fftlib +# local_options += "-DFFTLIB_USE_MKL " # use symbols from MKL's fft library +# local_options += "-DFFTLIB_BYPASS " # bypass fftlib's internal logic +# local_options += "-DFFTLIB_OWN_LOCK " # use fftlib's reader/writer lock +# local_options += "-DFFTLIB_UNSAFE_OPT " # activate unsafe optimizations in fftlib +# local_options += "-DFFTLIB_DEBUG " # print debug messages (infos and warnings) +# local_options += "-DFFTLIB_WARNINGS_ONLY " # print warnings only +# local_options += "-DFFTLIB_COMPOSED_FFT " # split 3d FFT computation into 2d+1d FFT start_dir = 'src' parallel = False -build_cmd = "$CXX $CXXFLAGS -I../include -I$EBROOTFFTW/include %s -c fftlib.cpp -o fftlib.o" % _options +build_cmd = "$CXX $CXXFLAGS -I../include -I$EBROOTFFTW/include %s -c fftlib.cpp -o fftlib.o" % local_options files_to_copy = [(['fftlib.o'], 'lib')] From 9b3eb72eb339da0da041e5d8cc626843513297ad Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 4 Jan 2021 15:25:07 -0800 Subject: [PATCH 0197/2365] ubuntu requires pkg-config --- .../GObject-Introspection-1.66.1-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb index 152dc3bc8e..c828437cf5 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb @@ -18,6 +18,7 @@ checksums = ['dd44a55ee5f426ea22b6b89624708f9e8d53f5cc94e5485c15c87cb30e06161d'] builddependencies = [ ('binutils', '2.35'), + ('pkg-config', '0.29.2'), ('Meson', '0.55.3'), ('Ninja', '1.10.1'), ('flex', '2.6.4'), From 2b745d6dbad153105af25aa2bbed30f7125ab604 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 4 Jan 2021 19:26:09 -0800 Subject: [PATCH 0198/2365] update OpenJPEG --- .../OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a3a6498b28 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchenson Cancer Research Center Seattle WA +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.4.0' + +homepage = 'http://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/openjpeg/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8702ba68b442657f11aaeb2b338443ca8d5fb95b0d845757968a7be31ef7f16d'] + +separate_build_dir = True + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] + +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0') +] + +sanity_check_paths = { + 'files': ['bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From 083efa97ca8e3aa1b63e207fac9d28ce8e5c5c8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 Jan 2021 10:01:35 +0100 Subject: [PATCH 0199/2365] use https in homepage in OpenJPEG 2.4.0 easyconfig --- .../easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb index a3a6498b28..f82a18a53a 100644 --- a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'OpenJPEG' version = '2.4.0' -homepage = 'http://www.openjpeg.org/' +homepage = 'https://www.openjpeg.org/' description = """OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group From 354af1c9bfabd7c934615f47d266a5f5ea07768f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Jan 2021 15:25:05 +0100 Subject: [PATCH 0200/2365] fix source URL in expat easyconfigs (and consistently add custom sanity_check_paths) --- easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-10.2.0.eb index fdcc804030..73c40af988 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-10.2.0.eb @@ -14,8 +14,8 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] checksums = ['f1063084dc4302a427dabcca499c8312b3a32a29b7d2506653ecc8f950a9a237'] builddependencies = [('binutils', '2.35')] @@ -27,7 +27,7 @@ configopts = ['--without-docbook'] sanity_check_paths = { 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], - 'dirs': [] + 'dirs': [], } moduleclass = 'tools' From ff0c4bbb978486cc036168e83ee8c75be95a877c Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 7 Jan 2021 16:25:55 -0800 Subject: [PATCH 0201/2365] Pysam --- .../p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..aaf5db0046 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.16.0.1' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a61e98e299fa93ba121aab521081282b61bc978bb9052d33b26b38f8fe15573e'] + +dependencies = [ + ('Python', '3.8.6'), + ('ncurses', '6.2'), + ('cURL', '7.72.0'), + ('XZ', '5.2.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From c22c36f1c92dc71335ff3f6d9f6c714c16a0dac7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Jan 2021 12:31:56 +0100 Subject: [PATCH 0202/2365] {cae}[foss/2020b] OpenFOAM v8, ParaView v5.8.1, CGAL v5.2 --- .../c/CGAL/CGAL-5.2-gompi-2020b.eb | 38 ++++++++++++ .../o/OpenFOAM/OpenFOAM-8-foss-2020b.eb | 39 +++++++++++++ .../ParaView/ParaView-5.8.1-foss-2020b-mpi.eb | 58 +++++++++++++++++++ 3 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb new file mode 100644 index 0000000000..c03d9e13b1 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb @@ -0,0 +1,38 @@ +name = 'CGAL' +version = '5.2' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['744c86edb6e020ab0238f95ffeb9cf8363d98cde17ebb897d3ea93dac4145923'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Eigen', '3.3.8'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.8.6'), + ('Boost', '1.74.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('Qt5', '5.14.2'), +] + +configopts = "-DCGAL_HEADER_ONLY=OFF " +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb new file mode 100644 index 0000000000..58ae8e587c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb @@ -0,0 +1,39 @@ +name = 'OpenFOAM' +version = '8' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = [ + 'OpenFOAM-%(version)s-cleanup.patch', +] +checksums = [ + '94ba11cbaaa12fbb5b356e01758df403ac8832d69da309a5d79f76f42eb008fc', # version-8.tar.gz + 'e3fac8049611ee109f07eb5b0ed4b1526782a21b3f12435e03529d56c8483b9f', # OpenFOAM-8-cleanup.patch +] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('CGAL', '5.2'), + ('ParaView', '5.8.1', '-mpi'), +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb new file mode 100644 index 0000000000..da07b6c453 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.8.1' +versionsuffix = '-mpi' + +homepage = "https://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["ParaView-v%(version)s.tar.xz"] +checksums = ['7653950392a0d7c0287c26f1d3a25cdbaa11baa7524b0af0e6a1a0d7d487d034'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('XZ', '5.2.5'), + ('HDF5', '1.10.7'), + ('netCDF', '4.7.4'), + ('libGLU', '9.0.1'), + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('Qt5', '5.14.2'), + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.1'), + ('Szip', '2.1.1'), +] + +builddependencies = [('CMake', '3.18.4')] + +separate_build_dir = True + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' +configopts += '-DVTK_OPENGL_HAS_OSMESA=ON ' + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': ['lib64/python%(pyshortver)s/site-packages', 'lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' From 47f6dbc3ff66a3a9c078c82a237596c4feb8f0b4 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Fri, 8 Jan 2021 14:05:21 +0000 Subject: [PATCH 0203/2365] adding easyconfigs: networkx-2.5-foss-2020b.eb, networkx-2.5-fosscuda-2020b.eb --- .../n/networkx/networkx-2.5-foss-2020b.eb | 25 +++++++++++++++++++ .../n/networkx/networkx-2.5-fosscuda-2020b.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb new file mode 100644 index 0000000000..17140eeadb --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.5' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..5ed249495d --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.5' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 4a9f8bfb04bb78cfe3efc61bec89e18380f8ea2e Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Fri, 8 Jan 2021 16:14:42 +0000 Subject: [PATCH 0204/2365] adding easyconfigs: scikit-build-0.11.1-foss-2020b.eb, scikit-build-0.11.1-fosscuda-2020b.eb --- .../scikit-build-0.11.1-foss-2020b.eb | 34 +++++++++++++++++++ .../scikit-build-0.11.1-fosscuda-2020b.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb create mode 100755 easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb new file mode 100755 index 0000000000..01be14e317 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.11.1' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], +} + +exts_list = [ + ('distro', '1.5.0', { + 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], + }), + (name, version, { + 'modulename': 'skbuild', + 'checksums': ['da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb new file mode 100755 index 0000000000..e74ec50f16 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.11.1' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], +} + +exts_list = [ + ('distro', '1.5.0', { + 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], + }), + (name, version, { + 'modulename': 'skbuild', + 'checksums': ['da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c'], + }), +] + +moduleclass = 'lib' From a111b18bab7a52212047e0607d133ed08316a8ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Jan 2021 23:21:48 +0100 Subject: [PATCH 0205/2365] don't configure ParaView 5.8.1 with OSMESA support --- .../easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb index da07b6c453..4d1f402364 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb @@ -44,7 +44,6 @@ configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' # OpenGL & Mesa configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' -configopts += '-DVTK_OPENGL_HAS_OSMESA=ON ' sanity_check_paths = { 'files': ['bin/paraview', 'bin/pvpython'], From c2bfa0029be392e8ac92944eb7bf7f8e33c9c90f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Jan 2021 13:58:57 +0100 Subject: [PATCH 0206/2365] remove custom sanity_check_paths from Pysam v0.16.0.1 easyconfig, since it's the same as the default used by PythonPackage --- easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb index aaf5db0046..099b411c19 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb @@ -32,11 +32,7 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_pip_check = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} +sanity_pip_check = True moduleclass = 'bio' From 3d8a31a35b51eb684599bfa9ef83b6a65524d2c5 Mon Sep 17 00:00:00 2001 From: easybuild Date: Wed, 13 Jan 2021 11:23:08 +0000 Subject: [PATCH 0207/2365] adding easyconfigs: MariaDB-10.5.8-gompi-2020b.eb, MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb, Judy-1.0.5-GCCcore-10.2.0.eb, libaio-0.3.112-GCCcore-10.2.0.eb --- .../j/Judy/Judy-1.0.5-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ .../l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb | 31 +++++++++++++++++ ...riaDB-connector-c-3.1.11-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 3 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9988efaf33 --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..699303eba6 --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.112' +local_libversion = '1.0.1' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] + +builddependencies = [('binutils', '2.35')] + +files_to_copy = [ + (["src/libaio.a", "src/libaio.%s.%s" % (SHLIB_EXT, local_libversion)], "lib"), + (["src/libaio.h"], "include"), +] + +postinstallcmds = ["cd %%(installdir)s/lib; ln -s libaio.%s.%s libaio.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT)] + +sanity_check_paths = { + 'files': ['lib/libaio.a', 'lib/libaio.%s.%s' % (SHLIB_EXT, local_libversion), 'include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a7fe767d11 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB-connector-c' +version = '3.1.11' + +homepage = 'https://downloads.mariadb.org/connector-c/' +description = "MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/MariaDB/mariadb-connector-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2cd769afea447231588580234523121268eae7576f75a7bee25a7e6ec04282f8'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +# don't use gold linker, leads to error: "invalid use of VERSION in input file" +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd'" + +sanity_check_paths = { + 'files': ['lib/mariadb/libmariadbclient.a', 'lib/mariadb/libmariadb.%s' % SHLIB_EXT], + 'dirs': ['include/mariadb'], +} + +modextrapaths = { + 'CPATH': ['include/mariadb'], + 'LD_LIBRARY_PATH': ['lib/mariadb'], + 'LIBRARY_PATH': ['lib/mariadb'], +} + +moduleclass = 'lib' From 20e9aedca8ef93e506a55301011355cc66634fac Mon Sep 17 00:00:00 2001 From: easybuild Date: Wed, 13 Jan 2021 12:34:11 +0000 Subject: [PATCH 0208/2365] Lift MariaDB to GCC toolchain following Boost --- .../m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb new file mode 100644 index 0000000000..83ee345b1d --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.5.8' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + 'eb4824f6f2c532cd3fc6a6bce7bf78ea7c6b949f8bdd07656b2c84344e757be8', # mariadb-10.5.8.tar.gz + '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('libaio', '0.3.112'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.2'), # optional + ('XZ', '5.2.5'), # optional + ('jemalloc', '5.2.1'), # optional + ('snappy', '1.1.8'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.9.10'), # needed by Connect XML + ('Boost', '1.74.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=bundled " # using an external PCRE is broken, see https://bugs.exim.org/show_bug.cgi?id=2173 +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' From afd7caa34189f81b5d10a573ef09b572b8682006 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Jan 2021 19:34:10 +0100 Subject: [PATCH 0209/2365] adding easyconfigs: Arrow-0.17.1-intel-2020b.eb --- .../a/Arrow/Arrow-0.17.1-intel-2020b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb new file mode 100644 index 0000000000..c9e2a80a81 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '0.17.1' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings)), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [ + 'http://apache.belnet.be/arrow/arrow-%(version)s/', + 'https://www-eu.apache.org/dist/arrow/arrow-%(version)s/', +] +sources = ['apache-arrow-%(version)s.tar.gz'] +patches = ['Arrow-0.16.0_fix-intel.patch'] +checksums = [ + 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz + '7c1569087f93959a0dfc163d80e5f542edb4d7ed0b9d71a2a05b4081211ad2b9', # Arrow-0.16.0_fix-intel.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Autotools', '20200321'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('pkg-config', '0.29.2'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11',), # for numpy + ('Boost', '1.74.0'), +] + +separate_build_dir = True +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/python/development.html +configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' From 1573ff6986dd08eb6dd76d70b3fbf1ab817eaf72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Jan 2021 19:44:06 +0100 Subject: [PATCH 0210/2365] adding easyconfigs: Pysam-0.16.0.1-iccifort-2020.4.304.eb --- .../Pysam-0.16.0.1-iccifort-2020.4.304.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..cc0bc1b1e0 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute +# Modified by: Pavel Grochal +# INUITS + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.16.0.1' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a61e98e299fa93ba121aab521081282b61bc978bb9052d33b26b38f8fe15573e'] + +dependencies = [ + ('Python', '3.8.6'), + ('ncurses', '6.2'), + ('cURL', '7.72.0'), + ('XZ', '5.2.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' From 946f7bdf8eab27b2760f79c9c366b3e6d8ed9556 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Jan 2021 19:44:36 +0100 Subject: [PATCH 0211/2365] adding easyconfigs: Seaborn-0.11.1-intel-2020b.eb --- .../s/Seaborn/Seaborn-0.11.1-intel-2020b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb new file mode 100644 index 0000000000..25396ba969 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.11.1' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 97cebaa21c8003d855b28f2c9296572761999ef5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Jan 2021 19:45:05 +0100 Subject: [PATCH 0212/2365] adding easyconfigs: Biopython-1.78-intel-2020b.eb --- .../b/Biopython/Biopython-1.78-intel-2020b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020b.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020b.eb new file mode 100644 index 0000000000..b06996d99b --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.78' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From 3e5b3cfbfe0029cf4c2dcfde041a5e1fef8c488c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Jan 2021 19:47:22 +0100 Subject: [PATCH 0213/2365] adding easyconfigs: pauvre-0.1924-intel-2020b.eb --- .../p/pauvre/pauvre-0.1924-intel-2020b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb diff --git a/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb b/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb new file mode 100644 index 0000000000..1d15a6c810 --- /dev/null +++ b/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'pauvre' +version = '0.1924' + +homepage = 'https://github.com/conchoecia/pauvre' +description = "Tools for plotting Oxford Nanopore and other long-read data" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['0a5f4fab1cabf7a9dbe5ec0d21be1e2ab0fabc78c8a74453006b63677bcc038f'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), + ('scikit-learn', '0.23.2'), + ('matplotlib', '3.3.3'), +] + +download_dep_fail = True +use_pip = True + +# fix incorrect requirement, correct name is 'scikit-learn' +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/pauvre'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pauvre --help"] + +sanity_pip_check = True + +moduleclass = 'math' From e725dd667c933a44f50586fd155e43947e17e4aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Jan 2021 19:49:05 +0100 Subject: [PATCH 0214/2365] adding easyconfigs: statsmodels-0.12.1-intel-2020b.eb --- .../statsmodels-0.12.1-intel-2020b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb new file mode 100644 index 0000000000..2e655bfefd --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.12.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + (name, version, { + 'checksums': ['a271b4ccec190148dccda25f0cbdcbf871f408fc1394a10a7dc1af4a62b91c8e'], + }), +] + +moduleclass = 'math' From 0b6877baed559950d0073f6750fea9b481a26b8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Jan 2021 19:50:04 +0100 Subject: [PATCH 0215/2365] adding easyconfigs: NanoComp-1.13.1-intel-2020b.eb, NanoPlot-1.33.0-intel-2020b.eb, Kaleido-0.1.0-GCCcore-10.2.0.eb, nanomath-1.2.0-intel-2020b.eb, nanoget-1.15.0-intel-2020b.eb, joypy-0.2.4-intel-2020b.eb, plotly.py-4.14.3-GCCcore-10.2.0.eb, orca-1.3.1-GCCcore-10.2.0.eb --- .../j/joypy/joypy-0.2.4-intel-2020b.eb | 28 ++++++++++ .../k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb | 28 ++++++++++ .../n/NanoComp/NanoComp-1.13.1-intel-2020b.eb | 45 ++++++++++++++++ .../n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb | 52 +++++++++++++++++++ .../n/nanoget/nanoget-1.15.0-intel-2020b.eb | 30 +++++++++++ .../n/nanomath/nanomath-1.2.0-intel-2020b.eb | 35 +++++++++++++ .../plotly.py-4.14.3-GCCcore-10.2.0.eb | 32 ++++++++++++ 7 files changed, 250 insertions(+) create mode 100644 easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb create mode 100644 easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb b/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb new file mode 100644 index 0000000000..6dfe84c1af --- /dev/null +++ b/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb @@ -0,0 +1,28 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'joypy' +version = '0.2.4' + +homepage = 'https://github.com/sbebo/joypy' +description = "Joyplots in Python with matplotlib & pandas" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['55d268386a1d2d974aa90cbf6dcca3ad943d17075987dfb8c4a772852fbe79c7'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11',), + ('matplotlib', '3.3.3',), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..12c3d7ed2a --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Kaleido' +version = '0.1.0' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = ['kaleido-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'] +checksums = ['8d0403b1eb21080e09d6d728c1ea7170fd4763c415fe89dfea6edf35ec36f8e7'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [('Python', '3.8.6')] + +unpack_sources = False + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb new file mode 100644 index 0000000000..7a456e392c --- /dev/null +++ b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb @@ -0,0 +1,45 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'NanoComp' +version = '1.13.1' + +homepage = 'https://github.com/wdecoster/NanoComp' +description = "Comparing runs of Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e8af09f3f9462b045e1c7abe8d4110ea4aaf10e4a1ba0152ad27c1331eb9e389'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11',), + ('Pysam', '0.16.0.1'), + ('nanomath', '1.2.0',), + ('nanoget', '1.15.0',), + ('NanoPlot', '1.33.0',), + ('plotly.py', '4.14.3'), + ('orca', '1.3.1'), + ('joypy', '0.2.4'), +] + +download_dep_fail = True +use_pip = True + +# replace strict Seaborn & pauvre version requirement with minimal version requirements, +preinstallopts = "sed -i 's/==0/>=0/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/NanoComp'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoComp --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb new file mode 100644 index 0000000000..9af7556393 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb @@ -0,0 +1,52 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'NanoPlot' +version = '1.33.0' + +homepage = 'https://github.com/wdecoster/NanoPlot' +description = "Plotting suite for long read sequencing data and alignments" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['caf69a5789625e746814238cb4f0d510ed6768a094566e8f1dcaa77933c4d6fd'] + +# statsmodels and pauvre are locked to specific versions, although newer versions seems to work fine. +# replace '==' with '>=' which works fine with current latest versions +preinstallopts = "sed -i'' 's/==/>=/g' setup.py && " + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), + ('Pysam', '0.16.0.1'), + ('nanomath', '1.2.0'), + ('nanoget', '1.15.0'), + ('Seaborn', '0.11.1'), + ('plotly.py', '4.14.3'), + ('pauvre', '0.1924'), + ('statsmodels', '0.12.1'), + ('Arrow', '0.17.1'), # for pyarrow + ('Kaleido', '0.1.0'), +] + +download_dep_fail = True +use_pip = True + +# replace strict Seaborn & pauvre version requirement with minimal version requirements +preinstallopts = "sed -i 's/==0/>=0/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/NanoPlot'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoPlot --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb new file mode 100644 index 0000000000..4ea32dc852 --- /dev/null +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb @@ -0,0 +1,30 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'nanoget' +version = '1.15.0' + +homepage = 'https://github.com/wdecoster/nanoget' +description = "Functions to extract information from Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f6993855d5f1aa1e9271c61e39184b22fccd6a90e634ca88d2684ff85c8c22e5'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), + ('Pysam', '0.16.0.1'), + ('nanomath', '1.2.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb new file mode 100644 index 0000000000..cc6a8ed547 --- /dev/null +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'nanomath' +version = '1.2.0' + +homepage = 'https://github.com/wdecoster/nanomath' +description = "A few simple math function for other Oxford Nanopore processing scripts" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('Python-Deprecated', '1.1.0', { + 'modulename': 'deprecated', + 'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'], + }), + (name, version, { + 'checksums': ['b12bf23762fc30be4550d7a8582233bd6f128a1c97477ffb27730bbb8a77f606'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6366976289 --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '4.14.3' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [('Python', '3.8.6')] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('retrying', '1.3.3', { + 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], + }), + ('plotly', version, { + 'checksums': ['7d8aaeed392e82fb8e0e48899f2d3d957b12327f9d38cdd5802bc574a8a39d91'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From 667ac9154eb716f2a4c9f7d00fac9e513de3aed0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Jan 2021 10:53:02 +0100 Subject: [PATCH 0216/2365] fix description of Arrow-0.17.1-intel-2020b.eb --- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index c9e2a80a81..0fb5b5532b 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -4,7 +4,7 @@ name = 'Arrow' version = '0.17.1' homepage = 'https://arrow.apache.org' -description = """Apache Arrow (incl. PyArrow Python bindings)), a cross-language development platform +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.""" toolchain = {'name': 'intel', 'version': '2020b'} From 4fed616eb9f9d176d10cfe974fbf7b628fabd737 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 15 Jan 2021 09:07:13 +0000 Subject: [PATCH 0217/2365] adding easyconfigs: PyTorch-1.7.1-fosscuda-2020b.eb, typing-extensions-3.7.4.3-fosscuda-2020b.eb --- .../p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 314 ++++++++++++++++++ 1 file changed, 314 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..fb4f24f06b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -0,0 +1,314 @@ +name = 'PyTorch' +version = '1.7.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-11.1.1', True), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] + +# PyTorch pulls in a bunch of submodules that are not releases. +# We download the submodule revisions from their repos. +# The list is generated by easybuild-framework/easybuild/scripts/createSubmoduleDeps.sh +local_extract_cmd_pattern = 'tar -C pytorch-%%(version)s/third_party/%s --strip-components=1 -xf %%s' + +source_urls = ['https://github.com/pytorch/pytorch/archive'] +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], + 'download_filename': '4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz', + 'filename': 'FP16-20200514.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'FP16', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], + 'download_filename': 'b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz', + 'filename': 'FXdiv-20200417.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'FXdiv', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], + 'download_filename': '24b55303f5cf65d75844714513a0d1b1409809bd.tar.gz', + 'filename': 'NNPACK-20191007.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'NNPACK', + }, + { + 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], + 'download_filename': '7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz', + 'filename': 'QNNPACK-20190828.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'QNNPACK', + }, + { + 'source_urls': ['https://github.com/google/XNNPACK/archive'], + 'download_filename': '1b354636b5942826547055252f3b359b54acff95.tar.gz', + 'filename': 'XNNPACK-20200323.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'XNNPACK', + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', + 'filename': 'benchmark-20180606.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'benchmark', + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': '63b254577ed77a8004a9be6ac707f3dccc4e1fd9.tar.gz', + 'filename': 'cpuinfo-20200611.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'cpuinfo', + }, + { + 'source_urls': ['https://github.com/NVlabs/cub/archive'], + 'download_filename': 'd106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz', + 'filename': 'cub-20200512.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'cub', + }, + { + 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], + 'download_filename': 'd41dc4dd74acce21fb210e7625d5d135751fa9e5.tar.gz', + 'filename': 'eigen-20190125.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'eigen', + }, + { + 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], + 'download_filename': '1d710393d5b7588f5de3b83f51c22bbddf095229.tar.gz', + 'filename': 'fbgemm-20200914.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm', + }, + { + 'source_urls': ['https://github.com/asmjit/asmjit/archive'], + 'download_filename': '9057aa30b620f0662ff51e2230c126a345063064.tar.gz', + 'filename': 'asmjit-20200429.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/asmjit', + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': 'd5e37adf1406cf899d7d9ec1d317c47506ccb970.tar.gz', + 'filename': 'cpuinfo-20190201.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/cpuinfo', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '0fc5466dbb9e623029b1ada539717d10bd45e99e.tar.gz', + 'filename': 'googletest-20180925.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/googletest', + }, + { + 'source_urls': ['https://github.com/fmtlib/fmt/archive'], + 'download_filename': 'cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz', + 'filename': 'fmt-20200806.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fmt', + }, + { + 'source_urls': ['https://github.com/houseroad/foxi/archive'], + 'download_filename': '4aba696ec8f31794fd42880346dc586486205e0a.tar.gz', + 'filename': 'foxi-20200922.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'foxi', + }, + { + 'source_urls': ['https://github.com/google/gemmlowp/archive'], + 'download_filename': '3fb5c176c17c765a3492cd2f0321b0dab712f350.tar.gz', + 'filename': 'gemmlowp-20181126.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'gemmlowp/gemmlowp', + }, + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': '3dc0328fe6a9d47bd47c0c6ca145a0d8a21845c6.tar.gz', + 'filename': 'gloo-20200918.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'gloo', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'googletest', + }, + { + 'source_urls': ['https://github.com/intel/ideep/archive'], + 'download_filename': 'ba885200dbbc1f144c7b58eba487378eb324f281.tar.gz', + 'filename': 'ideep-20200915.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'ideep', + }, + { + 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], + 'download_filename': '5ef631a030a6f73131c77892041042805a06064f.tar.gz', + 'filename': 'mkl-dnn-20200909.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'ideep/mkl-dnn', + }, + { + 'source_urls': ['https://github.com/onnx/onnx/archive'], + 'download_filename': 'a82c6a7010e2e332d8f74ad5b0c726fd47c85376.tar.gz', + 'filename': 'onnx-20200531.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'onnx', + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': 'e776aa0275e293707b6a0901e0e8d8a8a3679508.tar.gz', + 'filename': 'benchmark-20180525.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'onnx/third_party/benchmark', + }, + { + 'source_urls': ['https://github.com/onnx/onnx-tensorrt/archive'], + 'download_filename': 'c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz', + 'filename': 'onnx-tensorrt-20190916.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'onnx-tensorrt', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], + 'download_filename': '072586a71b55b7f8c584153d223e95687148a900.tar.gz', + 'filename': 'psimd-20200517.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'psimd', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], + 'download_filename': '029c88620802e1361ccf41d1970bd5b07fd6b7bb.tar.gz', + 'filename': 'pthreadpool-20200615.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'pthreadpool', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], + 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', + 'filename': 'PeachPy-20180218.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'python-peachpy', + }, + { + 'source_urls': ['https://github.com/shibatch/sleef/archive'], + 'download_filename': '7f523de651585fe25cade462efccca647dcc8d02.tar.gz', + 'filename': 'sleef-20190730.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'sleef', + }, + { + 'source_urls': ['https://github.com/01org/tbb/archive'], + 'download_filename': 'a51a90bc609bb73db8ea13841b5cf7aa4344d4a9.tar.gz', + 'filename': 'tbb-20181009.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tbb', + }, + { + 'source_urls': ['https://github.com/pytorch/tensorpipe/archive'], + 'download_filename': '95ff9319161fcdb3c674d2bb63fac3e94095b343.tar.gz', + 'filename': 'tensorpipe-20200928.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/googletest', + }, + { + 'source_urls': ['https://github.com/google/libnop/archive'], + 'download_filename': 'aa95422ea8c409e3f078d2ee7708a5f59a8b9fa2.tar.gz', + 'filename': 'libnop-20200723.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/libnop', + }, + { + 'source_urls': ['https://github.com/libuv/libuv/archive'], + 'download_filename': '02a9e1be252b623ee032a3137c0b0c94afbe6809.tar.gz', + 'filename': 'libuv-20200419.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/libuv', + }, +] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_fix_altivec_defines.patch', + 'PyTorch-1.7.0_fix_test_DistributedDataParallel.patch', + 'PyTorch-1.7.0_fix-fbgemm-not-implemented-issue.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', +] +checksums = [ + 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz + '90f20492621d5ed80b442aa682ff92d7ccf333ac8fac4a10e7e02afb159f3c13', # FP16-20200514.tar.gz + '9ccf554541666b5c089ad5dd465141d671c99971f36d72f313652f5c49ffce14', # FXdiv-20200417.tar.gz + '1f11dbbfad78d0a4c39fe94e52a28c0821cb25f9880420bb304f6302f73fe002', # NNPACK-20191007.tar.gz + '0d752bd75f46ce4d7c6f0a60b0d6c0e5918a7b4683c825284f8db3706dd24f76', # QNNPACK-20190828.tar.gz + 'b55a6ef3a0b4c0d3c39ad5578eb4fa9a7b2d7ee1ef06592b8a808a59a8e6589b', # XNNPACK-20200323.tar.gz + '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz + '18a99130ced1eaacab2ba8f75a1435f9955aab54fa0436b60468f020876ee902', # cpuinfo-20200611.tar.gz + 'd87f6737be1b544c299340b64b9303c1d6ec0447b49b3aaf6642838b4f8280d7', # cub-20200512.tar.gz + '2ec954f18cec50a7063a7358ce555f7e11788a7f6d4e7e597d83687dc2f3b989', # eigen-20190125.tar.gz + 'e7e495fee65a73fa40cf1644f5b9496a6498c7a4209ce4b6b4d7d80f3d3941a4', # fbgemm-20200914.tar.gz + '5c7ecb03ede09a38fa9bcf2527a0f1454cd67a34c0e6fd939ae4d93b276ce982', # asmjit-20200429.tar.gz + '3f2dc1970f397a0e59db72f9fca6ff144b216895c1d606f6c94a507c1e53a025', # cpuinfo-20190201.tar.gz + 'e99b904983d08ac8e9bddb5b0d21196b78ad9499e3c5d12192cee2ddd2b7515c', # googletest-20180925.tar.gz + '0654ea5a1899f373fee87ae00ca3478aef227c3cf23916572421c6ce25d274bc', # fmt-20200806.tar.gz + '10a3774a2ebef7a09dd5c9a6b7bfdc9d3e4eb153711572864d4cc560637727c3', # foxi-20200922.tar.gz + 'fdd6f08bdb33d33f4df516ffb91730fdb163479c19502cfc983083fd9cf43bfa', # gemmlowp-20181126.tar.gz + '9c6bace1c2af3ee186a84c791ba61a6ba92ecbe8a3990839d895771219a73ebc', # gloo-20200918.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + 'f205584378d9b0b6aeae9558b9d578469235f4e394e71b44ead616881e5fb210', # ideep-20200915.tar.gz + '4234ce25fd8bb64899493bb21c2473559d6bcfe098309fe74e351945475da930', # mkl-dnn-20200909.tar.gz + 'c3bf8cc8091b24c43aa205a1f2037a518d249eb5997bea7f543b7fc880e80e21', # onnx-20200531.tar.gz + 'c7682e9007ddfd94072647abab3e89ffd9084089460ae47d67060974467b58bf', # benchmark-20180525.tar.gz + '314cde420a7cf692bdb6877bc6af6bc514805f6cdb8bee90f32566ed08d94b1c', # onnx-tensorrt-20190916.tar.gz + 'f6c4dab91ae9a03b3019e7cab0572743afd0e1b6e75b97fcca50259c737c924e', # psimd-20200517.tar.gz + 'd13818a10a645d557202aa005606337b2a0cdf690e5655253800ab11abb0c076', # pthreadpool-20200615.tar.gz + '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180218.tar.gz + '8cb5fae822077ca9cbc14dcc7bba9a3a35ad519284fc5169f9a176672c63860a', # sleef-20190730.tar.gz + # checksum for original download of tbb-20181009.tar.gz from https://github.com/intel/tbb/archive + ('dc0a8d8d96cb8765782aa6ac1b509ad4db955d9bbb58fa5cc2265f0292756d72', + # checksum for download of tbb-20181009.tar.gz from https://github.com/01org/tbb/archive + 'be111cf161b587812fa3b106fe550efb6f129b8b0b702fef32fac23af9580e5e'), + '0039658ffed8d4ff21575651a6f5258853cf8e1ca8bf564822b51f94da28b7fd', # tensorpipe-20200928.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + '9ee3f3b1efc629dbc3703ece3892e7e05c7048eed7031d06020e38bb30bee3ab', # libnop-20200723.tar.gz + '5ca4e9091f3231d8ad8801862dc4e851c23af89c69141d27723157776f7291e7', # libuv-20200419.tar.gz + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + '98a32023292772984aa53ef739e444ec8b20617b72bd7593c62e884f5d8b2e6c', # PyTorch-1.7.0_fix_altivec_defines.patch + # PyTorch-1.7.0_fix_test_DistributedDataParallel.patch + '5e70e6aecb1916bb8369b8d3f5e4b3cbf7e2b7a015f8099eea330b42775e25c5', + # PyTorch-1.7.0_fix-fbgemm-not-implemented-issue.patch + '97febb91ae2d051db9541e1e4c5924c77555ab73ee49ad7d62ef3e4714110297', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + # PyTorch-1.7.0_increase-distributed-test-timeout.patch + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch +] + +excluded_tests = { + '': [ + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! + # https://github.com/pytorch/pytorch/issues/43209 + 'test_quantization', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From 322c58e89ca4c84b70a93131c9f6e71c7d0bb2ab Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 15 Jan 2021 10:16:55 +0000 Subject: [PATCH 0218/2365] add 8.0 to cuda compute capabilities MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index fb4f24f06b..fa3c257ff6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -34,7 +34,7 @@ dependencies = [ ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) -cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] # PyTorch pulls in a bunch of submodules that are not releases. # We download the submodule revisions from their repos. From 87bec1d5adb0fcfc586c6f99c4c5a780c1f97e3b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 15 Jan 2021 14:03:19 +0100 Subject: [PATCH 0219/2365] patch of a missing include file. this bug has been fixed in 1.75.0 https://github.com/boostorg/serialization/issues/219 --- easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index fe7439b16c..68da86b69d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -9,7 +9,14 @@ toolchainopts = {'pic': True} source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5'] + +# patch of a missing include file that has been fixed in 1.75.0 https://github.com/boostorg/serialization/issues/219 +patches = ['Boost-%(version)s-library_version_type_serialization.patch'] +checksums = [ + 'afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5', # boost_1_74_0.tar.gz + # Boost-1.74.0-library_version_type_serialization.patch + '882b4bdf1029ff0a31d092a0a92d920f5b5f0cea40feb153256bfb5a9098936d', +] dependencies = [ ('bzip2', '1.0.8'), From 4bb24595c059646c83b95d6411029d8ee01c6ec3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Jan 2021 14:39:28 +0100 Subject: [PATCH 0220/2365] {devel}[foss/2020b] PyTorch v1.7.1 w/ Python 3.8.6 --- .../p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 313 ++++++++++++++++++ ...yping-extensions-3.7.4.3-GCCcore-10.2.0.eb | 21 ++ 2 files changed, 334 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb new file mode 100644 index 0000000000..38b0c7f28a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -0,0 +1,313 @@ +name = 'PyTorch' +version = '1.7.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] + +# PyTorch pulls in a bunch of submodules that are not releases. +# We download the submodule revisions from their repos. +# The list is generated by easybuild-framework/easybuild/scripts/createSubmoduleDeps.sh +local_extract_cmd_pattern = 'tar -C pytorch-%%(version)s/third_party/%s --strip-components=1 -xf %%s' + +source_urls = ['https://github.com/pytorch/pytorch/archive'] +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], + 'download_filename': '4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz', + 'filename': 'FP16-20200514.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'FP16', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], + 'download_filename': 'b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz', + 'filename': 'FXdiv-20200417.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'FXdiv', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], + 'download_filename': '24b55303f5cf65d75844714513a0d1b1409809bd.tar.gz', + 'filename': 'NNPACK-20191007.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'NNPACK', + }, + { + 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], + 'download_filename': '7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz', + 'filename': 'QNNPACK-20190828.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'QNNPACK', + }, + { + 'source_urls': ['https://github.com/google/XNNPACK/archive'], + 'download_filename': '1b354636b5942826547055252f3b359b54acff95.tar.gz', + 'filename': 'XNNPACK-20200323.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'XNNPACK', + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', + 'filename': 'benchmark-20180606.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'benchmark', + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': '63b254577ed77a8004a9be6ac707f3dccc4e1fd9.tar.gz', + 'filename': 'cpuinfo-20200611.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'cpuinfo', + }, + { + 'source_urls': ['https://github.com/NVlabs/cub/archive'], + 'download_filename': 'd106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz', + 'filename': 'cub-20200512.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'cub', + }, + { + 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], + 'download_filename': 'd41dc4dd74acce21fb210e7625d5d135751fa9e5.tar.gz', + 'filename': 'eigen-20190125.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'eigen', + }, + { + 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], + 'download_filename': '1d710393d5b7588f5de3b83f51c22bbddf095229.tar.gz', + 'filename': 'fbgemm-20200914.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm', + }, + { + 'source_urls': ['https://github.com/asmjit/asmjit/archive'], + 'download_filename': '9057aa30b620f0662ff51e2230c126a345063064.tar.gz', + 'filename': 'asmjit-20200429.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/asmjit', + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': 'd5e37adf1406cf899d7d9ec1d317c47506ccb970.tar.gz', + 'filename': 'cpuinfo-20190201.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/cpuinfo', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '0fc5466dbb9e623029b1ada539717d10bd45e99e.tar.gz', + 'filename': 'googletest-20180925.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/googletest', + }, + { + 'source_urls': ['https://github.com/fmtlib/fmt/archive'], + 'download_filename': 'cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz', + 'filename': 'fmt-20200806.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'fmt', + }, + { + 'source_urls': ['https://github.com/houseroad/foxi/archive'], + 'download_filename': '4aba696ec8f31794fd42880346dc586486205e0a.tar.gz', + 'filename': 'foxi-20200922.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'foxi', + }, + { + 'source_urls': ['https://github.com/google/gemmlowp/archive'], + 'download_filename': '3fb5c176c17c765a3492cd2f0321b0dab712f350.tar.gz', + 'filename': 'gemmlowp-20181126.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'gemmlowp/gemmlowp', + }, + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': '3dc0328fe6a9d47bd47c0c6ca145a0d8a21845c6.tar.gz', + 'filename': 'gloo-20200918.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'gloo', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'googletest', + }, + { + 'source_urls': ['https://github.com/intel/ideep/archive'], + 'download_filename': 'ba885200dbbc1f144c7b58eba487378eb324f281.tar.gz', + 'filename': 'ideep-20200915.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'ideep', + }, + { + 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], + 'download_filename': '5ef631a030a6f73131c77892041042805a06064f.tar.gz', + 'filename': 'mkl-dnn-20200909.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'ideep/mkl-dnn', + }, + { + 'source_urls': ['https://github.com/onnx/onnx/archive'], + 'download_filename': 'a82c6a7010e2e332d8f74ad5b0c726fd47c85376.tar.gz', + 'filename': 'onnx-20200531.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'onnx', + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': 'e776aa0275e293707b6a0901e0e8d8a8a3679508.tar.gz', + 'filename': 'benchmark-20180525.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'onnx/third_party/benchmark', + }, + { + 'source_urls': ['https://github.com/onnx/onnx-tensorrt/archive'], + 'download_filename': 'c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz', + 'filename': 'onnx-tensorrt-20190916.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'onnx-tensorrt', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], + 'download_filename': '072586a71b55b7f8c584153d223e95687148a900.tar.gz', + 'filename': 'psimd-20200517.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'psimd', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], + 'download_filename': '029c88620802e1361ccf41d1970bd5b07fd6b7bb.tar.gz', + 'filename': 'pthreadpool-20200615.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'pthreadpool', + }, + { + 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], + 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', + 'filename': 'PeachPy-20180218.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'python-peachpy', + }, + { + 'source_urls': ['https://github.com/shibatch/sleef/archive'], + 'download_filename': '7f523de651585fe25cade462efccca647dcc8d02.tar.gz', + 'filename': 'sleef-20190730.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'sleef', + }, + { + 'source_urls': ['https://github.com/01org/tbb/archive'], + 'download_filename': 'a51a90bc609bb73db8ea13841b5cf7aa4344d4a9.tar.gz', + 'filename': 'tbb-20181009.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tbb', + }, + { + 'source_urls': ['https://github.com/pytorch/tensorpipe/archive'], + 'download_filename': '95ff9319161fcdb3c674d2bb63fac3e94095b343.tar.gz', + 'filename': 'tensorpipe-20200928.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/googletest', + }, + { + 'source_urls': ['https://github.com/google/libnop/archive'], + 'download_filename': 'aa95422ea8c409e3f078d2ee7708a5f59a8b9fa2.tar.gz', + 'filename': 'libnop-20200723.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/libnop', + }, + { + 'source_urls': ['https://github.com/libuv/libuv/archive'], + 'download_filename': '02a9e1be252b623ee032a3137c0b0c94afbe6809.tar.gz', + 'filename': 'libuv-20200419.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/libuv', + }, +] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_fix_altivec_defines.patch', + 'PyTorch-1.7.0_fix_test_DistributedDataParallel.patch', + 'PyTorch-1.7.0_fix-fbgemm-not-implemented-issue.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_el8_ppc64le.patch', +] +checksums = [ + 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz + '90f20492621d5ed80b442aa682ff92d7ccf333ac8fac4a10e7e02afb159f3c13', # FP16-20200514.tar.gz + '9ccf554541666b5c089ad5dd465141d671c99971f36d72f313652f5c49ffce14', # FXdiv-20200417.tar.gz + '1f11dbbfad78d0a4c39fe94e52a28c0821cb25f9880420bb304f6302f73fe002', # NNPACK-20191007.tar.gz + '0d752bd75f46ce4d7c6f0a60b0d6c0e5918a7b4683c825284f8db3706dd24f76', # QNNPACK-20190828.tar.gz + 'b55a6ef3a0b4c0d3c39ad5578eb4fa9a7b2d7ee1ef06592b8a808a59a8e6589b', # XNNPACK-20200323.tar.gz + '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz + '18a99130ced1eaacab2ba8f75a1435f9955aab54fa0436b60468f020876ee902', # cpuinfo-20200611.tar.gz + 'd87f6737be1b544c299340b64b9303c1d6ec0447b49b3aaf6642838b4f8280d7', # cub-20200512.tar.gz + '2ec954f18cec50a7063a7358ce555f7e11788a7f6d4e7e597d83687dc2f3b989', # eigen-20190125.tar.gz + 'e7e495fee65a73fa40cf1644f5b9496a6498c7a4209ce4b6b4d7d80f3d3941a4', # fbgemm-20200914.tar.gz + '5c7ecb03ede09a38fa9bcf2527a0f1454cd67a34c0e6fd939ae4d93b276ce982', # asmjit-20200429.tar.gz + '3f2dc1970f397a0e59db72f9fca6ff144b216895c1d606f6c94a507c1e53a025', # cpuinfo-20190201.tar.gz + 'e99b904983d08ac8e9bddb5b0d21196b78ad9499e3c5d12192cee2ddd2b7515c', # googletest-20180925.tar.gz + '0654ea5a1899f373fee87ae00ca3478aef227c3cf23916572421c6ce25d274bc', # fmt-20200806.tar.gz + '10a3774a2ebef7a09dd5c9a6b7bfdc9d3e4eb153711572864d4cc560637727c3', # foxi-20200922.tar.gz + 'fdd6f08bdb33d33f4df516ffb91730fdb163479c19502cfc983083fd9cf43bfa', # gemmlowp-20181126.tar.gz + '9c6bace1c2af3ee186a84c791ba61a6ba92ecbe8a3990839d895771219a73ebc', # gloo-20200918.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + 'f205584378d9b0b6aeae9558b9d578469235f4e394e71b44ead616881e5fb210', # ideep-20200915.tar.gz + '4234ce25fd8bb64899493bb21c2473559d6bcfe098309fe74e351945475da930', # mkl-dnn-20200909.tar.gz + 'c3bf8cc8091b24c43aa205a1f2037a518d249eb5997bea7f543b7fc880e80e21', # onnx-20200531.tar.gz + 'c7682e9007ddfd94072647abab3e89ffd9084089460ae47d67060974467b58bf', # benchmark-20180525.tar.gz + '314cde420a7cf692bdb6877bc6af6bc514805f6cdb8bee90f32566ed08d94b1c', # onnx-tensorrt-20190916.tar.gz + 'f6c4dab91ae9a03b3019e7cab0572743afd0e1b6e75b97fcca50259c737c924e', # psimd-20200517.tar.gz + 'd13818a10a645d557202aa005606337b2a0cdf690e5655253800ab11abb0c076', # pthreadpool-20200615.tar.gz + '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180218.tar.gz + '8cb5fae822077ca9cbc14dcc7bba9a3a35ad519284fc5169f9a176672c63860a', # sleef-20190730.tar.gz + # checksum for original download of tbb-20181009.tar.gz from https://github.com/intel/tbb/archive + ('dc0a8d8d96cb8765782aa6ac1b509ad4db955d9bbb58fa5cc2265f0292756d72', + # checksum for download of tbb-20181009.tar.gz from https://github.com/01org/tbb/archive + 'be111cf161b587812fa3b106fe550efb6f129b8b0b702fef32fac23af9580e5e'), + '0039658ffed8d4ff21575651a6f5258853cf8e1ca8bf564822b51f94da28b7fd', # tensorpipe-20200928.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + '9ee3f3b1efc629dbc3703ece3892e7e05c7048eed7031d06020e38bb30bee3ab', # libnop-20200723.tar.gz + '5ca4e9091f3231d8ad8801862dc4e851c23af89c69141d27723157776f7291e7', # libuv-20200419.tar.gz + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + '98a32023292772984aa53ef739e444ec8b20617b72bd7593c62e884f5d8b2e6c', # PyTorch-1.7.0_fix_altivec_defines.patch + # PyTorch-1.7.0_fix_test_DistributedDataParallel.patch + '5e70e6aecb1916bb8369b8d3f5e4b3cbf7e2b7a015f8099eea330b42775e25c5', + # PyTorch-1.7.0_fix-fbgemm-not-implemented-issue.patch + '97febb91ae2d051db9541e1e4c5924c77555ab73ee49ad7d62ef3e4714110297', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + # PyTorch-1.7.0_increase-distributed-test-timeout.patch + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + '2a94a9cc009f02469b843fc65a6ee2cb01873f783568b8bcc83c33ba8e6b1a58', # PyTorch-1.7.1_el8_ppc64le.patch +] + +excluded_tests = { + '': [ + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! + # https://github.com/pytorch/pytorch/issues/43209 + 'test_quantization', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1077cfc00c --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '3.7.4.3' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions – Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From b7030693c4f7a59474eab731f3fceb6147c86bfc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 15 Jan 2021 13:39:59 +0000 Subject: [PATCH 0221/2365] adding easyconfigs: iomkl-2020b.eb, imkl-2020.4.304-iompi-2020b.eb, iompi-2020b.eb, OpenMPI-4.0.5-iccifort-2020.4.304.eb --- .../i/imkl/imkl-2020.4.304-iompi-2020b.eb | 39 +++++++++++++++++++ easybuild/easyconfigs/i/iomkl/iomkl-2020b.eb | 20 ++++++++++ easybuild/easyconfigs/i/iompi/iompi-2020b.eb | 19 +++++++++ .../OpenMPI-4.0.5-iccifort-2020.4.304.eb | 32 +++++++++++++++ 4 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-2020b.eb create mode 100644 easybuild/easyconfigs/i/iompi/iompi-2020b.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb new file mode 100644 index 0000000000..7536b65853 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.4.304' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iompi', 'version': '2020b'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2020b.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2020b.eb new file mode 100644 index 0000000000..994e712f40 --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2020b.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '2020b' + +homepage = 'https://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" + +toolchain = SYSTEM + +local_compver = '2020.4.304' + +dependencies = [ + ('iccifort', local_compver), + ('OpenMPI', '4.0.5', '', ('iccifort', local_compver)), + ('imkl', local_compver, '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2020b.eb b/easybuild/easyconfigs/i/iompi/iompi-2020b.eb new file mode 100644 index 0000000000..7a81cae9fa --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2020b.eb @@ -0,0 +1,19 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ +easyblock = "Toolchain" + +name = 'iompi' +version = '2020b' + +homepage = 'https://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" + +toolchain = SYSTEM + +local_compver = '2020.4.304' + +dependencies = [ + ('iccifort', local_compver), + ('OpenMPI', '4.0.5', '', ('iccifort', local_compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..b132e94d87 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -0,0 +1,32 @@ +name = 'OpenMPI' +version = '4.0.5' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('libevent', '2.1.12'), + ('UCX', '1.9.0'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 220c71b7f545e980cff0932a97ccac127a7cc1a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Jan 2021 14:50:17 +0100 Subject: [PATCH 0222/2365] drop cuda_compute_capabilities from PyTorch 1.7.1 easyconfig using foss/2020b --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index 38b0c7f28a..da0f7efcfe 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -30,9 +30,6 @@ dependencies = [ ('Pillow', '8.0.1'), ] -# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) -cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] - # PyTorch pulls in a bunch of submodules that are not releases. # We download the submodule revisions from their repos. # The list is generated by easybuild-framework/easybuild/scripts/createSubmoduleDeps.sh From bf2e2aca59eb56b2c8137f19173cdc1695179478 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Jan 2021 14:54:21 +0100 Subject: [PATCH 0223/2365] remove patch for PyTorch 1.7.1 that is no longer needed with foss(cuda)/2020b --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index da0f7efcfe..7b29d606cb 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -239,7 +239,6 @@ patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', - 'PyTorch-1.7.1_el8_ppc64le.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -289,7 +288,6 @@ checksums = [ # PyTorch-1.7.0_increase-distributed-test-timeout.patch 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - '2a94a9cc009f02469b843fc65a6ee2cb01873f783568b8bcc83c33ba8e6b1a58', # PyTorch-1.7.1_el8_ppc64le.patch ] excluded_tests = { From 1104e9c7e257138e485b3cc02ca1e4cbde3dad7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Jan 2021 15:18:22 +0100 Subject: [PATCH 0224/2365] add missing build dependency for typing-extensions v3.7.4.3 w/ GCCcore/10.2.0 --- .../typing-extensions-3.7.4.3-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb index 1077cfc00c..fc7c6a67ec 100644 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb @@ -12,6 +12,8 @@ source_urls = [PYPI_SOURCE] sources = ['typing_extensions-%(version)s.tar.gz'] checksums = ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'] +builddependencies = [('binutils', '2.35')] + dependencies = [('Python', '3.8.6')] use_pip = True From 02bb20ccd83ab136a6bacdaa549c352e8b4a21bc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 15 Jan 2021 15:37:33 +0000 Subject: [PATCH 0225/2365] qtlocation fix "error: 'runtime_error' is not a member of 'std'" in Qt5 --- easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb index 9a0f8bec84..bde35a1625 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb @@ -21,6 +21,7 @@ patches = [ 'Qt5-5.14.1_fix-OF-Gentoo.patch', 'Qt5-5.14.2_fix-missing-stdint.patch', 'Qt5-5.14.2_fix-webengine-bison.patch', + 'Qt5-5.14.2_fix-std-runtime_error.patch', ] checksums = [ 'c6fcd53c744df89e7d3223c02838a33309bd1c291fcb6f9341505fe99f7f19fa', # qt-everywhere-src-5.14.2.tar.xz @@ -29,6 +30,7 @@ checksums = [ '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch '648e2a92d5ea139543db5d01a80aa33d4721e52bb59c785490b64497b0ede4ab', # Qt5-5.14.2_fix-missing-stdint.patch '6ace4735e35dee95d6b6c7eea3a7c46c264589a319d745310282ee724f632861', # Qt5-5.14.2_fix-webengine-bison.patch + '290d91efe8fc7c6daedf01f4a055ff30123c987d41b1832a34920ef521579f5c', # Qt5-5.14.2_fix-std-runtime_error.patch ] builddependencies = [ From 218c005f978f0f1d6b02adc7e2818b205d35d9c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Jan 2021 20:07:04 +0100 Subject: [PATCH 0226/2365] add missing comment to patch for Boost 1.74.0, also apply patch in easyconfig using iccifort toolchain --- easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 4 +--- .../b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb | 7 ++++++- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index 68da86b69d..1708d2d677 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -9,13 +9,11 @@ toolchainopts = {'pic': True} source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] - -# patch of a missing include file that has been fixed in 1.75.0 https://github.com/boostorg/serialization/issues/219 patches = ['Boost-%(version)s-library_version_type_serialization.patch'] checksums = [ 'afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5', # boost_1_74_0.tar.gz # Boost-1.74.0-library_version_type_serialization.patch - '882b4bdf1029ff0a31d092a0a92d920f5b5f0cea40feb153256bfb5a9098936d', + 'ee61e889ce9473ad82b69c9a8cbe1bf9650d633b74fdf7e4f4a4825aa990feca', ] dependencies = [ diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb index 1391b652d5..b201695628 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb @@ -10,7 +10,12 @@ toolchainopts = {'pic': True, 'extra_cxxflags': '-DBOOST_ASIO_USE_TS_EXECUTOR_AS source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5'] +patches = ['Boost-%(version)s-library_version_type_serialization.patch'] +checksums = [ + 'afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5', # boost_1_74_0.tar.gz + # Boost-1.74.0-library_version_type_serialization.patch + 'ee61e889ce9473ad82b69c9a8cbe1bf9650d633b74fdf7e4f4a4825aa990feca', +] dependencies = [ ('bzip2', '1.0.8'), From fd8ae3e7bba27aed16313fbe2185d389442e5a14 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 15 Jan 2021 19:56:00 +0000 Subject: [PATCH 0227/2365] patch to validate number of gpus in distributed tests --- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index fa3c257ff6..feafbfb626 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -245,6 +245,7 @@ patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -294,6 +295,8 @@ checksums = [ # PyTorch-1.7.0_increase-distributed-test-timeout.patch 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch + 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', ] excluded_tests = { From a349e28041feb7c914a0f25afc4d1cdef5978c51 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 16 Jan 2021 16:54:26 +0000 Subject: [PATCH 0228/2365] patch to fix nan compare for complex in tests --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index feafbfb626..69a49e0242 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -246,6 +246,7 @@ patches = [ 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch', + 'PyTorch-1.7.1_fix-nan-compare.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -297,6 +298,7 @@ checksums = [ '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', + 'afed3d6043b015c0aeaedb9a75038ec22e63ee14e0be0146c9a31d9d55b123d7', # PyTorch-1.7.1_fix-nan-compare.patch ] excluded_tests = { From 8d5a324d62f41d828c44ac3698c18d02daffc745 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 17 Jan 2021 10:38:31 +0100 Subject: [PATCH 0229/2365] drop versionsuffix for GPyTorch --- .../g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb new file mode 100644 index 0000000000..a131fffa61 --- /dev/null +++ b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'GPyTorch' +version = '1.3.0' + +homepage = 'https://gpytorch.ai' +description = "GPyTorch is a Gaussian process library implemented using PyTorch." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9bc7aea1dee188b69ff181e3406aabf6fedfa4446b834ed6adf68b94b6ebebd5'] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', '1.7.1'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'lib' From f7e01186a4711e19e532e464a82826a174829353 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Jan 2021 09:19:40 +0100 Subject: [PATCH 0230/2365] remove duplicate 'preinstallopts' from NanoPlot easyconfig --- .../easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb index 9af7556393..4f8ea405c7 100644 --- a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb @@ -15,10 +15,6 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['caf69a5789625e746814238cb4f0d510ed6768a094566e8f1dcaa77933c4d6fd'] -# statsmodels and pauvre are locked to specific versions, although newer versions seems to work fine. -# replace '==' with '>=' which works fine with current latest versions -preinstallopts = "sed -i'' 's/==/>=/g' setup.py && " - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), From c46eeaff739f4cdb1a812b534a701536aa98900b Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 18 Jan 2021 19:26:22 +0100 Subject: [PATCH 0231/2365] fix download url for UDUNITS 2.2.26 --- .../easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb index db193785a1..f97a364b22 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb @@ -22,7 +22,7 @@ description = """UDUNITS supports conversion of unit specifications between form toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.unidata.ucar.edu/downloads/udunits'] +source_urls = ['https://fossies.org/linux/privat/legacy/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] From adaa1e1f4335e193397ac2a8634f1b196a4d04cd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 18 Jan 2021 21:55:44 +0100 Subject: [PATCH 0232/2365] rename orca-1.3.1-GCCcore-10.2.0.eb to plotly-orca-1.3.1-GCCcore-10.2.0.eb --- .../n/NanoComp/NanoComp-1.13.1-intel-2020b.eb | 2 +- .../plotly-orca-1.3.1-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 2 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb index 7a456e392c..cfa973108a 100644 --- a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb @@ -23,7 +23,7 @@ dependencies = [ ('nanoget', '1.15.0',), ('NanoPlot', '1.33.0',), ('plotly.py', '4.14.3'), - ('orca', '1.3.1'), + ('plotly-orca', '1.3.1'), ('joypy', '0.2.4'), ] diff --git a/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6815d1259d --- /dev/null +++ b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Binary' + +name = 'plotly-orca' +version = '1.3.1' + +homepage = 'https://github.com/plotly/orca' +description = """Orca is an Electron app that generates images and reports of Plotly things like +plotly.js graphs, dash apps, dashboards from the command line.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/plotly/orca/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['25ebf207d75769c140dcea033a984e7a3a6d919bb8e110a14c890c8cf430f14d'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('nodejs', '12.19.0'), +] + +install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s electron@6.1.4 v%(version)s.tar.gz' + +sanity_check_paths = { + 'files': ['bin/orca'], + 'dirs': ['lib/node_modules/orca'], +} +sanity_check_commands = ['orca --help'] + +moduleclass = 'vis' From d7218b2f2f6a790ffd0eefb062f3529f0fb0bd9d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 20 Jan 2021 17:19:15 +0000 Subject: [PATCH 0233/2365] Add Inline extension to recent Perl --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 9c2b7edb9a..b192f54ba0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -1788,6 +1788,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN/'], 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY/'], + 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], + }), ] moduleclass = 'lang' From 1ecb7c485da699f8c44fb530dcce3105e4e2d6db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Jan 2021 16:40:15 +0100 Subject: [PATCH 0234/2365] adding easyconfigs: gensim-3.8.3-foss-2020b.eb, gensim-3.8.3-intel-2020b.eb --- .../g/gensim/gensim-3.8.3-foss-2020b.eb | 32 +++++++++++++++++++ .../g/gensim/gensim-3.8.3-intel-2020b.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb diff --git a/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb new file mode 100644 index 0000000000..881669d3f1 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'gensim' +version = '3.8.3' + +homepage = 'https://radimrehurek.com/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy, pandas +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('smart_open', '4.1.2', { + 'checksums': ['4bbb6233364fc1173cc0af6b7a56ed76fce32509514f1978a995a5835f3177f1'], + }), + (name, version, { + 'checksums': ['786adb0571f75114e9c5f7a31dd2e6eb39a9791f22c8757621545e2ded3ea367'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb new file mode 100644 index 0000000000..8de87c4e0c --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'gensim' +version = '3.8.3' + +homepage = 'https://radimrehurek.com/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy, pandas +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('smart_open', '4.1.2', { + 'checksums': ['4bbb6233364fc1173cc0af6b7a56ed76fce32509514f1978a995a5835f3177f1'], + }), + (name, version, { + 'checksums': ['786adb0571f75114e9c5f7a31dd2e6eb39a9791f22c8757621545e2ded3ea367'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 127f093a4284f8b737020acc4add59b10b19c778 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 21 Jan 2021 20:01:39 +0000 Subject: [PATCH 0235/2365] correct fix nan compare patch and add complex half patch --- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 69a49e0242..0983bf4af1 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -247,6 +247,7 @@ patches = [ 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch', 'PyTorch-1.7.1_fix-nan-compare.patch', + 'PyTorch-1.7.1_complex32.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -298,7 +299,8 @@ checksums = [ '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', - 'afed3d6043b015c0aeaedb9a75038ec22e63ee14e0be0146c9a31d9d55b123d7', # PyTorch-1.7.1_fix-nan-compare.patch + 'b8f2d14ad8ea3e6809ab6f4c37f632c3d842f663ca0e4641589dc722a10f5411', # PyTorch-1.7.1_fix-nan-compare.patch + '6028bff2be720cf70acad2129db60fd10872e02c9e460c72bb274228cf90b320', # PyTorch-1.7.1_complex32.patch ] excluded_tests = { From 59d2f1e67e4edea7e72e54378e9a02fb91534998 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 25 Jan 2021 11:32:44 +0200 Subject: [PATCH 0236/2365] adding easyconfigs: ASE-3.21.1-foss-2020b.eb, GPAW-21.1.0-foss-2020b.eb --- .../a/ASE/ASE-3.21.1-foss-2020b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb new file mode 100644 index 0000000000..22f7a11c6b --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.21.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.3.3'), + ('spglib-python', '1.16.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('itsdangerous', '1.1.0', { + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Flask', '1.1.2', { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('ase', version, { + 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' From 1bcaabdf00de9187de191db296236fffc230e5d9 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 25 Jan 2021 12:14:29 +0200 Subject: [PATCH 0237/2365] Fix version suffix due to new ASE version. Update ASE dependencies. --- .../a/ASE/ASE-3.21.1-foss-2020b.eb | 2 + .../GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb | 49 +++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb index 22f7a11c6b..d6386e65ea 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb @@ -44,6 +44,8 @@ exts_list = [ ('Flask', '1.1.2', { 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], }), + ('pytest-mock', '3.5.1', { + }), ('ase', version, { 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], }), diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..6776283e38 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '21.1.0' +_aseversion = '3.21.1' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + '96843b68e04bd1c12606036c9f99b0ddfa5e6ee08ce46835e6bb347a6bd560a3', # gpaw-21.1.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('libxc', '4.3.4'), + ('libvdwxc', '0.4.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' From 060774617024d8d9b295acbd2077d91610d55889 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 25 Jan 2021 12:34:05 +0200 Subject: [PATCH 0238/2365] Forgotten checksum. --- easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb index d6386e65ea..55cc585912 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb @@ -45,6 +45,7 @@ exts_list = [ 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], }), ('pytest-mock', '3.5.1', { + 'checksums': ['a1e2aba6af9560d313c642dae7e00a2a12b022b80301d9d7fc8ec6858e1dd9fc'], }), ('ase', version, { 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], From 35db6d72d043ad6b1253026ad4fe48058e1c98f0 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 25 Jan 2021 13:58:03 +0200 Subject: [PATCH 0239/2365] Add Intel toolchain versions. --- .../a/ASE/ASE-3.21.1-intel-2020b.eb | 70 +++++++++++++++++++ .../GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb | 51 ++++++++++++++ 2 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb new file mode 100644 index 0000000000..528d78658c --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.21.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.3.3'), + ('spglib-python', '1.16.0'), +] + +use_pip = True +sanity_pip_check = True + +# required because we're building Python packages (MarkupSafe, +# ase-ext) using Intel compilers on top of Python built with GCC. +check_ldshared = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('itsdangerous', '1.1.0', { + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Flask', '1.1.2', { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('pytest-mock', '3.5.1', { + 'checksums': ['a1e2aba6af9560d313c642dae7e00a2a12b022b80301d9d7fc8ec6858e1dd9fc'], + }), + ('ase', version, { + 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..a2cc1f7494 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb @@ -0,0 +1,51 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '21.1.0' +_aseversion = '3.21.1' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + '96843b68e04bd1c12606036c9f99b0ddfa5e6ee08ce46835e6bb347a6bd560a3', # gpaw-21.1.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('libxc', '4.3.4'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC. +check_ldshared = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' From 3a3982e0c3e2db33c3a580ac48670a3a616a525f Mon Sep 17 00:00:00 2001 From: easybuilder Date: Mon, 25 Jan 2021 16:47:26 +0100 Subject: [PATCH 0240/2365] adding easyconfigs: bpytop-1.0.60-GCCcore-10.2.0.eb --- .../b/bpytop/bpytop-1.0.60-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/bpytop/bpytop-1.0.60-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/bpytop/bpytop-1.0.60-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bpytop/bpytop-1.0.60-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cbc86c851a --- /dev/null +++ b/easybuild/easyconfigs/b/bpytop/bpytop-1.0.60-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'bpytop' +version = '1.0.60' + +homepage = 'https://github.com/aristocratos/bpytop/' +description = """Resource monitor that shows usage and stats for processor, memory, disks, network and processes.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/aristocratos/bpytop/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7fc1a40ac6b9cb8f78f1e0e2e7bd58b9197c333ad4c5a4f2cb464d3f8183835b'] + +dependencies = [('Python', '3.8.6')] + +postinstallcmds = ['mv %(installdir)s/bpytop.py %(installdir)s/bpytop'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['bpytop'], + 'dirs': ['themes'], +} + +moduleclass = 'tools' From be1135524db90dbef047eb539ee93411364f61bc Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 25 Jan 2021 09:24:27 -0800 Subject: [PATCH 0241/2365] {lib}[GCC/10.2.0] libcroco 0.6.13 --- .../l/libcroco/libcroco-0.6.13-GCC-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCC-10.2.0.eb new file mode 100644 index 0000000000..29daab547e --- /dev/null +++ b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCC-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libcroco' +version = '0.6.13' + +homepage = 'https://gitlab.gnome.org/Archive/libcroco' +description = """Libcroco is a standalone css2 parsing and manipulation library.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + + +source_urls = ['https://download.gnome.org/sources/libcroco/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['767ec234ae7aa684695b3a735548224888132e063f92db585759b422570621d4'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), + ('GLib', '2.66.1'), +] + +sanity_check_paths = { + 'files': ['bin/csslint-%(version_major_minor)s', 'lib/libcroco-%%(version_major_minor)s.%s' % SHLIB_EXT, + 'lib/libcroco-%(version_major_minor)s.a'], + 'dirs': ['include/libcroco-%(version_major_minor)s', 'share'] +} + +moduleclass = 'lib' From 895311a483d598ead3bb179aed1ac0443d9273de Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 26 Jan 2021 16:38:21 +0000 Subject: [PATCH 0242/2365] STAR version 2.7.6a and 2.7.7a for gcc-10.2.0 Easyconfig files created, see also PR#12033 --- .../s/STAR/STAR-2.7.6a-GCC-10.2.0.eb | 42 +++++++++++++++++++ .../s/STAR/STAR-2.7.7a-GCC-10.2.0.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb new file mode 100644 index 0000000000..b1ec0ee6ab --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.3a-GCC-8.3.0.eb +# uploaded by J. Sassmannshausen + + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.6a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9320797c604673debea0fe8f2e3762db364915cc59755de1a0d87c8018f97d51'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/STAR', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb new file mode 100644 index 0000000000..0b9214740f --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.3a-GCC-8.3.0.eb +# uploaded by J. Sassmannshausen + + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.7a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a4be87223816f2a34b98ae89470d89caff60ecc8e6d49b5ae6c917b3cadf31bb'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/STAR', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' From 638ba507434d116df2a7127cc05557e2cd4a5c5b Mon Sep 17 00:00:00 2001 From: easybuilder Date: Tue, 26 Jan 2021 18:40:07 +0100 Subject: [PATCH 0243/2365] adding easyconfigs: gnuplot-5.4.1-GCCcore-10.2.0.eb, libcerf-1.14-GCCcore-10.2.0.eb, libgd-2.3.0-GCCcore-10.2.0.eb, Lua-5.4.2-GCCcore-10.2.0.eb --- .../g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb | 56 +++++++++++++++++++ .../l/Lua/Lua-5.4.2-GCCcore-10.2.0.eb | 28 ++++++++++ .../l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb | 33 +++++++++++ .../l/libgd/libgd-2.3.0-GCCcore-10.2.0.eb | 35 ++++++++++++ 4 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.4.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..67018fae58 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb @@ -0,0 +1,56 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.4.1' + +homepage = 'https://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['6b690485567eaeb938c26936e5e0681cf70c856d273cc2c45fabf64d8bc6590e'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), + ('Autotools', '20200321'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('cairo', '1.16.0'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('libgd', '2.3.0'), + ('Pango', '1.47.0'), + ('libcerf', '1.14'), + ('X11', '20201008'), + ('Qt5', '5.14.2'), + ('Lua', '5.4.2'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2179e5f542 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.4.2' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['11570d97e9d7303c0a59567ed1ac7c648340cd0db10d5fd594c09223ef2f524f'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('libreadline', '8.0'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a7b2d2b205 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '1.14' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['065346b3360943c9961517f8c49ae13fe956835f6fc3b53e9d307e41feec3a34'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dc2c2c7aa9 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.0' + +homepage = 'https://libgd.github.io/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['32590e361a1ea6c93915d2448ab0041792c11bae7b18ee812514fe08b2c6a342'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('fontconfig', '2.13.92'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' From 4a9feb13b5aaa800af53787d3700c0fff6a9e2e0 Mon Sep 17 00:00:00 2001 From: Mormacill <31103546+Mormacill@users.noreply.github.com> Date: Tue, 26 Jan 2021 23:46:21 +0100 Subject: [PATCH 0244/2365] ssl not reachable, changed back to non-ssl --- easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb index 67018fae58..cd32053b88 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'gnuplot' version = '5.4.1' -homepage = 'https://gnuplot.sourceforge.net/' +homepage = 'http://gnuplot.sourceforge.net/' description = """Portable interactive, function plotting utility""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From fe7f254934f2f575d6003b7f3975cf2d186d5da0 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 27 Jan 2021 18:40:14 -0800 Subject: [PATCH 0245/2365] user foss toolchain --- .../i/igraph/igraph-0.8.5-foss-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb new file mode 100644 index 0000000000..4572d2cbde --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'igraph' +version = '0.8.5' + +homepage = 'http://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['2e5da63a2b8e9bb497893a17cf77c691df1739c298664f8adb1310a01218f95b'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), + ('binutils', '2.35'), +] + +dependencies = [ + ('GLPK', '4.65'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), +] + +preconfigopts = 'autoreconf -i && ' +# Remove hardcoded links to BLAS/LAPACK +preconfigopts += "sed -i 's/-lblas/$LIBBLAS/' configure && " +preconfigopts += "sed -i 's/-llapack/$LIBLAPACK/' configure && " + +configopts = "--with-external-blas --with-external-lapack --with-external-glpk" + +sanity_check_paths = { + 'files': ['lib/libigraph.%s' % SHLIB_EXT, 'lib/libigraph.la', 'lib/pkgconfig/igraph.pc'] + + ['include/igraph/%s' % x for x in ['igraph_version.h', 'igraph_types.h', 'igraph_constants.h']], + 'dirs': [], +} + +moduleclass = 'lib' From cc441700235c35f02e80c176b814787b25b933d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Jan 2021 14:30:37 +0100 Subject: [PATCH 0246/2365] ad fmri and AnalyzeFMRI extensions to R v4.0.3 --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 62902ac0d0..01414465fa 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2773,6 +2773,15 @@ exts_list = [ ('blavaan', '0.3-12', { 'checksums': ['9a44a21343e1dcced0c65c3117edc5ab2412513c258f1422fd39852e4d9cd706'], }), + ('metafor', '2.4-0', { + 'checksums': ['b64a678b762e91f1e0a6360b15e79fe19159b243c9f40ad9cc0be833bb4ba9ac'], + }), + ('fmri', '1.9.6', { + 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + }), + ('AnalyzeFMRI', '1.1-23', { + 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], + }), ] moduleclass = 'lang' From 74aa45b744bf70d31586591ac2e1ea67c7fdfaf7 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 29 Jan 2021 09:16:27 +0100 Subject: [PATCH 0247/2365] Fix OS deps Depend on InfiniBand packages rather than OpenSSL. --- .../easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb index 3518074350..e95e33215a 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -osdependencies = [OS_PKG_OPENSSL_DEV] +osdependencies = [OS_PKG_IBVERBS_DEV] # Disable deprecated "sockets" provider configopts = "--disable-sockets" From fa408a07093f2d9f4ab34cb41f39f0fe01b9a21c Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 29 Jan 2021 13:32:35 +0000 Subject: [PATCH 0248/2365] [esl] fdict update to 0.8.0 and foss 2020b --- .../f/fdict/fdict-0.8.0-GCC-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..d4ec2b5be5 --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ + A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. + """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +files_to_copy = [(['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), (['settings.bash'], 'bin')] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['bin'], +} + +moduleclass = 'data' From c83c6ae3c56167397cb85d835acad457f0d9d793 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 29 Jan 2021 13:11:38 +0000 Subject: [PATCH 0249/2365] [esl] update flook to version 0.8.1 and foss2020b --- .../f/flook/flook-0.8.1-GCC-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..6b9f747a77 --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """ + The fortran-Lua-hook library. + """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +checksums = ['beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'] + +dependencies = [('libreadline', '8.0')] + +buildopts = ' liball ' +parallel = 1 + +files_to_copy = [(['libflookall.a', 'libflook.a'], 'lib'), (['flook.mod'], 'include')] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' From 7a25219003d33a765f5bcd0933785db1e7f16cd6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 1 Feb 2021 12:54:05 +0200 Subject: [PATCH 0250/2365] adding easyconfigs: ESMF-8.0.1-foss-2020b.eb --- .../e/ESMF/ESMF-8.0.1-foss-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb new file mode 100644 index 0000000000..695ef6c559 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb @@ -0,0 +1,34 @@ +name = 'ESMF' +version = '8.0.1' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'optarch': False, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['%%(name)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '9172fb73f3fe95c8188d889ee72fdadb4f978b1d969e1d8e401e8d106def1d84', # ESMF_8_0_1.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +dependencies = [ + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('netCDF-C++4', '4.3.1'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' From 9c26f8dcf34bd14123fe745f40902d03ea11287f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 1 Feb 2021 13:20:37 +0200 Subject: [PATCH 0251/2365] adding easyconfigs: NCO-4.9.7-foss-2020b.eb, libdap-3.20.7-GCCcore-10.2.0.eb, ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb, libtirpc-1.3.1-GCCcore-10.2.0.eb --- .../ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb | 33 +++++++++++++++++ .../l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb | 36 ++++++++++++++++++ .../libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb | 28 ++++++++++++++ .../easyconfigs/n/NCO/NCO-4.9.7-foss-2020b.eb | 37 +++++++++++++++++++ 4 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-4.9.7-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb new file mode 100644 index 0000000000..7f7064ef51 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +builddependencies = [('binutils', '2.35')] +dependencies = [('Java', '11', '', True)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bea8e38be8 --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.20.7' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '7.72.0'), + ('libxml2', '2.9.10'), + ('libtirpc', '1.3.1'), + ('PCRE', '8.44'), + ('util-linux', '2.36'), +] + +configopts = 'TIRPC_LIBS="-ltirpc"' + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9752901816 --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.1' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['245895caf066bec5e3d4375942c8cb4366adad184c29c618d97f724ea309ee17'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.35') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.9.7-foss-2020b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.9.7-foss-2020b.eb new file mode 100644 index 0000000000..8c82c365bf --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.9.7-foss-2020b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '4.9.7' + +homepage = "https://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['eade5b79f3814b11ae3f52c34159567e76a73f05f0ab141eccaac68f0ca94aee'] + +builddependencies = [ + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.26'), + ('expat', '2.2.9'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.7'), + ('GSL', '2.6'), + ('netCDF', '4.7.4'), + ('ESMF', '8.0.1'), # ncremap needs ESMF_RegridWeightGen +] + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 5f91bc400bd0cc7e9a0512e70585fd730d162531 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 1 Feb 2021 17:11:02 +0200 Subject: [PATCH 0252/2365] adding easyconfigs: JasPer-2.0.24-GCCcore-10.2.0.eb --- .../j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a010c5cecb --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.24' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['d2d28e115968d38499163cf8086179503668ce0d71b90dd33855b3de96a1ca1d'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'vis' From 5a945f3152eaaad38248731b29fec3ecdd88f051 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 1 Feb 2021 17:13:51 +0100 Subject: [PATCH 0253/2365] add sanity check command to JasPer-2.0.24-GCCcore-10.2.0.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb index a010c5cecb..3f19f8a808 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb @@ -30,5 +30,5 @@ sanity_check_paths = { 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], 'dirs': ['include'], } - +sanity_check_commands = ['jasper --version'] moduleclass = 'vis' From a00d5c460fd617b12b27dade3a2272876fb91bad Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Mon, 1 Feb 2021 18:07:17 +0100 Subject: [PATCH 0254/2365] Update JasPer-2.0.24-GCCcore-10.2.0.eb add empty lines before/after sanity_check_commands --- easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb index 3f19f8a808..2398c04fb1 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb @@ -30,5 +30,7 @@ sanity_check_paths = { 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], 'dirs': ['include'], } + sanity_check_commands = ['jasper --version'] + moduleclass = 'vis' From 9c803619402f5b9175a4e791c9a09cd8960e8ff4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Feb 2021 20:52:29 +0100 Subject: [PATCH 0255/2365] adding easyconfigs: BLAST+-2.11.0-gompi-2020b.eb --- .../b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb new file mode 100644 index 0000000000..4a191ea283 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb @@ -0,0 +1,57 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.11.0' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE2', '10.35'), + ('Boost', '1.74.0'), + ('GMP', '6.2.0'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), +] + + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' From 070abdab865c36591a1c7186d4ea32ec44b40883 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 1 Feb 2021 20:54:14 +0100 Subject: [PATCH 0256/2365] enable optarch in ESMF-8.0.1-foss-2020b.eb --- easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb index 695ef6c559..159058ef8b 100644 --- a/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb @@ -6,7 +6,7 @@ description = """The Earth System Modeling Framework (ESMF) is a suite of softwa high-performance, multi-component Earth science modeling applications.""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True, 'optarch': False, 'cstd': 'c++11', 'pic': True} +toolchainopts = {'usempi': True, 'optarch': True, 'cstd': 'c++11', 'pic': True} source_urls = ['https://github.com/esmf-org/esmf/archive/'] sources = ['%%(name)s_%s.tar.gz' % '_'.join(version.split('.'))] From 4bfbcdd6df5001043247bedb47f2a5a4d2a0e492 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Feb 2021 21:05:42 +0100 Subject: [PATCH 0257/2365] {bio}[foss/2020b] OrthoFinder v2.5.2, FastME v2.1.6.1, MCL v14.137, ... w/ Python 3.8.6 --- .../f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb | 32 ++++++++++++++ .../m/MCL/MCL-14.137-GCCcore-10.2.0.eb | 41 +++++++++++++++++ .../OrthoFinder-2.5.2-foss-2020b.eb | 44 +++++++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..4d4476d110 --- /dev/null +++ b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FastME' +version = '2.1.6.1' + +homepage = 'http://www.atgc-montpellier.fr/fastme/' +description = "FastME: a comprehensive, accurate and fast distance-based phylogeny inference program." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://gite.lirmm.fr/atgc/FastME/-/archive/v%(version)s/'] +sources = ['FastME-v%(version)s.tar.gz'] +checksums = ['fae0609576873cb137ad4f63529b3ccba8f747b857c23c7870236aba440076ca'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +# install-sh, missing, config.sub, depcomp scripts included in source tarball are symlinks into /usr/share/... +local_scripts = "config.sub depcomp install-sh missing" +preconfigopts = "rm %s && " % local_scripts +preconfigopts += "for x in %s; do ln -s $EBROOTAUTOMAKE/share/automake-*/$x; done && " % local_scripts + +sanity_check_paths = { + 'files': ['bin/fastme'], + 'dirs': [] +} + +sanity_check_commands = ["fastme --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9aaca698b9 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '14.137' + +homepage = 'https://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +patches = ['%(name)s-%(version)s_fixperl.patch'] +checksums = [ + 'b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497', # mcl-14-137.tar.gz + '46988a287b2ee400a54fa485176d043b2a2d6589b6257cc6cf9c21689ea3842d', # MCL-14.137_fixperl.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Perl', '5.32.0'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -fcommon" && ' +configopts = '--enable-blast ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['clm', 'clmformat', 'clxdo', 'mcl', 'mclblastline', 'mclcm', 'mclpipeline', 'mcx', + 'mcxarray', 'mcxassemble', 'mcxdeblast', 'mcxdump', 'mcxi', 'mcxload', 'mcxmap', + 'mcxrand', 'mcxsubs']], + 'dirs': ['share'] +} + +sanity_check_commands = ["mcl --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb new file mode 100644 index 0000000000..ff9a4ad647 --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonPackage' + +name = 'OrthoFinder' +version = '2.5.2' + +homepage = 'https://github.com/davidemms/OrthoFinder' +description = "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'davidemms' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e85c1fb920179655bf1611b6c0cb17efdf1fd26caf07667ae7eefe05be3fbc35'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('BLAST+', '2.11.0'), + ('DIAMOND', '2.0.6'), + ('FastME', '2.1.6.1'), + ('MCL', '14.137'), + ('MMseqs2', '12-113e3'), +] + +download_dep_fail = True +use_pip = True + +# see https://github.com/davidemms/OrthoFinder/pull/500 +preinstallopts = 'sed -i "s/ExampleDataset/ExampleData/g" setup.py && ' + +options = {'modulename': 'scripts_of'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['convert_orthofinder_tree_ids', 'make_ultrametric', 'orthofinder', + 'primary_transcript']], + 'dirs': ['ExampleData', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["orthofinder --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 49d97d4cb0ec1067fa876c48ddb71addf50108a1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 2 Feb 2021 00:11:59 +0200 Subject: [PATCH 0258/2365] adding easyconfigs: ecCodes-2.18.0-gompi-2020a.eb, ecCodes-2.20.0-gompi-2020b.eb --- .../e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb new file mode 100644 index 0000000000..54cb9105d3 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.20.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': False, 'openmp': True} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['207a3d7966e75d85920569b55a19824673e8cd0b50db4c4dac2d3d52eacd7985'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('netCDF', '4.7.4'), + ('JasPer', '2.0.24'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +# Python bindings are now provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_OMP_THREADS=ON" + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 4333a6d9b157d9c3cb66936454980c110b4c35cf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 2 Feb 2021 00:24:22 +0200 Subject: [PATCH 0259/2365] adding easyconfigs: eccodes-python-1.0.0-foss-2020a-Python-3.8.2.eb, eccodes-python-1.1.0-foss-2020b.eb --- .../eccodes-python-1.1.0-foss-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb new file mode 100644 index 0000000000..30df322fee --- /dev/null +++ b/easybuild/easyconfigs/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'eccodes-python' +version = '1.1.0' + +homepage = 'https://github.com/ecmwf/eccodes-python' +description = "Python 3 interface to decode and encode GRIB and BUFR files via the ECMWF ecCodes library." + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'ecmwf' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['c1b4986f2e44a1e5e37d9a38cb41ac97a4bd994edad1f8fce0342522f58b947e'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ecCodes', '2.20.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'eccodes'} + +moduleclass = 'tools' From 6d47df5564176b9b2942eb9d96bca3e054be3202 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 2 Feb 2021 00:41:51 +0200 Subject: [PATCH 0260/2365] downgrade dependency on JasPer to v2.0.14 in ecCodes-2.20.0-gompi-2020b.eb --- easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb index 54cb9105d3..f0104f79df 100644 --- a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb @@ -19,7 +19,7 @@ builddependencies = [('CMake', '3.18.4')] dependencies = [ ('netCDF', '4.7.4'), - ('JasPer', '2.0.24'), + ('JasPer', '2.0.14'), ('libjpeg-turbo', '2.0.5'), ('libpng', '1.6.37'), ('zlib', '1.2.11'), From aea9d970e8865561d69c5e9b348e7e2900d0ee56 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Feb 2021 09:29:55 +0100 Subject: [PATCH 0261/2365] add missing Perl build dep for (recent) libcerf versions, required for 'pod2html' command --- easybuild/easyconfigs/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb index a7b2d2b205..863a2d13b9 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb @@ -21,6 +21,7 @@ checksums = ['065346b3360943c9961517f8c49ae13fe956835f6fc3b53e9d307e41feec3a34'] builddependencies = [ ('binutils', '2.35'), ('CMake', '3.18.4'), + ('Perl', '5.32.0'), # required for pod2html ] separate_build_dir = True From f9bb2b0470eca866ca0342c4b841cf222a4d4efb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Feb 2021 10:44:27 +0100 Subject: [PATCH 0262/2365] stick to PCRE as dep for BLAST+ --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb index 4a191ea283..27565c0c39 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb @@ -30,7 +30,7 @@ checksums = ['d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954'] dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.8'), - ('PCRE2', '10.35'), + ('PCRE', '8.44'), ('Boost', '1.74.0'), ('GMP', '6.2.0'), ('libpng', '1.6.37'), From 474dbe131c15b416aa9ccbfab69a156b00e6afd9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Feb 2021 10:55:15 +0100 Subject: [PATCH 0263/2365] use autoreconf rather than symlinking Automake scripts for FastME --- easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb index 4d4476d110..7b8029d378 100644 --- a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb @@ -17,10 +17,7 @@ builddependencies = [ ('Autotools', '20200321'), ] -# install-sh, missing, config.sub, depcomp scripts included in source tarball are symlinks into /usr/share/... -local_scripts = "config.sub depcomp install-sh missing" -preconfigopts = "rm %s && " % local_scripts -preconfigopts += "for x in %s; do ln -s $EBROOTAUTOMAKE/share/automake-*/$x; done && " % local_scripts +preconfigopts = "autoreconf -if && " sanity_check_paths = { 'files': ['bin/fastme'], From 3fe11c87ecfca131157521c51197a258361cb707 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 2 Feb 2021 12:16:24 +0200 Subject: [PATCH 0264/2365] Fix version prefixes --- .../ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb | 37 +++++++++++++++++ .../ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb | 40 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb create mode 100644 easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..1e10aa955c --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'ASAP3' +version = '3.12.2' +_aseversion = '3.21.1' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/asap/' +description = """ASAP is a calculator for doing large-scale classical molecular +dynamics within the Campos Atomic Simulation Environment (ASE).""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b6c03c790ba4c9f0d231659078c26ce8193fa21314bf2fe4adaa7899d5cd9dbe'] + +builddependencies = [ + ('pkgconfig', '1.5.1', '-python'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('ASE', _aseversion), + ('kim-api', '2.2.1'), +] + +use_pip = False +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..bb202034ac --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb @@ -0,0 +1,40 @@ +easyblock = "PythonPackage" + +name = 'ASAP3' +version = '3.12.2' +_aseversion = '3.21.1' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/asap/' +description = """ASAP is a calculator for doing large-scale classical molecular +dynamics within the Campos Atomic Simulation Environment (ASE).""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b6c03c790ba4c9f0d231659078c26ce8193fa21314bf2fe4adaa7899d5cd9dbe'] + +builddependencies = [ + ('pkgconfig', '1.5.1', '-python'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('ASE', _aseversion), + ('kim-api', '2.2.1'), +] + +use_pip = False +download_dep_fail = True + +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'phys' From 2a9cc4c5faaf891f64057996d453bfcb23953861 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 2 Feb 2021 13:40:15 +0200 Subject: [PATCH 0265/2365] use_pip can be set true from this version of Asap. --- .../easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb | 2 +- .../easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb index 1e10aa955c..163e1efb68 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb @@ -26,7 +26,7 @@ dependencies = [ ('kim-api', '2.2.1'), ] -use_pip = False +use_pip = True download_dep_fail = True sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb index bb202034ac..ecc1f16f73 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb @@ -26,7 +26,7 @@ dependencies = [ ('kim-api', '2.2.1'), ] -use_pip = False +use_pip = True download_dep_fail = True # required because we're building Python packages using Intel compilers on top of Python built with GCC From 978bb6810fe207ec659052afa806bca194a44146 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 2 Feb 2021 18:47:52 +0200 Subject: [PATCH 0266/2365] Enable sanity_pip_check. --- .../easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb | 1 + .../easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb index 163e1efb68..6601e03e9d 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb @@ -28,6 +28,7 @@ dependencies = [ use_pip = True download_dep_fail = True +sanity_pip_check = True sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb index ecc1f16f73..ad8a03e528 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb @@ -28,6 +28,7 @@ dependencies = [ use_pip = True download_dep_fail = True +sanity_pip_check = True # required because we're building Python packages using Intel compilers on top of Python built with GCC check_ldshared = True From bcd0731eea14e5d950af9bdd90741ae1adce7468 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 3 Feb 2021 22:55:10 +0000 Subject: [PATCH 0267/2365] adding easyconfigs: gobff-2020b.eb, BLIS-0.8.0-GCC-10.2.0.eb, HPL-2.3-gobff-2020b.eb, libFLAME-5.2.0-GCC-10.2.0.eb, make-4.3-GCC-10.2.0.eb, ScaLAPACK-2.1.0-gompi-2020b-bf.eb --- easybuild/easyconfigs/g/gobff/gobff-2020b.eb | 31 ++++++++++++++ .../easyconfigs/h/HPL/HPL-2.3-gobff-2020b.eb | 21 ++++++++++ .../ScaLAPACK-2.1.0-gompi-2020b-bf.eb | 41 +++++++++++++++++++ 3 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/g/gobff/gobff-2020b.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-gobff-2020b.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb diff --git a/easybuild/easyconfigs/g/gobff/gobff-2020b.eb b/easybuild/easyconfigs/g/gobff/gobff-2020b.eb new file mode 100644 index 0000000000..c3c1fc3e46 --- /dev/null +++ b/easybuild/easyconfigs/g/gobff/gobff-2020b.eb @@ -0,0 +1,31 @@ +easyblock = "Toolchain" + +name = 'gobff' +version = '2020b' + +homepage = '(none)' +description = 'GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPACK and FFTW.' + +toolchain = SYSTEM + +local_comp_name = 'GCC' +local_comp_version = '10.2.0' +local_comp = (local_comp_name, local_comp_version) +local_blisver = '0.8.0' +local_libflamever = '5.2.0' + +# toolchain used to build dependencies +local_comp_mpi_tc_name = 'gompi' +local_comp_mpi_tc = (local_comp_mpi_tc_name, version) + +# compiler toolchain dependencies +dependencies = [ + local_comp, + ('OpenMPI', '4.0.5', '', local_comp), # part of gompi toolchain + ('BLIS', local_blisver, '', local_comp), + ('libFLAME', local_libflamever, '', local_comp), + ('ScaLAPACK', '2.1.0', '-bf', local_comp_mpi_tc), + ('FFTW', '3.3.8', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-gobff-2020b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-gobff-2020b.eb new file mode 100644 index 0000000000..45ff15f21a --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-gobff-2020b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gobff', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb new file mode 100644 index 0000000000..70f985aba6 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb @@ -0,0 +1,41 @@ +name = 'ScaLAPACK' +version = '2.1.0' +versionsuffix = '-bf' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = ['61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('BLIS', '0.8.0'), + ('libFLAME', '5.2.0'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' +configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From 3d20eb69b65ca4b483186264ff64ab2faa39353b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 4 Feb 2021 02:59:00 +0200 Subject: [PATCH 0268/2365] enable openmp in ESMF-8.0.1-foss-2020b.eb --- easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb index 159058ef8b..8fc38d9f4e 100644 --- a/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-foss-2020b.eb @@ -6,7 +6,7 @@ description = """The Earth System Modeling Framework (ESMF) is a suite of softwa high-performance, multi-component Earth science modeling applications.""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True, 'optarch': True, 'cstd': 'c++11', 'pic': True} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} source_urls = ['https://github.com/esmf-org/esmf/archive/'] sources = ['%%(name)s_%s.tar.gz' % '_'.join(version.split('.'))] From 20c1eaa84afcf827957c0b47bbd95ed12d35d745 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 4 Feb 2021 09:31:09 +0000 Subject: [PATCH 0269/2365] Addind checksums for ScaLAPACK-2.1.0-gompi-2020b-bf.eb --- .../s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb index 70f985aba6..1a51184125 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] -checksums = ['61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6'] +checksums = [ + '61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6', # scalapack-2.1.0.tgz + 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch +] builddependencies = [ ('CMake', '3.18.4'), From ef0e1869ee90c477187564ce7dd477b4922ed67a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 5 Feb 2021 02:47:04 +0200 Subject: [PATCH 0270/2365] adding easyconfigs: BEEF-0.1.1-iccifort-2020.4.304.eb --- .../b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..818445eea0 --- /dev/null +++ b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'BEEF' +version = '0.1.1' + +homepage = 'svn://suncatls1.slac.stanford.edu/beef' +description = """BEEF is a library-based implementation of the Bayesian +Error Estimation Functional, suitable for linking against by Fortran- +or C-based DFT codes. A description of BEEF can be found at +http://dx.doi.org/10.1103/PhysRevB.85.235149.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://confluence.slac.stanford.edu/download/attachments/146704476/'] +sources = ['libbeef-%(version)s.tar.gz'] + +configopts = 'CC="$CC"' + +sanity_check_paths = { + 'files': ['bin/bee', 'lib/libbeef.a'], + 'dirs': [], +} + +moduleclass = 'chem' From 4409c4321b1181f311cba5687573d5b23b69cd24 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 6 Feb 2021 14:37:48 +0000 Subject: [PATCH 0271/2365] bypass two tests, as known failing --- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 0983bf4af1..8095ba5b21 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -246,8 +246,8 @@ patches = [ 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch', - 'PyTorch-1.7.1_fix-nan-compare.patch', 'PyTorch-1.7.1_complex32.patch', + 'PyTorch-1.7.1_bypass-nan-compare.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -299,8 +299,8 @@ checksums = [ '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', - 'b8f2d14ad8ea3e6809ab6f4c37f632c3d842f663ca0e4641589dc722a10f5411', # PyTorch-1.7.1_fix-nan-compare.patch '6028bff2be720cf70acad2129db60fd10872e02c9e460c72bb274228cf90b320', # PyTorch-1.7.1_complex32.patch + '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch ] excluded_tests = { @@ -313,7 +313,7 @@ excluded_tests = { ] } -runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' +runtest = 'cd test ' # && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' sanity_check_commands = ["python -c 'import caffe2.python'"] tests = ['PyTorch-check-cpp-extension.py'] From f1cb50de082a2668ad778c6f53610730a03294b7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 6 Feb 2021 14:53:42 +0000 Subject: [PATCH 0272/2365] remove debug change --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 8095ba5b21..39324bc2fe 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -313,7 +313,7 @@ excluded_tests = { ] } -runtest = 'cd test ' # && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' sanity_check_commands = ["python -c 'import caffe2.python'"] tests = ['PyTorch-check-cpp-extension.py'] From b9039401181972c30f90d7612d5c2379c00ce895 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 8 Feb 2021 08:53:30 +0100 Subject: [PATCH 0273/2365] adding easyconfigs: imbalanced-learn-0.7.0-foss-2020b.eb --- .../imbalanced-learn-0.7.0-foss-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb new file mode 100644 index 0000000000..ad59b47535 --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'imbalanced-learn' +version = '0.7.0' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['da59de0d1c0fa66f62054dd9a0a295a182563aa1abbb3bf9224a3678fcfe8fa4'] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-learn', '0.23.2'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'imblearn'} + +sanity_pip_check = True + +moduleclass = 'tools' From 00a7378b44ec7693ecadc573ed7b4d5875a88b1e Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 8 Feb 2021 11:31:01 +0200 Subject: [PATCH 0274/2365] adding easyconfigs: scikit-image-0.18.1-foss-2020b.eb, scikit-image-0.18.1-intel-2020b.eb, dask-2021.2.0-foss-2020b.eb, dask-2021.2.0-intel-2020b.eb, bokeh-2.2.3-foss-2020b.eb, bokeh-2.2.3-intel-2020b.eb --- .../b/bokeh/bokeh-2.2.3-foss-2020b.eb | 42 ++++++++++ .../b/bokeh/bokeh-2.2.3-intel-2020b.eb | 47 +++++++++++ .../d/dask/dask-2021.2.0-foss-2020b.eb | 74 ++++++++++++++++++ .../d/dask/dask-2021.2.0-intel-2020b.eb | 78 +++++++++++++++++++ .../scikit-image-0.18.1-foss-2020b.eb | 49 ++++++++++++ .../scikit-image-0.18.1-intel-2020b.eb | 57 ++++++++++++++ 6 files changed, 347 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb new file mode 100644 index 0000000000..d51f0e5893 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.2.3' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('Pillow', '8.0.1'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('typing-extensions', '3.7.4.3', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'], + }), + (name, version, { + 'checksums': ['c4a3f97afe5f525019dd58ee8c4e3d43f53fe1b1ac264ccaae9b02c07b2abc17'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb new file mode 100644 index 0000000000..2d673ba427 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.2.3' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('Pillow', '8.0.1'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +# required because we're building Python packages (tornado) +# using Intel compilers on top of Python built with GCC. +check_ldshared = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('typing-extensions', '3.7.4.3', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'], + }), + (name, version, { + 'checksums': ['c4a3f97afe5f525019dd58ee8c4e3d43f53fe1b1ac264ccaae9b02c07b2abc17'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb new file mode 100644 index 0000000000..68e934e86d --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb @@ -0,0 +1,74 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2021.2.0' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('SciPy-bundle', '2020.11'), + ('bokeh', '2.2.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('fsspec', '0.8.5', { + 'checksums': ['890c6ce9325030f03bd2eae81389ddcbcee53bdd475334ca064595e1e45f92a6'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('locket', '0.2.1', { + 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + }), + ('partd', '1.1.0', { + 'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.0.0', { + 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + (name, version, { + 'checksums': ['e7054b8d685205e95c789900ae87d6174550180cbe38a3cb1142e10c73004c22'], + }), + ('distributed', version, { + 'checksums': ['9150b99b2c28e7c238c486b117154abd545c6990080d084aaff02f803f86f75e'], + }), + ('dask-mpi', '2.21.0', { + 'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'], + }), + ('docrep', '0.3.1', { + 'checksums': ['ef6e7433716c0d2c59889aae8bff800b48e82d7e759dfd934b93100dc7bccaa1'], + }), + ('dask-jobqueue', '0.7.2', { + 'checksums': ['1767f4146b2663d9d2eaef62b882a86e1df0bccdb8ae68ae3e5e546aa6796d35'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb new file mode 100644 index 0000000000..50775be1d6 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2021.2.0' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('SciPy-bundle', '2020.11'), + ('bokeh', '2.2.3'), +] + +use_pip = True +sanity_pip_check = True + +# required because we're building Python packages (msgpack) +# using Intel compilers on top of Python built with GCC. +check_ldshared = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('fsspec', '0.8.5', { + 'checksums': ['890c6ce9325030f03bd2eae81389ddcbcee53bdd475334ca064595e1e45f92a6'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('locket', '0.2.1', { + 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + }), + ('partd', '1.1.0', { + 'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.0.0', { + 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + (name, version, { + 'checksums': ['e7054b8d685205e95c789900ae87d6174550180cbe38a3cb1142e10c73004c22'], + }), + ('distributed', version, { + 'checksums': ['9150b99b2c28e7c238c486b117154abd545c6990080d084aaff02f803f86f75e'], + }), + ('dask-mpi', '2.21.0', { + 'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'], + }), + ('docrep', '0.3.1', { + 'checksums': ['ef6e7433716c0d2c59889aae8bff800b48e82d7e759dfd934b93100dc7bccaa1'], + }), + ('dask-jobqueue', '0.7.2', { + 'checksums': ['1767f4146b2663d9d2eaef62b882a86e1df0bccdb8ae68ae3e5e546aa6796d35'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb new file mode 100644 index 0000000000..f2c19ac26b --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.18.1' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('Pillow', '8.0.1'), + ('dask', '2021.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('networkx', '2.5', { + 'checksums': ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'], + }), + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imageio', '2.9.0', { + 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.3.0', { + 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], + }), + ('tifffile', '2021.2.1', { + 'checksums': ['6793787742e18cf2116bc65e17c51cd9c14cd27a4a6033a8ddd5bf801a637615'], + }), + (name, version, { + 'modulename': 'skimage', + 'checksums': ['fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb new file mode 100644 index 0000000000..1e623b7aae --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.18.1' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('Pillow', '8.0.1'), + ('dask', '2021.2.0'), +] + +use_pip = True +sanity_pip_check = True + +# required because we're building Python packages +# using Intel compilers on top of Python built with GCC. +check_ldshared = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('networkx', '2.5', { + 'checksums': ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'], + }), + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imageio', '2.9.0', { + 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.3.0', { + 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], + }), + ('tifffile', '2021.2.1', { + 'checksums': ['6793787742e18cf2116bc65e17c51cd9c14cd27a4a6033a8ddd5bf801a637615'], + }), + (name, version, { + 'modulename': 'skimage', + 'checksums': ['fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171'], + # avoid building with OpenMP support, since that triggers a nasty internal compiler error with + # icpc 19.0.5.281 and 19.1.3.304: Segmentation violation + 'preinstallopts': "sed -i 's/-fopenmp//g' setup.py && " + + }), +] + +moduleclass = 'vis' From 552c5983f64c6ad32ca7555fc77ae348359375aa Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 8 Feb 2021 11:45:53 +0200 Subject: [PATCH 0275/2365] Remove duplicate parameter. --- easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb | 2 +- easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb index d51f0e5893..f83db1d939 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb @@ -16,6 +16,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} @@ -37,6 +38,5 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_pip_check = True moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb index 2d673ba427..aa1444c33a 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb @@ -42,6 +42,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_pip_check = True - moduleclass = 'tools' From 10d55942e25353e3d6c652d51a770852685cca92 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 8 Feb 2021 13:23:45 +0200 Subject: [PATCH 0276/2365] fix checksums of NCO-4.9.7-foss-2020b.eb --- easybuild/easyconfigs/n/NCO/NCO-4.9.7-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.9.7-foss-2020b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.9.7-foss-2020b.eb index 8c82c365bf..cc1f44d3a1 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.9.7-foss-2020b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.9.7-foss-2020b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/nco/nco/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['eade5b79f3814b11ae3f52c34159567e76a73f05f0ab141eccaac68f0ca94aee'] +checksums = ['934e247d9592f3e6087ea8985507077873559b52679b9c9a1ecae40668a352dc'] builddependencies = [ ('Bison', '3.7.1'), From 58b6d41943b4c2997af67b8a6df89df6ca86772c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 8 Feb 2021 13:43:25 +0100 Subject: [PATCH 0277/2365] fix checksums of libdap-3.20.7-GCCcore-10.2.0.eb --- easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb index bea8e38be8..88a8de8e31 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://www.opendap.org/pub/source/'] sources = [SOURCE_TAR_GZ] +checksums = ['6856813d0b29e70a36e8a53e9cf20ad680d21d615952263e9c6586704539e78c'] builddependencies = [ ('binutils', '2.35'), From 876fbefb09e38a375da98e4f1fd5d9133187d72a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 9 Feb 2021 16:28:04 +0100 Subject: [PATCH 0278/2365] Drop typing-extensions to GCCcore and fix module class --- .../typing-extensions-3.7.4.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb index fc7c6a67ec..87343f80b2 100644 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb @@ -20,4 +20,4 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -moduleclass = 'bio' +moduleclass = 'devel' From 0376420586f39a110106fa1eea345af3ba47458d Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 9 Feb 2021 15:37:22 +0000 Subject: [PATCH 0279/2365] Jansson bumped up to version 2.13.1 with gcc-10.2.0 --- .../j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..bb0f51fe42 --- /dev/null +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb @@ -0,0 +1,34 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'Jansson' +version = "2.13.1" + +homepage = 'http://www.digip.org/jansson/' +description = """Jansson is a C library for encoding, decoding and manipulating JSON data. + Its main features and design principles are: + * Simple and intuitive API and data model + * Comprehensive documentation + * No dependencies on other libraries + * Full Unicode support (UTF-8) + * Extensive test suite""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/akheron/jansson/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f22901582138e3203959c9257cf83eba9929ac41d7be4a42557213a22ebcc7a0'] + +preconfigopts = 'autoreconf -i && ' + +sanity_check_paths = { + 'files': ['lib/libjansson.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +runtest = 'check' + +moduleclass = 'devel' From 1d4ea49f019d2dddb07ec4540690575efd7c679b Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 9 Feb 2021 15:49:36 +0000 Subject: [PATCH 0280/2365] libzip bumped up to version 1.7.3 with gcc-10.2.0 --- .../l/libzip/libzip-1.7.3-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/libzip/libzip-1.7.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.7.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.7.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fed83245aa --- /dev/null +++ b/easybuild/easyconfigs/l/libzip/libzip-1.7.3-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'libzip' +version = '1.7.3' + +homepage = 'https://libzip.org/' +description = "libzip is a C library for reading, creating, and modifying zip archives." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/nih-at/libzip/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c0a086901dfc8bda0fb8695f2d3c8050ed140b7899536b9348bcc72b47b2f307'] # libzip-1.7.3.tar.gz + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': [ + 'bin/zipcmp', + 'bin/zipmerge', + 'bin/ziptool', + 'lib64/libzip.%s' % SHLIB_EXT, + ], + 'dirs': ['include', 'lib/pkgconfig'], +} + +moduleclass = 'lib' From ee3094c21281933c81aa2208849afd7983598e48 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 9 Feb 2021 15:54:21 +0000 Subject: [PATCH 0281/2365] http to https change --- easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb index bb0f51fe42..7a1da55ff1 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb @@ -7,7 +7,7 @@ easyblock = 'ConfigureMake' name = 'Jansson' version = "2.13.1" -homepage = 'http://www.digip.org/jansson/' +homepage = 'https://www.digip.org/jansson/' description = """Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model From ba9bda5ca03edad948dcfdcdac594bd3b33d03f9 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 9 Feb 2021 21:37:49 -0800 Subject: [PATCH 0282/2365] Update HTSlib --- .../h/HTSlib/HTSlib-1.11-GCC-10.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.11-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.11-GCC-10.2.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.11-GCC-10.2.0.eb new file mode 100644 index 0000000000..341fd40e5f --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.11-GCC-10.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.11' + +homepage = "https://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['cffadd9baa6fce27b8fe0b01a462b489f06a5433dfe92121f667f40f632538d7'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.72.0'), +] + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 52e1638c76b5de173f59ef53e1e9aa079b184ee5 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 10 Feb 2021 10:16:14 +0100 Subject: [PATCH 0283/2365] adding easyconfigs: SWAT+-60.5.1-iccifort-2020.4.304.eb --- .../SWAT+/SWAT+-60.5.1-iccifort-2020.4.304.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWAT+/SWAT+-60.5.1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/s/SWAT+/SWAT+-60.5.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/SWAT+/SWAT+-60.5.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..a58153e87b --- /dev/null +++ b/easybuild/easyconfigs/s/SWAT+/SWAT+-60.5.1-iccifort-2020.4.304.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'SWAT+' +version = '60.5.1' +local_commit = 'e2aa3c7' + +homepage = 'https://swatplus.gitbook.io' +description = """ +The Soil & Water Assessment Tool (SWAT) is a small watershed to river +basin-scale model used to simulate the quality and quantity of surface and +ground water and predict the environmental impact of land use, land management +practices, and climate change. In order to face present and future challenges +in water resources modeling SWAT code has undergone major modifications over +the past few years, resulting in SWAT+, a completely revised version of the +model. SWAT+ provides a more flexible spatial representation of interactions +and processes within a watershed.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://bitbucket.org/blacklandgrasslandmodels/modular_swatplus/get/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}] +patches = [ + ('SWAT+_add-cmakelists.patch', 0), + 'SWAT+-60.4.1_fix-implicits.patch', +] +checksums = [ + '6574b8145351117d82c0e9206d9958d09a93cd2271b1ebf89e8ce0d82908fe6c', # SWAT+-60.5.1.tar.gz + '777be052b815f48b4c448636bb9e4e7bd8a0bc6e4691ddcd0363fc7116d632ae', # SWAT+_add-cmakelists.patch + 'b424232b482b5be96462e036835672696e04e41ea03cca883cd10b5c0aba3b5f', # SWAT+-60.4.1_fix-implicits.patch +] + +builddependencies = [('CMake', '3.18.4')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/swatplus'], + 'dirs': ['share/%s' % d for d in ['data', 'database_files', 'documentation', 'example_data_descriptions', + 'modular_database_table', 'revision_notes']], +} + +moduleclass = 'geo' From ff3faec77f00098245a1fc0f00341e0b871e8deb Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 11 Feb 2021 22:18:32 -0800 Subject: [PATCH 0284/2365] {data}[GCCcore/10.2.0] PostgreSQL 13.2 --- .../PostgreSQL-13.2-GCCcore-10.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ba342dc037 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '13.2' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3386a40736332aceb055c7c9012ecc665188536d874d967fcc5a33e7992f8080'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('libreadline', '8.0'), + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' From 64e8c5370c8fa96824180017db4b9f5b4eeb89aa Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 12 Feb 2021 12:46:42 +0100 Subject: [PATCH 0285/2365] adding easyconfigs: Bazel-3.7.2-GCCcore-10.2.0.eb, flatbuffers-1.12.0-GCCcore-10.2.0.eb, flatbuffers-python-1.12-GCCcore-10.2.0.eb and patches: flatbuffers-1.12.0_replace-usage-of-memset.patch, flatbuffers-1.12.0_silence-str-op-false-positive.patch --- .../b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb | 38 +++++++++++++ .../flatbuffers-python-1.12-GCCcore-10.2.0.eb | 27 +++++++++ .../flatbuffers-1.12.0-GCCcore-10.2.0.eb | 57 +++++++++++++++++++ 3 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6b259a49b4 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +name = 'Bazel' +version = '3.7.2' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = [ + '%(name)s-3.4.1-fix-grpc-protoc.patch', + 'Bazel-3.7.1_fix-protobuf-env.patch', +] +checksums = [ + 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', # bazel-3.7.2-dist.zip + 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', # Bazel-3.4.1-fix-grpc-protoc.patch + '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', # Bazel-3.7.1_fix-protobuf-env.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), + ('Zip', '3.0'), +] +dependencies = [('Java', '11', '', True)] + +runtest = True +testopts = ' '.join([ + '--', + '//examples/cpp:hello-success_test', + '//examples/py/...', + '//examples/py_native:test', + '//examples/shell/...', +]) + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7d9f73d559 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'flatbuffers-python' +version = '1.12' + +homepage = 'https://github.com/google/flatbuffers/' +description = """Python Flatbuffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers'] +sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['63bb9a722d5e373701913e226135b28a6f6ac200d5cc7b4d919fa38d73b44610'] + +dependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3eac90f1d2 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb @@ -0,0 +1,57 @@ +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '1.12.0' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'flatbuffers-1.12.0_replace-usage-of-memset.patch', + 'flatbuffers-1.12.0_silence-str-op-false-positive.patch', +] +checksums = [ + '62f2223fb9181d1d6338451375628975775f7522185266cd5296571ac152bc45', + # flatbuffers-1.12.0_replace-usage-of-memset.patch + '094a98b5a7debbc2c60c2b235942c79e505ec76f9281f87c95d15e9ad8a97c52', + # flatbuffers-1.12.0_silence-str-op-false-positive.patch + '4a9a18abc776407f3f97e02c40f349cfb24fe7ddb41df952271d894777a31c88', +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Ninja', '1.10.1'), + ('Python', '3.8.6'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +# exts_defaultclass = 'PythonPackage' +# +# exts_list = [ +# (name, version, { +# 'source_urls': [PYPI_SOURCE], +# 'sources': { +# 'filename': '%(name)s-python-%(version)s.tar.gz', +# 'download_filename': '%(name)s-%(version_major_minor)s.tar.gz' +# }, +# 'checksums': ['63bb9a722d5e373701913e226135b28a6f6ac200d5cc7b4d919fa38d73b44610'], +# 'download_dep_fail': True, +# 'use_pip': True, +# 'sanity_pip_check': False, # Doesn't work yet when Python is only a build dep +# 'preinstallopts': 'VERSION=%(version)s ', +# }), +# ] + +moduleclass = 'devel' From 735fc26c195f5a5f93fac86e3dcb6dc466045a94 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 12 Feb 2021 16:05:01 +0000 Subject: [PATCH 0286/2365] adding easyconfigs: R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb, ncdf4-1.17-foss-2020b-R-4.0.3.eb --- .../n/ncdf4/ncdf4-1.17-foss-2020b-R-4.0.3.eb | 29 + ...le-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 967 ++++++++++++++++++ 2 files changed, 996 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2020b-R-4.0.3.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..01ddd2ceed --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2020b-R-4.0.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.17' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/%(name)s' +description = "ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6'] + +dependencies = [ + ('R', '4.0.3'), + ('netCDF', '4.7.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..e6438f280f --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -0,0 +1,967 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.12' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('R', '4.0.3'), + ('Boost', '1.74.0'), # for mzR + ('GSL', '2.6'), # for flowClust + ('HDF5', '1.10.7'), # for rhdf5 + # ('MariaDB-connector-c', '3.1.7'), # for RMySQL + ('ncdf4', '1.17', versionsuffix), # for mzR +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.12/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.12/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.12/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on 12th February 2021 +exts_list = [ + ('BiocGenerics', '0.36.0', { + 'checksums': ['384197246060ff43032ccd3666b5f4419dbdd0cf0bc93f76b2c089ffac7a37f9'], + }), + ('Biobase', '2.50.0', { + 'checksums': ['a441d8442c6734b6ac7585cd4d040b69eb89282a650083421c95724f1d616f86'], + }), + ('S4Vectors', '0.28.1', { + 'checksums': ['30839d2f118c91cf3638e15dfe5ef154fde90d79d6c0afe83b35e6ee34250e3a'], + }), + ('IRanges', '2.24.1', { + 'checksums': ['a2704c1600ff0d15e587ac6389f440e6f5cbc99c40de02ce7fa36d819421bd06'], + }), + ('GenomeInfoDbData', '1.2.4', { + 'checksums': ['9a9ecee1d03b7a859bd00640c952862781398a1f06bd63667c1cb9c746172972'], + }), + ('GenomeInfoDb', '1.26.2', { + 'checksums': ['fb38a15c6ed0cf3daef6b7f85ed7f9cd84a682e8182c528d83b2ab9a08fb5124'], + }), + ('AnnotationDbi', '1.52.0', { + 'checksums': ['993efd2ffca433085d243e28d8f1dde577459cd07a0b2d82cfc89b6e077c1d7f'], + }), + ('zlibbioc', '1.36.0', { + 'checksums': ['afc369ac424b010153201b4da910a7573e283b65ac5bd852a8db7ea0756b6654'], + }), + ('XVector', '0.30.0', { + 'checksums': ['989aeac1929409ec78964f85efed086015fcf83fa394faf859d238f2669414df'], + }), + ('Biostrings', '2.58.0', { + 'checksums': ['0577271fccd6996202bd724455c882231eab7c9448f40ce20bd9c13a8e8678e5'], + }), + ('GenomicRanges', '1.42.0', { + 'checksums': ['9108d8842b7b2bff1a99cc8fd9582534c9521eec1d6245612f43b66b5ef19748'], + }), + ('BiocParallel', '1.24.1', { + 'checksums': ['55c7f472ab94c614214043b648a438760a1c21ae89dc9984ccec2956378b3ec7'], + }), + ('Rhtslib', '1.22.0', { + 'checksums': ['44795c065c4aa74107786f200e7d156bbe90d56eee4ed9d10146b56ba5788aa3'], + }), + ('Rsamtools', '2.6.0', { + 'checksums': ['a4144f71022410410ed57b4f4f711c1b48651beb87590c92e786d1c7e77b1710'], + }), + ('MatrixGenerics', '1.2.1', { + 'checksums': ['2bcffc10cbc49f647f61dfd4fd70022b3dd6140cb637c91e1ac06c36c6076e98'], + }), + ('DelayedArray', '0.16.1', { + 'checksums': ['6dd0a32d5edce34b6797127064c42c3410725524ca5cb9176c67070561fee5b4'], + }), + ('SummarizedExperiment', '1.20.0', { + 'checksums': ['fa864028b2231d7aa1027be71407981f69373613d3b83ae9337f5bcd2a69a613'], + }), + ('GenomicAlignments', '1.26.0', { + 'checksums': ['794180a9b935cd4c01c61c1cc7232d9767daeeffa5a4ae4857da6aa34dbf25e1'], + }), + ('ShortRead', '1.48.0', { + 'checksums': ['69badfa1ca5c075ff29adda33d6bd71a2b62433640dcea45ae15180347439570'], + }), + ('graph', '1.68.0', { + 'checksums': ['c4dfe47143152f5ce758c6db1e59a3154d49c90076fcf476d6236eadae902773'], + }), + ('affyio', '1.60.0', { + 'checksums': ['70206db67322b998d86c914372a4a8aae7ca5e7349150c658fafbf9d7bfeb693'], + }), + ('preprocessCore', '1.52.1', { + 'installopts': "--configure-args='--disable-threading'", + 'checksums': ['94da71e954204c6edca9899452488c0a9c5c5771c24faad8de9f29a62fcde7c3'], + }), + ('BiocManager', '1.30.10', { + 'checksums': ['f3b7a412b42be0ab8df5fcd9bf981876ba9e5c55bc5faaca7af7ede3b6d0c90e'], + }), + ('affy', '1.68.0', { + 'checksums': ['062cc13461ad66fe46e913a989ce6ce2efdf7c9914762b6d9862fec510299f7b'], + }), + ('GO.db', '3.12.1', { + 'checksums': ['e0316959d3d32096f9432c897413dff74fce53e15ead7917a7724467d971dab9'], + }), + ('limma', '3.46.0', { + 'checksums': ['dff5651fdc8aef4af640290244f73b1f1e6c5b99679fede44a37ce804722bbf7'], + }), + ('RBGL', '1.66.0', { + 'checksums': ['5fe38c3792ffdb46839392e7794eee0c5bfbacd12b0711ff956fac1edff7db04'], + }), + ('org.Hs.eg.db', '3.12.0', { + 'checksums': ['48a1ab5347ec7a8602c555d9aba233102b61ffa2765826e5c8890ff0003249bb'], + }), + ('AnnotationForge', '1.32.0', { + 'checksums': ['a75fe48bf9ab3beed407e447752f6729eb8b9fe9b9a55f294fe0f33d1b106878'], + }), + ('KEGG.db', '3.2.4', { + 'checksums': ['2e60d1b664cbd1491cc00ed13a22904706c5a4651150f70daca04bf3ba9ead88'], + }), + ('annaffy', '1.62.0', { + 'checksums': ['91c49ac634e11c97ac58fbca6de6e27aa40ce9013459d3e76817254cc7c8f4eb'], + }), + ('gcrma', '2.62.0', { + 'checksums': ['00b8641da36645229e540c2f790c8bdf539e512ae2c7904f4fcc6cc6e3083dec'], + }), + ('oligoClasses', '1.52.0', { + 'checksums': ['fea100b75646d7e5b1deab3d49ed4f0a64e87a3676a55a4bab4555fb1880e6a6'], + }), + ('edgeR', '3.32.1', { + 'checksums': ['972d1444d4ee82a106dfd72a1506b61c7051dcef01365f17f0da28e3306251bd'], + }), + ('PFAM.db', '3.12.0', { + 'checksums': ['ec42d067522baf2d7d3ca78d4f8cc0dac08a4b98f1d890f52424e5d5b16f2fe9'], + }), + ('perm', '1.0-0.0', { + 'checksums': ['53c6ee598d5b7b04388915dddc5adf1f8f313b73c3bceb3708db7a632857e500'], + }), + ('baySeq', '2.24.0', { + 'checksums': ['25084dc5cfa60abba1b1ce366f4e394e9ba46f4cf26cf186779574c0a98d2691'], + }), + ('qvalue', '2.22.0', { + 'checksums': ['251223ab4fa1af6ebc2ca5bec0dfdf19b5f3e36958055c2bb962824f4de07c75'], + }), + ('impute', '1.64.0', { + 'checksums': ['aaefafb4c3eb17e54920936f47a32ccc8761e992a9e52f79af368598b856d2de'], + }), + ('shinyFiles', '0.9.0', { + 'checksums': ['51ad2aad61bcae22fb2c48a79d02bf6f86e36ffc49a3b64e26a76d133a955167'], + }), + ('samr', '3.0', { + 'checksums': ['25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506'], + }), + ('DEGseq', '1.44.0', { + 'checksums': ['163e7a785443047d847ad46eb9fc54adaadaa26a47b7af802c11e275c6e742f2'], + }), + ('hgu133plus2.db', '3.2.3', { + 'checksums': ['a56b247b69a6b8c81d23410e9def44f8d3e7c133aedf09fb1561798dca2c0549'], + }), + ('illuminaio', '0.32.0', { + 'checksums': ['5e39146fa22da82a7bb16364bd220739544ebb3a7750b5b8c747cdc2b11315fb'], + }), + ('rtracklayer', '1.50.0', { + 'checksums': ['a8df02d9508b112c8553d6862e8466ffd1fd5783e5ffcc036adfcbdf2eacf18b'], + }), + ('BiocFileCache', '1.14.0', { + 'checksums': ['e197e8f686955b3c80410d5f9be4b73e62b9a5006b6f70555f66983180120364'], + }), + ('biomaRt', '2.46.3', { + 'checksums': ['07574ef0703d7719601c2e9117b70382462a422dcf144606f40fec3b3d68953f'], + }), + ('GenomicFeatures', '1.42.1', { + 'checksums': ['1ac49eb97330fb9eaeee7ad194d4ecb376e87829b08d32bc09fc1ace606abe9d'], + }), + ('bumphunter', '1.32.0', { + 'checksums': ['735620c9273c203b46c5e8b0aa7133578bbda23e9efa7767d9cd77378140d441'], + }), + ('multtest', '2.46.0', { + 'checksums': ['78943ebbdee208f9ce7d49b934ea0f96f245d8b9e3d46958ee76401b50eb711b'], + }), + ('scrime', '1.3.5', { + 'checksums': ['5d97d3e57d8eb30709340fe572746029fd139456d7a955421c4e3aa75d825578'], + }), + ('siggenes', '1.64.0', { + 'checksums': ['fceceb9f1732297f8ce78cbb0ee01966b912e9adc38f5146d806747c4d149123'], + }), + ('DynDoc', '1.68.0', { + 'checksums': ['3cb09be25ebfb28796ab66926bdbead8cf301b719b36502c12f6fb1897318c68'], + }), + ('genoset', '1.45.1', { + 'checksums': ['ead640cba1366ca8af2cc4e104243332aeb610d96fdd7c7fb473aa7d5bc93106'], + }), + ('NOISeq', '2.34.0', { + 'checksums': ['0e75002e4e96247c715ca11a4d6c1a5e43e918a92ad255c898ff5136d5561423'], + }), + ('Rgraphviz', '2.34.0', { + 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], + 'checksums': [ + 'e728b8a67d14ca1ac5ef0cb05a7bff43c9ebf9c84608f5cfee658ba9a6ce16cc', # Rgraphviz_2.34.0.tar.gz + # Rgraphviz-2.28.0_fno-tree-vectorize.patch + '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9', + ], + }), + ('RNASeqPower', '1.30.0', { + 'checksums': ['c7183f17ea0ccd9ee934d7cffe1b020d20345e52a432ff6acc55394ffc469f5b'], + }), + ('annotate', '1.68.0', { + 'checksums': ['d4fc1309f27b560a7438e2b8ec60f99aad09a79bad2b625115a398d2432a14e7'], + }), + ('GSEABase', '1.52.1', { + 'checksums': ['d1f48f887b09593a1d824d1326ef19a2e00cafd0429e536510c9b82a67805c35'], + }), + ('genefilter', '1.72.1', { + 'checksums': ['3693641d6eca6c6c3cf54ac17e30c80884a5b753bb6c88cf491ade2d2d1ed0b0'], + }), + ('Category', '2.56.0', { + 'checksums': ['79726414a27c9ef9bb6dd768ca930effd14bd48baa49955414102816ede5e754'], + }), + ('GOstats', '2.56.0', { + 'checksums': ['d2ccce0296bc1966ecaf0a31e3bba72d99dc3197cece2ebfc982bab41db808a3'], + }), + ('BSgenome', '1.58.0', { + 'checksums': ['9893e5fe00181c6234fbffce3e9d86647a6ed9ba9a3f0cf7abfa946c72af7bbd'], + }), + ('VariantAnnotation', '1.36.0', { + 'checksums': ['bcc63970244de88da06a57d87c5a2543cc0281aa5fdb8084a4cfd102b6a180ea'], + }), + ('interactiveDisplayBase', '1.28.0', { + 'checksums': ['016c6a263f7aca6e2807ebac70c2b6e00f491400bdd1d8c8905d6bd227142d22'], + }), + ('BiocVersion', '3.12.0', { + 'checksums': ['330f6ba08f6d1e2972918eca5e239ff02901ab9f80c355086e737de23cd749b2'], + }), + ('AnnotationHub', '2.22.0', { 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['605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f'], + }), + ('methylumi', '2.36.0', { + 'checksums': ['d08aa9ec9ec5a978badeddf8f7c5d47c737ed51d63da1f9d332ec7df9d538503'], + }), + ('lumi', '2.42.0', { + 'checksums': ['63e3679d834c998a2035a4f3925a50ba8503783d14e5bb3d446f54b8d1555aa5'], + }), + ('widgetTools', '1.68.0', { + 'checksums': ['5cb8cda157195ff4a08a8d432f6bd4562dede4ef959d52b4a6a95dadeb054e9c'], + }), + ('tkWidgets', '1.68.0', { + 'checksums': ['d1f32ba1d51985269fc6b43b0b22d9488575227c1335661e1a11b482fecf0fef'], + }), + ('Mfuzz', '2.50.0', { + 'checksums': ['9fbe9587fbf760211d95a18e9fa7527ff4b2f83b5eda6a39d9096497cc1ace2e'], + }), + ('admisc', '0.11', { + 'checksums': ['d0f7a50a132ab4b2406d68c5575a0a8b8e33a3a5275b7bdfbc895761729fa2a2'], + }), + ('venn', '1.9', { + 'checksums': ['19c96cd7daad83267c666106ceea742dbc1eed917922ce61b2088b9198e45b34'], + }), + ('maSigPro', '1.62.0', { + 'checksums': ['d0024b16600f9de5b6abbf1a3a065b1fa9b8c3e26226647d7115bc15a1b8f4ec'], + }), + ('SPIA', '2.42.0', { + 'checksums': ['b209a37a653540ad75fba75f4226e9fd3a5fa4a09dbe00c243e32133a207e832'], + }), + ('Gviz', '1.34.0', { + 'checksums': ['026e720178eaa20410a780130d1218ba8b18a4a48240554aceb685b40cf9eb6c'], + }), + ('cummeRbund', '2.32.0', { + 'checksums': ['f2b55b18b2d73920e1998222386095cd0b84458a4019aa8c61215e058a5ff9f4'], + }), + ('GenomicFiles', '1.26.0', { + 'checksums': ['5f624f2d6930d33482ebab9f2ab7e5a6f633d3ef8e25b879e2ecfc1b2a70962b'], + }), + ('derfinderHelper', '1.24.1', { + 'checksums': ['8b5d3a23f9f403c50b212996d3b525cfa6086d3f74c99cfaae92840a72ded5c8'], + }), + ('derfinder', '1.24.2', { + 'checksums': ['f2ca20d636e68c821c5a5a615f80ff18672ed11f1a37a9e2efa4688e4d395b09'], + }), + ('polyester', '1.26.0', { + 'checksums': ['93432ffb8d2dea79ffc183378a90b4ceeaf318e5a4e18c8eb78e66c6b71e01bd'], + }), + ('Rsubread', '2.4.2', { + 'checksums': ['2a677970e9249f62bf9c0326db29c74dfbb993c6b8e5d160213d99250bcf9ff1'], + }), + ('pcaMethods', '1.82.0', { + 'checksums': ['c0bd8bfe3ee6ed7bdeb7b7cb166d6ff2bfb273c2314430282a181a3fe526ab13'], + }), + ('marray', '1.68.0', { + 'checksums': ['5e65b295358f7fada0d4ed4238e2f5157dc5e0a8ea6f542e9274ff674cd86fce'], + }), + ('CGHbase', '1.50.0', { + 'checksums': ['a4b3cc26619d3256dc86d21bacfbe84766f84f5a927bbb8064c3b8a16995f083'], + }), + ('Wrench', '1.8.0', { + 'checksums': ['bdc57c05c35bec643183fb2f28d1c27a1b4ca5bb8ebfdec6529719eb52cbe707'], + }), + ('lpsymphony', '1.18.0', { + 'checksums': ['a977e5b7e0314c13a3878df552fefb80d403ef1d5f5aa6791d3edc7cb6933839'], + }), + ('IHW', '1.18.0', { + 'checksums': ['80474cc48ca846d0c758828bfbd0ab627e0764b571487459ef51b222d7785f13'], + }), + ('metagenomeSeq', '1.32.0', { + 'checksums': ['dd6a70d19cd3023764722c7326870005787c5c838d58139bfb00a8e3ea4236f3'], + }), + ('gdsfmt', '1.26.1', { + 'checksums': ['163d3e9d501e35f96ba29573317f9cb313060b72f9699136fbea7f5720b2bb38'], + }), + ('SNPRelate', '1.24.0', { + 'checksums': ['3b6a46fc969573ba6791b5cc7737839883ce1a6099bc3f9d82fc8f61027ad4e7'], + }), + ('biomformat', '1.18.0', { + 'checksums': ['ecb60b0a0962bbf285f512a713178e541c86798e386e9b5aeb9a9d0eaf02b780'], + }), + ('phyloseq', '1.34.0', { + 'checksums': ['b4b4d1ad377bda0f872e7cfef154ca15533533dd53bf1a3cba1473e03c9bfcd7'], + }), + ('NADA', '1.6-1.1', { + 'checksums': ['670ff6595ba074ed0a930b7a09624d5ef20616379a20e768c1a7b37332aee44a'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('zCompositions', '1.3.4', { + 'checksums': ['ae22c86fe92368a26265933f42eecc518b9b69e7d9b698bc31bfaabfc3c48e95'], + }), + ('ALDEx2', '1.22.0', { + 'checksums': ['ba51da140ff183e5e10695bf642610ff20ba5dc9f2d3a3a540232cdc8e9ec91a'], + }), + ('dada2', '1.18.0', { + 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], + 'checksums': [ + '400160de67e6afbe5cc806acfb072b6efc7d08cc13301415c4e04c7009e00453', # dada2_1.18.0.tar.gz + # dada2-1.16.0-remove-sse-on-aarch64.patch + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + ], + }), + ('LEA', '3.2.0', { + 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], + 'checksums': [ + '5fde04a8aab6467a2641447099688d520b772faf1488e5febbd51d1b86c911d5', # LEA_3.2.0.tar.gz + # LEA-3.0.0_support_aarch64_and_ppc64le.patch + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + ], + }), + ('tximport', '1.18.0', { + 'checksums': ['6460ef739edc7e5268922d3be877de63d92efca7408aa3ba4843ec48e8a6b6db'], + }), + ('SingleCellExperiment', '1.12.0', { + 'checksums': ['a26242172a2c10497cc3a0c988e47dc71120bcf31101caeba58cf60eb358ef72'], + }), + ('beachmat', '2.6.4', { + 'checksums': ['51ca7ac7a937e0f9270723a15d774a9454fc16131ed6e7e10b5b4851d86c786d'], + }), + ('RcppAnnoy', '0.0.18', { + 'checksums': ['e4e7ddf071109b47b4fdf285db6d2155618ed73da829c30d8e64fc778e63c858'], + }), + ('RcppHNSW', '0.3.0', { + 'checksums': ['a0eb4eea65e28ba31e8306a1856f7e617a192bd448b148f88abe99181cbde007'], + }), + ('BiocNeighbors', '1.8.2', { + 'checksums': ['a711fb56fd227ba165da8aab81e4d285678406b310c8078b6fbe387a42a2fea5'], + }), + ('rsvd', '1.0.3', { + 'checksums': ['13560e0fc3ae6927c4cc4d5ad816b1f640a2a445b712a5a612ab17ea0ce179bb'], + }), + ('BiocSingular', '1.6.0', { + 'checksums': ['d10ea057e2b62b885a8e8c7e7803d1f94e6c319ef859cd3e4ca19100438f9fc1'], + }), + ('scuttle', '1.0.4', { + 'checksums': ['888addbb0ba1e326830a4c1fba0234415eef83ef6b68301f2ea2f880b6efd06d'], + }), + ('scater', '1.18.3', { + 'checksums': ['651456bbdb8a8ed3590c5d4122fee7f7473b9ca690f25359edd3db7304f7c791'], + }), + ('sitmo', '2.0.1', { + 'checksums': ['0c90d357af334d5c99c8956739dc12623ddd87dda5efa59f4a43f7393c87ed2a'], + }), + ('dqrng', '0.2.1', { + 'checksums': ['e149c105b1db31e7f46b1aebf31d911a109e380923f3696fc56a53197fc1e866'], + }), + ('bluster', '1.0.0', { + 'checksums': ['c15c79f82a5424c639b5bb75a9085c2a2f3189d6b2f812d5cbdefe520572f947'], + }), + ('scran', '1.18.5', { + 'checksums': ['c1f7c053433124ef48b277d95e081c08654eb3feb69cab948a6afd798f5e6456'], + }), + ('SC3', '1.18.0', { + 'checksums': ['e73effd89bfa8bf3aa60b2bc65ab6e22bfd701e72c03696a26667a8ca71ce4df'], + }), + ('ComplexHeatmap', '2.6.2', { + 'checksums': ['bd3caa8426d16074aab92fdc567ebb05515d47dfd5a50d528a3b7f846fefa1db'], + }), + ('GENIE3', '1.12.0', { + 'checksums': ['c5495b748bb71beac6e365c4a61afb5036be8f36bff5c320bda2b7c7c09ef8fc'], + }), + ('dupRadar', '1.20.0', { + 'checksums': ['a422ece6c2dfb4a53b397fffec95e5b4f5436ea536fef348881f256b2f5ee2d4'], + }), + ('DNAcopy', '1.64.0', { + 'checksums': ['0c16de79da073c1e1bd6cecceebc53d21051627b748ce497a940211e8953a54e'], + }), + ('sva', '3.38.0', { + 'checksums': ['fe8fd0aa333a11da1d2a93074a649a4fcec848c2afd4f0f8446dbe8cc7fbffc2'], + }), + ('ballgown', '2.22.0', { + 'checksums': ['a75ce0ccb506ff60bd1ef94d491c4fef402fcf279c2c43ccc204a9358f536e1a'], + }), + ('DropletUtils', '1.10.3', { + 'checksums': ['782d33ae853b6102d987d633b6b95d3f822de8035c92a325ce272058d3c6f94c'], + }), + ('DeconRNASeq', '1.32.0', { + 'checksums': ['5e2549ba8f2b7a65187fd6b0e6cdafa76cd5d45768d8700fd06a350512b1d81a'], + }), + ('GSVA', '1.38.2', { + 'checksums': ['b35f7b921b02164b8edd751a0f8011def6f8cf7032e7477064fde44a1235d1ac'], + }), + ('PureCN', '1.20.0', { + 'checksums': ['2fc659f13c13d193016bc5aec0b373b457bd220439c07524418ff335f4a377c2'], + }), + ('globaltest', '5.44.0', { + 'checksums': ['c7dd30502778cf83eada4b35735cede49728f34819f447e27e9a4e4f17e4bdce'], + }), + ('GlobalAncova', '4.8.0', { + 'checksums': ['b001146f4e2737930402929f9662091f9c7b1df2f8fbd97954e813e1f10bfc41'], + }), + ('SSPA', '2.30.0', { + 'checksums': ['a82a48386481693e8abd8cabd5c2746d8334df00160042416f96787e89bf5fd3'], + }), + ('vsn', '3.58.0', { + 'checksums': ['8b6641eb70da5db8947b9cf60414361b3bbad28faed68f3d87d7de16a973d935'], + }), + ('mzID', '1.28.0', { + 'checksums': ['02df69fafbcf4d08475babce8144f6d18f44af6e191a6ba21dfb441a3e33ed68'], + }), + ('ncdf4', '1.17', { + 'checksums': ['db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6'], + }), + ('mzR', '2.24.1', { + 'patches': ['mzR-2.22.0_use-external-boost.patch'], + 'checksums': [ + '4f0b126e27c34f81cc1100d439ffc70fdca694b0908194ea2d19cd0d65f66046', # mzR_2.24.1.tar.gz + '8b5ba4f0c4efbbab9b4801d7da3fb04a490a5d95af1cefb489f209afa4d14fb4', # mzR-2.22.0_use-external-boost.patch + ], + }), + ('MSnbase', '2.16.1', { + 'checksums': ['7034911cbbc5ddbeb0737c7e40a1cfed067fa186080d7c72c7dc4bfa7fd2bf43'], + }), + ('MassSpecWavelet', '1.56.0', { + 'checksums': ['63ff4f6558b0263d7c1993c06c0357e242b903b13475e075c32aa351585f7def'], + }), + ('MsCoreUtils', '1.2.0', { + 'checksums': ['6018803eda335d47942612129ab3c58f6323f4b7f768c9912fee57261c5b4339'], + }), + ('xcms', '3.12.0', { + 'checksums': ['db213637490bdbbf2060dfd82200279ccf5a53b8b2baa5c503b28e04e4f27e9e'], + }), + ('CAMERA', '1.46.0', { + 'checksums': ['241ce0fbceebb4fe16d026f7e1feab9b1db41f773253403c223ff8d8c7eeb504'], + }), + ('fgsea', '1.16.0', { + 'checksums': ['1619d0f5fbc2597a1f412887b9dcd9efecdd3669bd0ae63d0575f4a5bc9ab34a'], + }), + ('GWASExactHW', '1.01', { + 'checksums': ['e850ed40fbf14b02eb3798603cfb111fe3718bb69d74c0ff4cb6f679209a15a7'], + }), + ('quantsmooth', '1.56.0', { + 'checksums': ['d9817070c31adbafc4f9463efce0b30981ba8e0a7cb6c342d2577986dc2fed93'], + }), + ('GWASTools', '1.36.0', { + 'checksums': ['66e7d342f8e3ba5b82d8263907091ff8a1cb16b367fa546301956bfe153efc9a'], + }), + ('SeqArray', '1.30.0', { + 'checksums': ['e230413b5159384352f9c6596531bae4f46702a1d369f16fdf0967003c56ea40'], + }), + ('SeqVarTools', '1.28.1', { + 'checksums': ['a66b6e6baf4a352cb80f43fca3b23b27b67f8c222f38ad0ca0678d6c595200d6'], + }), + ('GENESIS', '2.20.1', { + 'checksums': ['a7c089bc107a934b1f3c01614a5a13a9572ce8e1b10e4b722099d0216c05e673'], + }), + ('MLInterfaces', '1.70.0', { + 'checksums': ['79e02236071044f2f83bf7e47f0f87ee5a23c2fc33efd09e2a2c9f62020422c9'], + }), + ('pRoloc', '1.30.0', { + 'checksums': ['d3f3b48b162782ce5d6685e0c4c8653f74e27661c3ea8b53f10bf0e0efe1fb0c'], + }), + ('pRolocdata', '1.28.0', { + 'checksums': ['4e3c6f05d9202731f5507b8571444cff3fc2b7a2518855e0668e51d5a8b0f672'], + }), + ('shinydashboardPlus', '0.7.5', { + 'checksums': ['3eae1281c9416c81a2eab4d40894a7db4cfe1a033a2e25f06197b6f30fe00c3c'], + }), + ('shinyhelper', '0.3.2', { + 'checksums': ['f7ed62543ab4d05a34b69a9183517a09e93e1b2da85b113282de0f9982db90b0'], + }), + ('shinyWidgets', '0.5.7', { + 'checksums': ['eb385c8dadb73aded7cb2d24218a7fd2962dcd711c69a22562a8003607f7c890'], + }), + ('pRolocGUI', '2.0.0', { + 'checksums': ['f6f57c0611eb758f2109310b0218e04244b774f3cf5dc358d174c7c63f33e43c'], + }), + ('EBImage', '4.32.0', { + 'checksums': ['9c13b81ab5f659da254b4b03596af910c9455bdc0e4a3a8e864aaed2e35a2862'], + }), + ('GenomicScores', '2.2.0', { + 'checksums': ['599aeedaeb8b87dac81aaf3198ae1108eb62d4a83c696fb26ee2a9a773ec2291'], + }), + ('BSgenome.Mmusculus.UCSC.mm10', '1.4.0', { + 'checksums': ['6e2eb3bce208cc7766f0e0ef1e14465289d5463b34d94c9a9279256545b5408b'], + }), + ('TxDb.Mmusculus.UCSC.mm10.knownGene', '3.10.0', { + 'checksums': ['696281749d01737c94894564d62093433045bc007a4528cc3d94f205edb54977'], + }), + ('regioneR', '1.22.0', { + 'checksums': ['b1493b9f81a9e9255ce6aff10e8e5c4bd10b43d2072c2319327ef897bd835330'], + }), + ('RcppZiggurat', '0.1.6', { + 'checksums': ['9c78255ca476c945c05a564d1e4da363de714d890e0e27f3b252fd73c50eed71'], + }), + ('Rfast', '2.0.1', { + 'checksums': ['a8a4305e3ec56321ead1c696cc2d26aa2277ba7e8d386339c45bc3441eab03b3'], + }), + ('ChIPpeakAnno', '3.24.1', { + 'checksums': ['f29560f34de88b8e380a7ac699c8d6c97f7fb68c9089f7ea0ccd108db6e4b361'], + }), + ('seqLogo', '1.56.0', { + 'checksums': ['01db7c1a0c1f261b19d0597ddeaadbe231742a1367efe538a79095e7a4fc370b'], + }), + ('rGADEM', '2.38.0', { + 'checksums': ['fce3140b033710a3a0e0dcf1b72f86afbe65fc7f186c6035264f5a361f7d2374'], + }), + ('MotifDb', '1.32.0', { + 'checksums': ['652bcadd070ee1a8ce750002d1399b71ef89e5bfbfb96a19f1a2bdc35f0bd33d'], + }), + ('motifStack', '1.34.0', { + 'checksums': ['8bcacef91f59f5eb5e2ca87e5b0ecd49978885a1ab3c88da0aa3a9f556bb58df'], + }), + ('ATACseqQC', '1.14.4', { + 'checksums': ['c9ae3accd8698e54ebf3d97e98cd84f9318e098335978fb72c11984ae8075613'], + }), + ('ResidualMatrix', '1.0.0', { + 'checksums': ['e13c57469ab48f8e7792328905c21ad1cdd2b59f26918f5cf83671ec6af65fda'], + }), + ('batchelor', '1.6.2', { + 'checksums': ['b970219d713e977dbf66c9668c005d9b3a612a62a84ee9b607f5540a9e41d20b'], + }), + ('gsmoothr', '0.1.7', { + 'checksums': ['b75ffd2a4a0f357762e02e46e355b45cc90ea637830f0a1b01f216bb4541e903'], + }), + ('Ringo', '1.54.0', { + 'checksums': ['865ce9693b8466999681eeb6be4ef16e3a396eaf93c023c5d0d83d61a55c0398'], + }), + ('R.devices', '2.17.0', { + 'checksums': ['c2d4b12949e0faab414c9f7575e39ee9dbf50ea12d858143df529f15ea365fb6'], + }), + ('R.filesets', '2.14.0', { + 'checksums': ['707dd7c099aeadbecebbd2ba57e6400405aa44487c641f3729ce06c4c642bb23'], + }), + ('aroma.light', '3.20.0', { + 'checksums': ['401581a5823831749f2a8c3da65b47231d76dc583dd0d378ba4440ec683e235e'], + }), + ('PSCBS', '0.65.0', { + 'checksums': ['3365065d5375c599eb024bfff12c5f6b10a6b1a4fe4ba6f200f7e83618dd399a'], + }), + ('aroma.core', '3.2.2', { + 'checksums': ['35e0312e403a1894da036afac12d1d727c937e666d7eb400bfe4018b21244855'], + }), + ('R.huge', '0.9.0', { + 'checksums': ['f12d113a965603cfdbbb46e1a57331d267916235555b22f2bbc06caa302ae58e'], + }), + ('aroma.apd', '0.6.0', { + 'checksums': ['87513774baeed8e1d43f819e615c85278aef748ebc842f1ee50686c3392e37d1'], + }), + ('aroma.affymetrix', '3.2.0', { + 'checksums': ['d279cf13cf6ed8369cfdf6682ace12924379bad578003453449aa1ccec31b0a7'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('Repitools', '1.36.0', { + 'checksums': ['e6166de4ac92c0d4124f89a2a091a272f790964d36d83db6f33f71f6650b82c6'], + }), + ('BSgenome.Hsapiens.UCSC.hg38', '1.4.3', { + 'checksums': ['c29911ca93935e3b9aa6a67e894337dc2ad707405da1500c9898bd0578519ecc'], + }), + ('MEDIPS', '1.42.0', { + 'checksums': ['7d4457e586ec68e4c521c1966f07e095dce76ffee2c4ebd0c66fc2d68c21e4e1'], + }), + ('RProtoBufLib', '2.2.0', { + 'checksums': ['1f537a4434286f056425984119f1d170f0df9215396792975072baea87b7c426'], + }), + ('cytolib', '2.2.1', { + 'checksums': ['f9c0295001cfcb1e52a4d9bace6ce8a19ea1a47f74e5e434542b41395eee1579'], + }), + ('flowCore', '2.2.0', { + 'checksums': ['28f771b8246928ff60ec55f9bcfab76784c3039d58b6cb3fa04d2b41f3643100'], + }), + ('mutoss', '0.1-12', { + 'checksums': 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['63d1246f88a498f3db0321b46a552163631b288a25b24400935db41326636e87'], + }), + ('fds', '1.8', { + 'checksums': ['203a5e7671e542dcb83d4c75d0f4012aaebc32d54f94657afaf9e71e99dd0489'], + }), + ('fda', '5.1.9', { + 'checksums': ['c8bdf4bd285100c4c7ee89bb67df96dbf1132c1cf2c9ee85c59cad52b696597a'], + }), + ('flowStats', '4.2.0', { + 'checksums': ['ddf418c43f64ebe73566d62741ea1905397efcb546bf7c31b18bcc5218cfd6c4'], + }), + ('flowClust', '3.28.0', { + 'installopts': "--configure-args='--with-gsl=${EBROOTGSL} --enable-bundled-gsl=false'", + 'checksums': ['38333d7944074384a20fa4bf62ebe76b15b9d2d19fc8424ff64b228379f183d6'], + }), + ('openCyto', '2.2.0', { + 'checksums': ['1b109b0fd2a84ec08eda26d148543e53d5625ad84d0e8a2f699203e58aafbe09'], + }), + ('ggcyto', '1.18.0', { + 'checksums': ['35e4b7e96b120503d46d37cfe11ff2cc96f7931b6a525b60646949992adcd257'], + }), + ('CytoML', '2.2.1', { + 'checksums': ['d89bff3d46b9ac5b7ac9951b9ae40588aa7a72511e9a42fa0ebd248655221db5'], + }), + ('FlowSOM', '1.22.0', { + 'checksums': ['8e3f5de400a59f245aea6bb2341ffad6bb6f88c92b4d53066f6ae26fb0b9cd3f'], + }), + ('HMMcopy', '1.32.0', { + 'checksums': ['4b128a0fb77a076f955f9069704e4492a7f91d514af876655fc641494cd50374'], + }), + ('diffcyt', '1.10.0', { + 'checksums': ['c95ee8f4acad7baf4bf19536c4d2eac10698ea5c5f46417189db573a32d81019'], + }), + ('blme', '1.0-5', { + 'checksums': ['679a4f19d34a584c2390ffab37810a31f6834b913fceaa2409d297ccdf912310'], + }), + ('colorRamps', '2.3', { + 'checksums': ['3f10eab0602a42a2e5a79c7c04638be06cbf1e6f23979a1bd95d853e10940b6a'], + }), + ('variancePartition', '1.20.0', { + 'checksums': ['50411cba28f49014992192bf9f6398040a1ba630fa079a7e4ebea35d1a563a3a'], + }), + ('muscat', '1.4.0', { + 'checksums': ['871b65d1614977c5183956d0ead57747c4639d4b58458f0687f3da8d6f0952bf'], + }), + ('IlluminaHumanMethylation450kmanifest', '0.4.0', { + 'checksums': ['41b2e54bac3feafc7646fe40bce3aa2b92c10871b0a13657c5736517792fa763'], + }), + ('IlluminaHumanMethylationEPICmanifest', '0.3.0', { + 'checksums': ['e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a'], + }), + ('IlluminaHumanMethylation450kanno.ilmn12.hg19', '0.6.0', { + 'checksums': ['249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15'], + }), + ('IlluminaHumanMethylationEPICanno.ilm10b2.hg19', '0.6.0', { + 'checksums': ['4decdbc78a6a8d02bf8aecb0d6e1d81134ae9dbc2375add52574f07829e8cd69'], + }), + ('IlluminaHumanMethylationEPICanno.ilm10b4.hg19', '0.6.0', { + 'checksums': ['2c8128126b63e7fa805a5f3b02449367dca9c3be3eb5f6300acc718826590719'], + }), + ('conumee', '1.24.0', { + 'checksums': ['38941f7735acc137bf2bb64f2e40000bd4039ef8d83d84d2ed6cddfb70a106fc'], + }), + ('BSgenome.Cfamiliaris.UCSC.canFam3', '1.4.0', { + 'checksums': ['99c55b6f7808822a3dae6679e60ecfb88a2b618159484bc35303c000bd4820c7'], + }), + ('ExperimentHub', '1.16.0', { + 'checksums': ['6faa70a2fed185c35313776b60a10f10bb809a24b4e74ff311120607b3de27fe'], + }), + ('SingleR', '1.4.1', { + 'checksums': ['6f11a8caff8d88b95e2163bb5cfdc7c9f64a5ca79b9df537e495df7ec37f24ff'], + }), + ('FlowSorted.Blood.EPIC', '1.8.0', { + 'checksums': ['a98636b86394cfd82ddebb68cb638aa3f50877a665ef13c916ad3a3295fc702c'], + }), + ('FlowSorted.CordBloodCombined.450k', '1.6.0', { + 'checksums': ['1ed4da1a91bdb9a92f8fa3cd29b6567d352650c01a9d29c1f5d8299e5b45d5fd'], + }), + ('DRIMSeq', '1.18.0', { + 'checksums': ['676a1813ee7cd1d04d18f3bfcd55ba3a4d90ea61ab7a3f6bd473ed320f593b27'], + }), + ('stageR', '1.12.0', { + 'checksums': ['b57e7935dba7619b1f496bb7c37adfbfcf069c794472f0adfe3b501e932288a1'], + }), + ('isva', '1.9', { + 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], + }), + ('org.Mm.eg.db', '3.12.0', { + 'checksums': ['745341c40fda3a1f3b1970a55492e421cf96ae110a5c39a0d96c0b7856326c04'], + }), + ('org.Rn.eg.db', '3.12.0', { + 'checksums': ['4bdd645761fc0954dfeb04ef85dc4f74c4920dc1774d963b4c8e5036dd5a46c5'], + }), + ('ROC', '1.66.0', { + 'checksums': ['890d427fb977c2ef12581500ccbc85369d56e3c6f40dd76e7759cef105b16909'], + }), + ('wateRmelon', '1.34.0', { + 'checksums': ['6e5cb3f2d7465abe675a8af5b1d39c354e6756b9c24f8839ddd7a9955eb782e9'], + }), + ('GLAD', '2.54.0', { + 'checksums': ['b2727e430daf417d3f74331667c11948358f72ed6b23918459f1e275f0a2da1a'], + }), + ('missMethyl', '1.24.0', { + 'checksums': ['e5443e8a2503d861f0b38972f693662f0adb08262fc9be36a260440aebf3b635'], + }), + ('MethylSeekR', '1.30.0', { + 'checksums': ['f3e73ccae68e7fc6ebb024f3e32a074533f03dbe3f080d49202d91eca58c5974'], + }), + ('affxparser', '1.62.0', { + 'checksums': ['9708bbd894c1c3a878d93d26bb6883eb35fbc3fa0f18975aec8fbf3d358f048e'], + }), + ('ccdata', '1.16.0', { + 'checksums': ['fff13441f6e743791bc0811c66208ab1d1dfc04a51fa2ea4a3123f79d4f6f889'], + }), + ('xgboost', '1.3.2.1', { + 'checksums': ['2ff462b81ad51a4810bd7860cb014b9b88831a8b1d45774249a808547147f884'], + }), + ('lsa', '0.73.2', { + 'checksums': ['cb0017bbda9b0eb1d05b451e0f557d02f789f65b2f8bf005606b63a3708e63a8'], + }), + ('ccmap', '1.16.0', { + 'checksums': ['93e49a0540f2bc5e78cf80838ba5c3d5d1add258f69233fc216c7da1e041055e'], + }), + ('oligo', '1.54.1', { + 'checksums': ['631e8adbb8b378ba5a11399cfdd33f5265e6280613441accb0ea447bfb9eee32'], + }), + ('SMVar', '1.3.3', { + 'checksums': ['17625e89eb8be7a6dbb77e6bd9daca1ea1acff69026049f213e30edf2325999f'], + }), + ('metaMA', '3.1.2', { + 'checksums': ['01851d9632cdf1988d6a43ba44500e51477b9b25d5df1e1da488cd800df85ed6'], + }), + ('randomcoloR', '1.1.0.1', { + 'checksums': ['cbae51a47a92b2cc3d5ab48877818404429fb73fc795430ec622a8dff20f1067'], + }), + ('shinyBS', '0.61', { + 'checksums': ['51be29541e066d30c66e243393f20b0da705eba1b7ce7eeadea993bb2aa91166'], + }), + ('shinypanel', '0.1.4', { + 'checksums': ['f98644118a582aed4149920beaeac12851ae2cacbd3cbe46f547620f9dbcae41'], + }), + ('crossmeta', '1.16.1', { + 'checksums': ['5b212b400c2abe2a8037825471500b91a46d94981673dc00df3698caf2be5b9e'], + }), + ('snpStats', '1.40.0', { + 'checksums': ['4438873cd22b6ab31e057c314c2f0a6840a66e9bd8cde4fc285b71aec3512889'], + }), + ('coloc', '3.2-1', { + 'checksums': ['b01c8fd81e4c4d766606e546482482d07ebe9e46e12538a1661bc685a2aca26a'], + }), + ('SCANVIS', '1.4.0', { + 'checksums': ['35e8b8f86a70db6e0dd7dceae8023058535e70e11ade54660a8db3c158c7d3ba'], + }), + ('EnsDb.Hsapiens.v86', '2.99.0', { + 'checksums': ['552c07bcc2a1420089d4330deafaeb5303e03d0fa75c96b78075dfd67eeee7be'], + }), + ('agricolae', '1.3-3', { + 'checksums': ['e9b16317f7f97c8af5d5edcf414ff209114bfc76329e06701fffc279eaa21f8e'], + }), + ('bookdown', '0.21', { + 'checksums': ['47c0fa7a65da83753c2f445e0e972913f9203460f1daae3ab255d0d4b30eba76'], + }), + ('BiocStyle', '2.18.1', { + 'checksums': ['17e7c9210c5dd551de5497d272465a9b9cd3fba45520b605e929b54694f55d67'], + }), + ('estimability', '1.3', { + 'checksums': ['a33179c5fbd6a1a623d90cb6f1743148f92c09429fac466867f3ea70946a2e32'], + }), + ('emmeans', '1.5.4', { + 'checksums': ['c10cc4879f64d8c7822371e8aaf717ff373cc7a4b454a52fcf5fb921341d70e5'], + }), + ('ggdendro', '0.1.22', { + 'checksums': ['f0a65f3498c1abc3076df0fb56364b63bdf5d212d8931f85bcc6997510916b6a'], + }), + ('pmp', '1.2.0', { + 'checksums': ['fe8916e9b567ab3a0c75a4249121aec48c2c44b7c5547a0e35982a76ba49ab95'], + }), + ('MultiDataSet', '1.18.1', { + 'checksums': ['4429e689167168b4dc18b0ebadf9522760f9a73c817c71ee3fece6f7e695746c'], + }), + ('ropls', '1.22.0', { + 'checksums': ['457a6e5db897e739a11bcfbb65affb3445eb6c94fbf479a19ed9290d13d2e6c0'], + }), + ('ontologyIndex', '2.7', { + 'checksums': ['33f4918cafb983635f9f831553daf15e10103dc375475e170f104a8eaf0e7048'], + }), + ('struct', '1.2.0', { + 'checksums': ['6d5a9140a1f127625e3467097da68c4c0d93ee1975122b9a89f8105baa548977'], + }), + ('ggthemes', '4.2.4', { + 'checksums': ['7b35168cf5b68f6f52dd533a1b345ec87e09d1a85ca68e8dc5377cdf95718567'], + }), + ('structToolbox', '1.2.0', { + 'checksums': ['01e19570ba21945874b70d310019de253e61bd69ad14d5eb0c624f088777f8b2'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' From c292b697f5cc8664b4c78bf7c8b9dd718e4345a0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 12 Feb 2021 16:21:50 +0000 Subject: [PATCH 0287/2365] Downgrade one package due to deps --- .../R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index e6438f280f..6db88f75dc 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -17,7 +17,6 @@ dependencies = [ ('Boost', '1.74.0'), # for mzR ('GSL', '2.6'), # for flowClust ('HDF5', '1.10.7'), # for rhdf5 - # ('MariaDB-connector-c', '3.1.7'), # for RMySQL ('ncdf4', '1.17', versionsuffix), # for mzR ] @@ -88,8 +87,8 @@ exts_list = [ ('Rsamtools', '2.6.0', { 'checksums': ['a4144f71022410410ed57b4f4f711c1b48651beb87590c92e786d1c7e77b1710'], }), - ('MatrixGenerics', '1.2.1', { - 'checksums': ['2bcffc10cbc49f647f61dfd4fd70022b3dd6140cb637c91e1ac06c36c6076e98'], + ('MatrixGenerics', '1.2.0', { + 'checksums': ['6c7fa4223149656077cd4ce5298f22e5dcc5feb43e533e1acda61514d2e17aa8'], }), ('DelayedArray', '0.16.1', { 'checksums': ['6dd0a32d5edce34b6797127064c42c3410725524ca5cb9176c67070561fee5b4'], From b56da3478366fb0e9a88fcc24493f8ddb49bfc2a Mon Sep 17 00:00:00 2001 From: John Dey Date: Fri, 12 Feb 2021 09:49:37 -0800 Subject: [PATCH 0288/2365] Update easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb index ba342dc037..49bfb5df88 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb @@ -38,7 +38,7 @@ dependencies = [ # ('OpenSSL', '1.0.2h'), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [OS_PKG_OPENSSL_DEV] configopts = '--with-python --with-openssl' From 63344cc8c078d343a927b4de33881937b73e601e Mon Sep 17 00:00:00 2001 From: John Dey Date: Fri, 12 Feb 2021 09:50:03 -0800 Subject: [PATCH 0289/2365] Update easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb index 49bfb5df88..4aee97b7c9 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb @@ -35,7 +35,7 @@ dependencies = [ ('zlib', '1.2.11'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.0.2h'), + # ('OpenSSL', '1.1.1h'), ] osdependencies = [OS_PKG_OPENSSL_DEV] From 76e00a2d6eec9c33e1f32e5a201cc3b890a36579 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2021 19:24:49 +0100 Subject: [PATCH 0290/2365] {math}[intel/2020b] PyMC3 v3.11.0, Theano v1.0.5 + dependencies --- .../netcdf4-python-1.5.5.1-intel-2020b.eb | 44 +++++++++++++++++++ .../t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb | 23 ++++++++++ .../x/xarray/xarray-0.16.2-intel-2020b.eb | 27 ++++++++++++ 3 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb new file mode 100644 index 0000000000..07b7940a68 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.5.5.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('netCDF', '4.7.4'), + ('cURL', '7.72.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('cftime', '1.2.0', { + 'checksums': ['ff0a175edda260357ff7d24a32bbe0a8c72eafd5f6a404ce487127f9d01836db'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'd957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd', # netCDF4-1.5.5.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9dc227ef7a --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.56.2' + +homepage = "https://github.com/tqdm/tqdm" +description = """A fast, extensible progress bar for Python and CLI""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['11d544652edbdfc9cc41aa4c8a5c166513e279f3f2d9f1a9e1c89935b51de6ff'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb new file mode 100644 index 0000000000..98f20a0441 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.16.2' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['38e8439d6c91bcd5b7c0fca349daf8e0643ac68850c987262d53526e9d7d01e4'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'data' From 22523c5171eaee4e2d4bbe016fc137f160b9e24a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 12 Feb 2021 18:27:15 +0000 Subject: [PATCH 0291/2365] cytolib requires newer BH --- .../R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index 6db88f75dc..2dff369b6b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -704,6 +704,9 @@ exts_list = [ ('RProtoBufLib', '2.2.0', { 'checksums': ['1f537a4434286f056425984119f1d170f0df9215396792975072baea87b7c426'], }), + ('BH', '1.75.0-0', { + 'checksums': ['ae4c10992607dd697663f60675a46a5770851da159330bb63c4a68890bdd6f5a'], + }), ('cytolib', '2.2.1', { 'checksums': ['f9c0295001cfcb1e52a4d9bace6ce8a19ea1a47f74e5e434542b41395eee1579'], }), From 20beb27c8102e4de6c28f7e26d12daef9f926936 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2021 19:53:00 +0100 Subject: [PATCH 0292/2365] adding easyconfigs: SuiteSparse-5.8.1-foss-2020b-METIS-5.1.0.eb --- ...uiteSparse-5.8.1-foss-2020b-METIS-5.1.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-foss-2020b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-foss-2020b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-foss-2020b-METIS-5.1.0.eb new file mode 100644 index 0000000000..cf6bd920e1 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-foss-2020b-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '5.8.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['06726e471fbaa55f792578f9b4ab282ea9d008cf39ddcc3b42b73400acddef40'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From 60bbcc3e15a3fb5763f7fdbae5c4fd511c055b73 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 12 Feb 2021 10:57:36 -0800 Subject: [PATCH 0293/2365] https fix --- easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb index 4572d2cbde..098e05b12a 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'igraph' version = '0.8.5' -homepage = 'http://igraph.org' +homepage = 'https://igraph.org' description = """igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.""" From 85ec6f15c89c068ce87f0a33b5584211b1d4ed30 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 12 Feb 2021 11:06:42 -0800 Subject: [PATCH 0294/2365] {lang}[GCC/10.2.0] SOCI 4.0.1 --- .../s/SOCI/SOCI-4.0.1-GCC-10.2.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOCI/SOCI-4.0.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.1-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..834cef5f74 --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.1-GCC-10.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.1' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1979b4084ba644125da29dbfbd132798f7742a56caf5a0edb16756a5dbad0f31'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Boost', '1.74.0'), + ('SQLite', '3.33.0'), + ('PostgreSQL', '13.2'), +] + +# Matches RStudio (1.4.1101) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' From 031a335cee47d09882d33fc3561c2194905c3478 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 12 Feb 2021 20:37:37 +0000 Subject: [PATCH 0295/2365] Seurat requires newer sctransform --- .../R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index 2dff369b6b..2434d2015d 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -4,6 +4,8 @@ name = 'R-bundle-Bioconductor' version = '3.12' versionsuffix = '-R-%(rver)s' +local_biocver = 3.12 + homepage = 'https://bioconductor.org' description = """Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.""" @@ -728,6 +730,9 @@ exts_list = [ ('scattermore', '0.7', { 'checksums': ['f36280197b8476314d6ce81a51c4ae737180b180204043d2937bc25bf3a5dfa2'], }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), ('SeuratObject', '4.0.0', { 'checksums': ['313eb25f2083ff708d14abbf340d4860f68102ee9709255d3d9e9bf3ce3f620e'], }), From b23ce92f31f71be2379792d7e985a2ff16126245 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 12 Feb 2021 20:39:20 +0000 Subject: [PATCH 0296/2365] remove item needed for easy_update --- .../R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index 2434d2015d..b7f5016bcb 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -4,8 +4,6 @@ name = 'R-bundle-Bioconductor' version = '3.12' versionsuffix = '-R-%(rver)s' -local_biocver = 3.12 - homepage = 'https://bioconductor.org' description = """Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.""" From b452446e07bbadef18ce41d6772ae1ff7ff53144 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2021 23:25:10 +0100 Subject: [PATCH 0297/2365] fix source URL in UDUNITS easyconfigs + add sources.easybuild.io fallback source URL --- .../easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb index f97a364b22..006876aac2 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb @@ -22,7 +22,10 @@ description = """UDUNITS supports conversion of unit specifications between form toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://fossies.org/linux/privat/legacy/'] +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/', + 'http://sources.easybuild.io/u/UDUNITS/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] From 97f4f945718b5994c742e3dd6dbd29785a79ff6f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Feb 2021 15:12:54 +0100 Subject: [PATCH 0298/2365] remove commented out Python binding in flatbuffers easyconfig (available via separate flatbuffers-python easyconfig) --- .../flatbuffers-1.12.0-GCCcore-10.2.0.eb | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb index 3eac90f1d2..8f9764b10b 100644 --- a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb @@ -37,21 +37,4 @@ sanity_check_paths = { 'dirs': ['lib/cmake'], } -# exts_defaultclass = 'PythonPackage' -# -# exts_list = [ -# (name, version, { -# 'source_urls': [PYPI_SOURCE], -# 'sources': { -# 'filename': '%(name)s-python-%(version)s.tar.gz', -# 'download_filename': '%(name)s-%(version_major_minor)s.tar.gz' -# }, -# 'checksums': ['63bb9a722d5e373701913e226135b28a6f6ac200d5cc7b4d919fa38d73b44610'], -# 'download_dep_fail': True, -# 'use_pip': True, -# 'sanity_pip_check': False, # Doesn't work yet when Python is only a build dep -# 'preinstallopts': 'VERSION=%(version)s ', -# }), -# ] - moduleclass = 'devel' From 8765dc9caaf51cf160f14a089a8380258fbb23bd Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 13 Feb 2021 20:44:25 +0000 Subject: [PATCH 0299/2365] sync patch list with 2019b version --- .../p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 39324bc2fe..085d5c7b7a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -245,9 +245,14 @@ patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch', + 'PyTorch-1.7.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch', 'PyTorch-1.7.1_complex32.patch', 'PyTorch-1.7.1_bypass-nan-compare.patch', + 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.7.1_el8_ppc64le.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -295,12 +300,19 @@ checksums = [ '97febb91ae2d051db9541e1e4c5924c77555ab73ee49ad7d62ef3e4714110297', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch # PyTorch-1.7.0_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + # PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch + '96241088dbfcd4db93bd5faadecabce6259a495ffd24b75101444cd0e164c12b', + '12be5139e4e7aeec214bb38b123b09b391cd1ca72ce5ded6e61590cfae801824', # PyTorch-1.7.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch - 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', + 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', '6028bff2be720cf70acad2129db60fd10872e02c9e460c72bb274228cf90b320', # PyTorch-1.7.1_complex32.patch '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch + # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch + '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', ] excluded_tests = { From 11f514944c893389e134f81ae078f0d511c65318 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 13 Feb 2021 20:47:32 +0000 Subject: [PATCH 0300/2365] remove accidentally added patch and stray spaces --- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 085d5c7b7a..0cbcb57798 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -252,7 +252,6 @@ patches = [ 'PyTorch-1.7.1_complex32.patch', 'PyTorch-1.7.1_bypass-nan-compare.patch', 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', - 'PyTorch-1.7.1_el8_ppc64le.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -308,7 +307,7 @@ checksums = [ '96241088dbfcd4db93bd5faadecabce6259a495ffd24b75101444cd0e164c12b', '12be5139e4e7aeec214bb38b123b09b391cd1ca72ce5ded6e61590cfae801824', # PyTorch-1.7.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch - 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', + 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', '6028bff2be720cf70acad2129db60fd10872e02c9e460c72bb274228cf90b320', # PyTorch-1.7.1_complex32.patch '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch From 7ff6405fa8ad1f5ad4131d46857f5eedf8d561a8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 13 Feb 2021 20:53:37 +0000 Subject: [PATCH 0301/2365] more trailing whitespace ... --- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 0cbcb57798..bba354dab6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -302,9 +302,9 @@ checksums = [ '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch - 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', # PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch - '96241088dbfcd4db93bd5faadecabce6259a495ffd24b75101444cd0e164c12b', + '96241088dbfcd4db93bd5faadecabce6259a495ffd24b75101444cd0e164c12b', '12be5139e4e7aeec214bb38b123b09b391cd1ca72ce5ded6e61590cfae801824', # PyTorch-1.7.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', From 95a88416afc0ed6c68827b68b7e7565134e0f71c Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 13 Feb 2021 21:07:06 +0000 Subject: [PATCH 0302/2365] switch to using cudaver for cuDNN and NCCL --- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index bba354dab6..2debc8f748 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -28,9 +28,9 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), ('magma', '2.5.4'), - ('NCCL', '2.8.3', '-CUDA-11.1.1', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) From d5d3cadcaca6002229136aef5207f1d14ff10720 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 12 Feb 2021 12:49:26 +0100 Subject: [PATCH 0303/2365] adding easyconfigs: TensorFlow-2.4.1-fosscuda-2020b.eb and patches: TensorFlow-2.4.0_add-default-shell-env.patch, TensorFlow-2.4.0_add-ldl.patch, TensorFlow-2.4.0_add-missing-llvm-deps.patch, TensorFlow-2.4.0_add-protobuf-deps.patch, TensorFlow-2.4.0_dont-use-var-lock.patch, TensorFlow-2.4.0_downgrade-required-versions.patch, TensorFlow-2.4.0_fix-absl-on-power.patch, TensorFlow-2.4.0_fix-eigen-on-power.patch, TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch --- .../TensorFlow-2.4.1-fosscuda-2020b.eb | 232 ++++++++++++++++++ 1 file changed, 232 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..cc2bff1205 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -0,0 +1,232 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.4.1' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), + ('NCCL', '2.8.3', '-CUDA-11.1.1', True), + ('Python', '3.8.6'), + # Next 2 are for h5py + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} +use_pip = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + # TF 2.4 needs h5py 2.10, later versions allow 3.x + ('h5py', '2.10.0', { + 'patches': ['h5py-%(version)s_avoid-mpi-init.patch'], + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch + ], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + }), + ('Markdown', '3.3.3', { + 'checksums': ['5d9f2b5ca24bc4c7a390d22323ca4bad200368612b5aaa7796babf971d2b2f18'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7', { + 'checksums': ['69805d6b69f56eb05b62daea3a7dbd7aa44324ad1306445e05da8060232d00f4'], + }), + ('cachetools', '4.2.0', { + 'checksums': ['3796e1de094f0eaca982441c92ce96c68c89cced4cd97721ab297ea4b16db90e'], + }), + ('google-auth', '1.24.0', { + 'modulename': 'google.auth', + 'checksums': ['0b0e026b412a0ad096e753907559e4bdb180d9ba9f68dd9036164db4fdc4ad2e'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.2', { + 'checksums': ['65b65bc39ad8cab15039b35e5898455d3d66296d0584d96fe0e79d67d04c51d9'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('absl-py', '0.10.0', { + 'modulename': 'absl', + 'checksums': ['b20f504a7871a580be5268a18fbad48af4203df5d33dbc9272426cb806245a45'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.32.0', { + 'modulename': 'grpc', + 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard', version, { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['7b8c53c396069b618f6f276ec94fc45d17e3282d668979216e5d30be472115e4'], + }), + ('tensorboard-plugin-wit', '1.8.0', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard-plugin-profile', '2.4.0', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', '2.4.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['5b7b7bf2debe19a8794adacc43e8ba6459daa4efaf54d3302623994a359b17f0'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.3.1_disable-float128-on-power.patch', + 'TensorFlow-2.4.0_add-default-shell-env.patch', + 'TensorFlow-2.4.0_fix-eigen-on-power.patch', + 'TensorFlow-2.4.0_downgrade-required-versions.patch', + 'TensorFlow-2.4.0_add-protobuf-deps.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', + 'TensorFlow-2.4.0_fix-absl-on-power.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Invalid alignment: https://github.com/tensorflow/tensorflow/issues/46460 + '-//tensorflow/core/kernels:sparse_matmul_op_test', + '-//tensorflow/core/kernels:sparse_matmul_op_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + 'checksums': [ + 'f681331f8fc0800883761c7709d13cda11942d4ad5ff9f44ad855e9dc78387e0', # v2.4.1.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + # TensorFlow-2.3.1_disable-float128-on-power.patch + 'a8369e92559cce4566ff831e615420fd98b83106c73ee3af7fbd5335c5fcd569', + # TensorFlow-2.4.0_add-default-shell-env.patch + '033a870b458406f4cabab878c4183cdf54cd7627648f24c8cc9f1964ff24d292', + # TensorFlow-2.4.0_fix-eigen-on-power.patch + '761303a9d5a0e78b833610891194e497a45f1218cfcb0ac4854a0d31d3156c2b', + # TensorFlow-2.4.0_downgrade-required-versions.patch + 'ac8f53662ad0bb660089c17bb433faf1ce3c2238234a2c3be7d92c8e02c1a8d6', + # TensorFlow-2.4.0_add-protobuf-deps.patch + '0ae2f4f1f1dc5b85f61edbe8a4a91dcffd5cf7588fa46c6a143455e4bc41a64e', + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_add-missing-llvm-deps.patch + 'ce8c41e75f9854e547d03de99ae72cf41afa967b20439e864bc4af3dd4f565c7', + # TensorFlow-2.4.0_fix-absl-on-power.patch + 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch + 'f384cd97e004673ae530b6e5cc826f8fddb46646991f1a228fc07b2aac87ee80', + ], + }), +] + +moduleclass = 'lib' From b9c39a4237028f41cd2d31ad0e1fa6e8b7b753a2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 15 Feb 2021 09:27:26 +0100 Subject: [PATCH 0304/2365] Hardcode h5py patch version --- .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index cc2bff1205..4e437f2822 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -56,7 +56,7 @@ use_pip = True exts_list = [ # TF 2.4 needs h5py 2.10, later versions allow 3.x ('h5py', '2.10.0', { - 'patches': ['h5py-%(version)s_avoid-mpi-init.patch'], + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], 'checksums': [ '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch From f4f7c591dce102e30aca488b1302ee8b1474c4c3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 15 Feb 2021 09:58:53 +0100 Subject: [PATCH 0305/2365] Exclude CUPTI test --- .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 4e437f2822..7650e2d84c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -182,6 +182,8 @@ exts_list = [ '//tensorflow/cc/...', '//tensorflow/c/...', '//tensorflow/python/...', + # Requires access to CUPTI (privileged!) + '-//tensorflow/core/profiler/internal/gpu:device_tracer_test', # Fails on some nodes but C API isn't installed anyway '-//tensorflow/c/eager:c_api_test_gpu', '-//tensorflow/c/eager:c_api_distributed_test', From 117cb89ba3095b24479989e150ba578c21b2c184 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 15 Feb 2021 11:50:05 +0100 Subject: [PATCH 0306/2365] FIRESTARTER: add gcccude/2020b too --- .../FIRESTARTER-2.0-gcccuda-2020b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb diff --git a/easybuild/easyconfigs/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb new file mode 100644 index 0000000000..349652c2ec --- /dev/null +++ b/easybuild/easyconfigs/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMakeCp' + +name = 'FIRESTARTER' +version = '2.0' + +homepage = 'https://github.com/tud-zih-energy/FIRESTARTER/' +description = """FIRESTARTER: A Processor Stress Test Utility. +FIRESTARTER maximizes the energy consumption of 64-Bit x86 processors by +generating heavy load on the execution units as well as transferring data +between the cores and multiple levels of the memory hierarchy.""" + +toolchain = {'name': 'gcccuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/tud-zih-energy/FIRESTARTER/releases/download/v2.0/'] +sources = ['FIRESTARTER_%(version)s.tar.gz'] +checksums = ['a3b09ac4ec29c3d24750bf161c58abe6b9c2f86d56f046d2657be72daf63b673'] +start_dir = 'sources' + +# Iterations don't work otherwise +unpack_options = ' && mkdir easybuild_obj' + +separate_build_dir = True + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +# All configopts, including default values +configopts = '-DFIRESTARTER_BUILD_TYPE=FIRESTARTER_CUDA' +configopts += ' -DFIRESTARTER_LINK_STATIC=ON' +configopts += ' -DFIRESTARTER_BUILD_HWLOC=ON' +configopts += ' -DFIRESTARTER_THREAD_AFFINITY=ON' + +files_to_copy = [(['FIRESTARTER'], 'bin')] + +sanity_check_commands = ['bin/FIRESTARTER -t 1'] +sanity_check_paths = { + 'files': ['bin/FIRESTARTER'], + 'dirs': ['bin'], +} + +moduleclass = 'tools' From bad71ac905ae55a898abc6b2890cd3631cd4e7b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Feb 2021 15:57:32 +0100 Subject: [PATCH 0307/2365] move make 4.3 easyconfigs to GCCcore toolchain --- .../m/make/make-4.3-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/make/make-4.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/make/make-4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..98544f1366 --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.3' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e05fdde47c5f7ca45cb697e973894ff4f5d79e13b750ed57d7b66d8defc78e19'] + +builddependencies = [('binutils', '2.35')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' From 24c491fcd120c52ecf88d85f133e1791a52a7020 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Feb 2021 16:21:40 +0100 Subject: [PATCH 0308/2365] move BLIS and libFLAME from GCC/10.2.0 to GCCcore/10.2.0 --- .../b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb | 34 ++++++++++++ .../libFLAME/libFLAME-5.2.0-GCCcore-10.2.0.eb | 53 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..92ff63b1db --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.8.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5e05868c4a6cf5032a7492f8861653e939a8f907a4fa524bbb6e14394e170a3d'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6751c8d65b --- /dev/null +++ b/easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'libFLAME' +version = '5.2.0' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame' +description = """libFLAME is a portable library for dense matrix computations, +providing much of the functionality present in LAPACK.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/flame/libflame/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['997c860f351a5c7aaed8deec00f502167599288fd0559c92d5bfd77d0b4d475c'] + +# '--enable-max-arg-list-hack --enable-dynamic-build' requires 'file' function from GNU Make 4.x +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), + ('make', '4.3'), # needed on Cent OS 7 where make 3 is installed +] + +dependencies = [('BLIS', '0.8.0')] + +# Use unset FLIBS to let configure pick up LDFLAGS +preconfigopts = 'unset FLIBS && ' +preconfigopts += 'LIBS="-lblis $LIBS" ' +preconfigopts += 'LDFLAGS="$LDFLAGS -L$EBROOTBLIS/lib -fopenmp -lm -lpthread" ' +preconfigopts += 'CFLAGS="$CFLAGS -I$EBROOTBLIS/include/blis" ' + +configopts = '--enable-max-arg-list-hack ' +configopts += '--enable-lapack2flame ' +configopts += '--enable-external-lapack-interfaces ' +configopts += '--enable-cblas-interfaces ' +configopts += '--enable-dynamic-build ' +configopts += '--enable-multithreading=openmp ' + +# libFLAME C++ Template API tests +# runtest = 'checkcpp LIBBLAS=$EBROOTBLIS/lib/libblis.a' + +# sanity_check_commands = [ +# 'cd %(builddir)s/%(namelower)s-%(version)s/test ' +# '&& make LIBBLAS=$EBROOTBLIS/lib/libblis-mt.so LDFLAGS="-fopenmp -lm -lpthread" ' +# '&& ./test_libfame.x' +# ] + +sanity_check_paths = { + 'files': ['include/FLAME.h', 'lib/libflame.a', 'lib/libflame.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'numlib' From 31a5b39cd90885a695c8e69ac6e905a1339216f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Feb 2021 17:19:54 +0100 Subject: [PATCH 0309/2365] fix dependencies in gobff easyconfigs --- easybuild/easyconfigs/g/gobff/gobff-2020b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gobff/gobff-2020b.eb b/easybuild/easyconfigs/g/gobff/gobff-2020b.eb index c3c1fc3e46..2ed4f4e1c2 100644 --- a/easybuild/easyconfigs/g/gobff/gobff-2020b.eb +++ b/easybuild/easyconfigs/g/gobff/gobff-2020b.eb @@ -11,8 +11,8 @@ toolchain = SYSTEM local_comp_name = 'GCC' local_comp_version = '10.2.0' local_comp = (local_comp_name, local_comp_version) -local_blisver = '0.8.0' -local_libflamever = '5.2.0' + +local_gcccore = ('GCCcore', local_comp_version) # toolchain used to build dependencies local_comp_mpi_tc_name = 'gompi' @@ -22,8 +22,8 @@ local_comp_mpi_tc = (local_comp_mpi_tc_name, version) dependencies = [ local_comp, ('OpenMPI', '4.0.5', '', local_comp), # part of gompi toolchain - ('BLIS', local_blisver, '', local_comp), - ('libFLAME', local_libflamever, '', local_comp), + ('BLIS', '0.8.0', '', local_gcccore), + ('libFLAME', '5.2.0', '', local_gcccore), ('ScaLAPACK', '2.1.0', '-bf', local_comp_mpi_tc), ('FFTW', '3.3.8', '', local_comp_mpi_tc), ] From 8ba6058e74db75368bf774ea52f541e3e24c7a21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Feb 2021 18:45:54 +0100 Subject: [PATCH 0310/2365] update to PyMC fork of Theano as dependency for PyMC3 + add sanity check command for Theano to catch missing mkl-service dependency --- .../mkl-service-2.3.0-intel-2020b.eb | 29 ++++++++++ .../p/PyMC3/PyMC3-3.11.1-intel-2020b.eb | 54 +++++++++++++++++++ .../t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb | 41 ++++++++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb diff --git a/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb b/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb new file mode 100644 index 0000000000..ec17aa2793 --- /dev/null +++ b/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'mkl-service' +version = '2.3.0' + +homepage = 'https://github.com/IntelPython/mkl-service' +description = "Python hooks for Intel(R) Math Kernel Library runtime control settings." + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://github.com/IntelPython/mkl-service/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['mkl-service-2.0.2_fix-mkl-lib.patch'] +checksums = [ + 'f0c61f44f29d1264a464c14791b042826f0f74da094c3355dcc295943c46fed5', # v2.3.0.tar.gz + 'e35045a5095a2b4056fe9ee3a52586f2cb5417b90eeddbcc9abae746ff40f2e5', # mkl-service-2.0.2_fix-mkl-lib.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'mkl'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb new file mode 100644 index 0000000000..9bf535a3dd --- /dev/null +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb @@ -0,0 +1,54 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'PyMC3' +version = '3.11.1' + +homepage = 'https://docs.pymc.io/' +description = """Probabilistic Programming in Python: +Bayesian Modeling and Probabilistic Machine Learning with Theano""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('Theano', '1.1.2', '-PyMC'), + ('matplotlib', '3.3.3'), + ('h5py', '3.1.0'), + ('tqdm', '4.56.2'), + ('netcdf4-python', '1.5.5.1'), + ('xarray', '0.16.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('typing_extensions', '3.7.4.3', { + 'checksums': ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'], + }), + ('arviz', '0.11.1', { + 'checksums': ['bb0730ab62223a44ec99072b12f9e9f24521a36e6b7ba2624df9f9908eba1d82'], + }), + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + ('dill', '0.3.3', { + 'source_tmpl': 'dill-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('fastprogress', '1.0.0', { + 'checksums': ['89e28ac1d2a5412aab18ee3f3dfd1ee8b5c1f2f7a44d0add0d0d4f69f0191bfe'], + }), + ('pymc3', version, { + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + 'checksums': ['501d48b9f5d033678de7a5918b9d055a6806adf84fe16a5a9d65eaa2dc71acd8'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb new file mode 100644 index 0000000000..9b07b02d78 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.1.2' +versionsuffix = '-PyMC' + +homepage = 'https://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/T/Theano%(versionsuffix)s'] +sources = ['Theano-PyMC-%(version)s.tar.gz'] +checksums = ['5da6c2242ea72a991c8446d7fe7d35189ea346ef7d024c890397011114bf10fc'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('mkl-service', '2.3.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] + +sanity_check_paths = { + 'files': ['bin/theano-cache'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +local_blas_warning = "Using NumPy C-API based implementation for BLAS functions" +sanity_check_commands = [ + # make sure that warning about falling back to (slow) NumPy C-API for BLAS functions is *not* printed + # mkl-service dependency is required to ensure this doesn't happen + "python -c 'import theano.tensor' 2>&1 | grep '%s'; test $? != 0" % local_blas_warning, +] + +moduleclass = 'math' From d6d6309dfe2338f80a8d21af65a5769872b77195 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Feb 2021 19:39:29 +0100 Subject: [PATCH 0311/2365] enable sanity_pip_check for mkl-service v2.3.0 easyconfig --- .../easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb b/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb index ec17aa2793..4c23f71ea9 100644 --- a/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb @@ -26,4 +26,6 @@ use_pip = True options = {'modulename': 'mkl'} +sanity_pip_check = True + moduleclass = 'data' From 9e8c86834f7dc1d97145deec0b3e5fdf1b4def97 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2021 14:25:34 +0100 Subject: [PATCH 0312/2365] add EnsDb.Hsapiens.v75 + Signac extensions to R-bundle-Bioconductor 3.12 --- .../R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index b7f5016bcb..f227bad343 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -960,6 +960,15 @@ exts_list = [ ('structToolbox', '1.2.0', { 'checksums': ['01e19570ba21945874b70d310019de253e61bd69ad14d5eb0c624f088777f8b2'], }), + ('EnsDb.Hsapiens.v75', '2.99.0', { + 'checksums': ['2c59f95959f344b2a3eaa65a00086b01a420823e30b0810fc81e49b08dcba64b'], + }), + ('ggseqlogo', '0.1', { + 'checksums': ['c14f145a982597f32264b37a5f2645206a0bee30dd2584a25cb8e3dc2f9b068f'], + }), + ('Signac', '1.1.1', { + 'checksums': ['ac49a45c0d6016d4239cf762c00fc1b58cbb65e05b58646de48e2f845e99b4da'], + }), ] modextrapaths = {'R_LIBS': ''} From 4ae87f72694024507ddd241b3debfabf61e72df0 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 16 Feb 2021 16:15:28 +0100 Subject: [PATCH 0313/2365] adding easyconfigs: texinfo-6.7-GCCcore-10.2.0.eb, GDB-10.1-GCCcore-10.2.0.eb, MPC-1.2.1-GCCcore-10.2.0.eb, ISL-0.23-GCCcore-10.2.0.eb --- .../g/GDB/GDB-10.1-GCCcore-10.2.0.eb | 44 +++++++++++++++++ .../i/ISL/ISL-0.23-GCCcore-10.2.0.eb | 22 +++++++++ .../m/MPC/MPC-1.2.1-GCCcore-10.2.0.eb | 34 +++++++++++++ .../t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb | 48 +++++++++++++++++++ 4 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ca0775a1e4 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '10.1' + +homepage = 'https://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['f82f1eceeec14a3afa2de8d9b0d3c91d5a3820e23e0a01bbb70ef9f0276b62c0'] + +builddependencies = [ + ('binutils', '2.35'), + ('texinfo', '6.7'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('expat', '2.2.9'), + ('Python', '3.8.6'), + ('ISL', '0.23'), + ('MPC', '1.2.1'), +] + +preconfigopts = "mkdir obj && cd obj && " +configure_cmd_prefix = '../' +prebuildopts = "cd obj && " +preinstallopts = prebuildopts + +configopts = '--with-system-zlib --with-system-readline --with-expat=$EBROOTEXPAT ' +configopts += '--with-python=$EBROOTPYTHON/bin/python --with-isl=$EBROOTISL --with-mpc=$EBROOTMPC ' +configopts += '--enable-tui --enable-plugins --disable-install-libbfd ' + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a746f49bac --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.23' + +homepage = 'http://isl.gforge.inria.fr/' +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GMP', '6.2.0')] +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..29b4a95e74 --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.2.1' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'] + +dependencies = [ + ('GMP', '6.2.0'), + ('MPFR', '4.1.0'), +] +builddependencies = [('binutils', '2.35')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c16f57a56e --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'texinfo' +version = '6.7' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [('binutils', '2.35')] + +osdependencies = ['texlive'] + +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" + +sanity_check_paths = { + 'files': [ + 'texmf/tex/texinfo/texinfo.tex', + 'bin/install-info', 'bin/makeinfo', 'bin/pdftexi2dvi', 'bin/pod2texi', 'bin/texi2pdf' + ], + 'dirs': ['bin', 'share', 'texmf'], +} + +moduleclass = 'devel' From 3fd2f6b098e12d53bb9290b5fb6cda67d8f23076 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 16 Feb 2021 17:56:45 +0100 Subject: [PATCH 0314/2365] Add checksum --- easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-10.2.0.eb index a746f49bac..0aac5d8b60 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.23-GCCcore-10.2.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['http://isl.gforge.inria.fr/'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d'] dependencies = [('GMP', '6.2.0')] builddependencies = [('binutils', '2.35')] From 84abd159c580585cd5e6bef4bf6093a45c2dcaf8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2021 18:04:57 +0100 Subject: [PATCH 0315/2365] adding easyconfigs: PyStan-2.19.1.1-intel-2020b.eb --- .../p/PyStan/PyStan-2.19.1.1-intel-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb new file mode 100644 index 0000000000..cf6cdc10a9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'PyStan' +version = '2.19.1.1' + +homepage = 'https://github.com/stan-dev/pystan' +description = """Python interface to Stan, a package for Bayesian inference + using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 45288780300f0bf45339ef82da3090c2f2235be7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 17 Feb 2021 09:06:11 +0100 Subject: [PATCH 0316/2365] Use makeinfo instead of texinfo --- .../m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb | 24 ++++++++++ .../t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb | 48 ------------------- 2 files changed, 24 insertions(+), 48 deletions(-) create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9af1d073ea --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.7' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb deleted file mode 100644 index c16f57a56e..0000000000 --- a/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exe Escobedo -# License:: -# -# Notes:: -## - -easyblock = 'ConfigureMake' - -name = 'texinfo' -version = '6.7' - -homepage = 'https://www.gnu.org/software/texinfo/' -description = """Texinfo is the official documentation format of the GNU project.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] - -builddependencies = [('binutils', '2.35')] - -osdependencies = ['texlive'] - -preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " - -# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency -modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} -modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" -modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" -modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" -modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" -modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" - -sanity_check_paths = { - 'files': [ - 'texmf/tex/texinfo/texinfo.tex', - 'bin/install-info', 'bin/makeinfo', 'bin/pdftexi2dvi', 'bin/pod2texi', 'bin/texi2pdf' - ], - 'dirs': ['bin', 'share', 'texmf'], -} - -moduleclass = 'devel' From eaa8902494853095affa167da8de1940debcc9a2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 17 Feb 2021 09:27:22 +0100 Subject: [PATCH 0317/2365] Update GDB EC to use makeinfo --- easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb index ca0775a1e4..ce54295778 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ checksums = ['f82f1eceeec14a3afa2de8d9b0d3c91d5a3820e23e0a01bbb70ef9f0276b62c0'] builddependencies = [ ('binutils', '2.35'), - ('texinfo', '6.7'), + ('makeinfo', '6.7'), ] dependencies = [ From ebbb137f44e2d37e2d5b293a5dd9cf4a4521e8b6 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Wed, 17 Feb 2021 11:18:17 +0100 Subject: [PATCH 0318/2365] {bio,devel}[foss/2020b,GCCcore-10.2.0,GCC-10.2.0] ABySS-2.2.5, sparsehash-2.0.4, VCFtools-0.1.16 --- .../a/ABySS/ABySS-2.2.5-foss-2020b.eb | 27 +++++++++++++++ .../sparsehash-2.0.4-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ .../v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb | 30 ++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb new file mode 100644 index 0000000000..b1ebe547c6 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '2.2.5' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['38e886f455074c76b32dd549e94cc345f46cb1d33ab11ad3e8e1f5214fc65521'] + +dependencies = [ + ('Boost', '1.74.0'), + ('sparsehash', '2.0.4'), + ('SQLite', '3.33.0'), +] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ce7e1010b2 --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Updated from previous easyconfig +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.4' + +homepage = 'https://github.com/sparsehash/sparsehash' +description = """ + An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! + The SparseHash library contains several hash-map implementations, including + implementations that optimize for space or speed. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8cd1a95827dfd8270927894eb77f62b4087735cbede953884647f16c521c7e58'] + +builddependencies = [ + ('binutils', '2.35'), +] + + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb new file mode 100644 index 0000000000..289ec97f00 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +dependencies = [ + ('Perl', '5.32.0'), + ('HTSlib', '1.11'), + ('zlib', '1.2.11'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' From 5684102b019183d4ec3c1084bae809a794c8a447 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 11:34:25 +0100 Subject: [PATCH 0319/2365] use https for UDUNITS fallback source URL --- .../easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb index 006876aac2..1ee9adeaf3 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ toolchainopts = {'pic': True} source_urls = [ 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/', - 'http://sources.easybuild.io/u/UDUNITS/', + 'https://sources.easybuild.io/u/UDUNITS/', ] sources = [SOURCELOWER_TAR_GZ] checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] From a71dd1f18b602c9a8fc6be6f9372640e17bba008 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Wed, 17 Feb 2021 11:37:55 +0100 Subject: [PATCH 0320/2365] {bio,devel}[foss/2020b] ABySS-2.2.5, sparsehash-2.0.4, VCFtools-0.1.16 - fix --- easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb index b1ebe547c6..e29efb36c8 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb @@ -9,7 +9,7 @@ description = """Assembly By Short Sequences - a de novo, parallel, paired-end s toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] +source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['38e886f455074c76b32dd549e94cc345f46cb1d33ab11ad3e8e1f5214fc65521'] From 06a915bfe8a66b750cb9145393569d117f118faa Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Wed, 17 Feb 2021 11:47:27 +0100 Subject: [PATCH 0321/2365] {bio,devel}[foss/2020b] ABySS-2.2.5, sparsehash-2.0.4, VCFtools-0.1.16 - fix 2 --- easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb index e29efb36c8..f201e60805 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'ABySS' version = '2.2.5' -homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss' description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" toolchain = {'name': 'foss', 'version': '2020b'} From a507a8a7381980895d51508e3b4cd712a867f98c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 13:49:01 +0100 Subject: [PATCH 0322/2365] {toolchain} iibff/2020b --- .../f/FFTW/FFTW-3.3.8-iimpi-2020b.eb | 26 +++++++++++ .../easyconfigs/h/HPL/HPL-2.3-iibff-2020b.eb | 21 +++++++++ easybuild/easyconfigs/i/iibff/iibff-2020b.eb | 32 ++++++++++++++ .../ScaLAPACK-2.1.0-iimpi-2020b-bf.eb | 44 +++++++++++++++++++ 4 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iimpi-2020b.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-iibff-2020b.eb create mode 100644 easybuild/easyconfigs/i/iibff/iibff-2020b.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iimpi-2020b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iimpi-2020b.eb new file mode 100644 index 0000000000..e9ebf6b3f2 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iimpi-2020b.eb @@ -0,0 +1,26 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +patches = ['FFTW-%(version)s_fix-icc-no-gcc.patch'] +checksums = [ + '6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303', # fftw-3.3.8.tar.gz + '1b3319b98a2ca4ead68290b3229385c0573e22749a5a2ffb49486a0bbb37dc1e', # FFTW-3.3.8_fix-icc-no-gcc.patch +] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-iibff-2020b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-iibff-2020b.eb new file mode 100644 index 0000000000..44e88d0c15 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-iibff-2020b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'iibff', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iibff/iibff-2020b.eb b/easybuild/easyconfigs/i/iibff/iibff-2020b.eb new file mode 100644 index 0000000000..9759ceacc9 --- /dev/null +++ b/easybuild/easyconfigs/i/iibff/iibff-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'Toolchain' + +name = 'iibff' +version = '2020b' + +homepage = '(none)' +description = 'GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPACK and FFTW.' + +toolchain = SYSTEM + +local_gccver = '10.2.0' +local_gcccore = ('GCCcore', local_gccver) + +local_comp_name = 'iccifort' +local_comp_version = '2020.4.304' +local_comp = (local_comp_name, local_comp_version) + +local_comp_mpi_tc_name = 'iimpi' +local_comp_mpi_tc = (local_comp_mpi_tc_name, version) + +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.35', '', local_gcccore), + ('iccifort', local_comp_version), + ('impi', '2019.9.304', '', local_comp), + ('BLIS', '0.8.0', '', local_gcccore), + ('libFLAME', '5.2.0', '', local_gcccore), + ('ScaLAPACK', '2.1.0', '-bf', local_comp_mpi_tc), + ('FFTW', '3.3.8', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb new file mode 100644 index 0000000000..33b69ea09a --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb @@ -0,0 +1,44 @@ +name = 'ScaLAPACK' +version = '2.1.0' +versionsuffix = '-bf' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6', # scalapack-2.1.0.tgz + 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('BLIS', '0.8.0'), + ('libFLAME', '5.2.0'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' +configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From 636b1b287dbdcee28dfc3f4524aca81ac14dcce7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 17 Feb 2021 15:15:45 +0100 Subject: [PATCH 0323/2365] Remove Pyver suffix --- ...-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb new file mode 100644 index 0000000000..7d4084ab69 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.21.1' +local_tf_version = '2.4.1' +versionsuffix = '-TensorFlow-%s' % local_tf_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('flatbuffers', '1.12.0'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('TensorFlow', local_tf_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('cloudpickle', '1.5.0', { + 'checksums': ['820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82'], + }), + ('horovod', version, { + 'checksums': ['874dd3ac469944464bb77e1a42296500d0028177183ad5ab5af8ec61a34a1ed7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From a0566276e59bfe91d400008f0e121c21c02468ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 15:25:41 +0100 Subject: [PATCH 0324/2365] {bio}[foss/2020b] SEPP v4.4.0, DendroPy v4.5.2 w/ Python 3.8.6 --- .../DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb | 44 +++++++++++++++++++ .../s/SEPP/SEPP-4.4.0-foss-2020b.eb | 42 ++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.4.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..482cdae8b9 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.5.2' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["sumtrees.py --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.4.0-foss-2020b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.4.0-foss-2020b.eb new file mode 100644 index 0000000000..7e693b99a6 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.4.0-foss-2020b.eb @@ -0,0 +1,42 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +name = 'SEPP' +version = '4.4.0' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['271cbac586fdbe27d6fc315f6e45b8ecb069c4531b94fe14ce2016ba87595e03'] + +dependencies = [ + ('Python', '3.8.6'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_abundance.py', 'run_sepp.py', 'run_tipp.py', + 'run_tipp_tool.py', 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From d1e489ebfcb48c9204c28d7bd4a787a55814ee1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 16:04:25 +0100 Subject: [PATCH 0325/2365] adding easyconfigs: MetaEuk-4-GCC-10.2.0.eb --- .../m/MetaEuk/MetaEuk-4-GCC-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.2.0.eb new file mode 100644 index 0000000000..16d2dcc3cc --- /dev/null +++ b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MetaEuk' +version = '4' +local_commit = 'a0f584d' + +homepage = 'https://metaeuk.soedinglab.org' +description = """MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic + metagenomic contigs.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/soedinglab/%(namelower)s/archive'] +sources = ['%%(version)s-%s.tar.gz' % local_commit] +checksums = ['d64eea5244bd1c73a8c229949b2e833ba77e530ea321d5bb1bdea13b759e6efd'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/metaeuk'], + 'dirs': [], +} + +sanity_check_commands = ["metaeuk --help"] + +moduleclass = 'bio' From b59876b45d75c0f6517961fa4f23f2150c1746f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 16:06:33 +0100 Subject: [PATCH 0326/2365] {bio}[foss/2020b] AUGUSTUS v3.4.0 + deps (BAMtools, BCFtools, SAMtools, lpsolve) --- .../a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb | 61 +++++++++++++++++++ .../b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb | 38 ++++++++++++ .../b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb | 19 ++++++ .../l/lpsolve/lpsolve-5.5.2.11-GCC-10.2.0.eb | 33 ++++++++++ .../s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb | 35 +++++++++++ 5 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb new file mode 100644 index 0000000000..79e747edac --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb @@ -0,0 +1,61 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.4.0' + +# HTTPS doesn't work +homepage = 'http://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'foss', 'version': '2020b'} + +# https://github.com/Gaius-Augustus/Augustus/archive +github_account = 'Gaius-Augustus' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch'] +checksums = [ + '2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8', # v3.4.0.tar.gz + '9e29770de3afe8827e35d0f93ffbdc3d41bd4df0563c01052fbb13176675c854', # AUGUSTUS-3.4.0_fix-hardcoding.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.74.0'), + ('GSL', '2.6'), + ('SAMtools', '1.11'), + ('HTSlib', '1.11'), # also provides tabix + ('BCFtools', '1.11'), + ('lpsolve', '5.5.2.11'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('BamTools', '2.5.1'), + ('SQLite', '3.33.0'), +] + +skipsteps = ['configure'] + +# run "make clean" to avoid using binaries included with the source tarball +prebuildopts = "make clean && " + +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" LINK.cc="$CXX" ' +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch', + 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} +sanity_check_commands = ['augustus --help'] + +modextrapaths = {'PATH': 'scripts'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb new file mode 100644 index 0000000000..17f091c140 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.11' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['3ceee47456ec481f34fa6c34beb6fe892b5b365933191132721fdf126e45a064'] + +dependencies = [ + ('zlib', '1.2.11'), + ('HTSlib', '1.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('GSL', '2.6'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['libexec/bcftools'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..df8599b794 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb @@ -0,0 +1,19 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.1' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc'] + +builddependencies = [('CMake', '3.18.4')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-10.2.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-10.2.0.eb new file mode 100644 index 0000000000..a4a64c04b9 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.11' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb new file mode 100644 index 0000000000..9fd7bf2d7a --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +## + +name = 'SAMtools' +version = '1.11' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['e283cebd6c1c49f0cf8a3ca4fa56e1d651496b4d2e42f80ab75991a9ece4e5b6'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.72.0'), +] + +moduleclass = 'bio' From 80c5f7f64480e2a4612f8a32bca7ea4b2a9da023 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 16:14:04 +0100 Subject: [PATCH 0327/2365] {bio}[foss/2020b] BUSCO v5.0.0 + HMMER v3.3.2 w/ Python 3.8.6 --- .../b/BUSCO/BUSCO-5.0.0-foss-2020b.eb | 54 +++++++++++++++ .../h/HMMER/HMMER-3.3.2-gompi-2020b.eb | 66 +++++++++++++++++++ 2 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb new file mode 100644 index 0000000000..b88e140a4d --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb @@ -0,0 +1,54 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'BUSCO' +version = '5.0.0' + +homepage = 'https://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2f4087b5385c5133966d5d33e060c46629949d3c5aca5d9e867b6d28c866858f'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for pandas + ('R', '4.0.3'), + ('Biopython', '1.78'), + ('BLAST+', '2.11.0'), + ('HMMER', '3.3.2'), + ('prodigal', '2.6.3'), + ('AUGUSTUS', '3.4.0'), + ('SEPP', '4.4.0'), + ('MetaEuk', '4'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/test_data %(installdir)s', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s', +] + +sanity_check_paths = { + 'files': ['bin/busco', 'bin/generate_plot.py'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages/busco'] +} + +sanity_check_commands = [ + "busco --help", + "busco -i %(installdir)s/test_data/bacteria/genome.fna --mode geno --out test_bacteria.out", + "busco -i %(installdir)s/test_data/eukaryota/genome.fna --mode geno --out test_eukaryota.out", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb new file mode 100644 index 0000000000..116dc59a97 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb @@ -0,0 +1,66 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] + +configopts = '--enable-mpi' + +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From e9357247cd697d0ba6df743f1b201f8f598187ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 16:17:37 +0100 Subject: [PATCH 0328/2365] add missing patch file for AUGUSTUS 3.4.0 --- easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb index 79e747edac..0a43f6938b 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb @@ -19,7 +19,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch'] checksums = [ '2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8', # v3.4.0.tar.gz - '9e29770de3afe8827e35d0f93ffbdc3d41bd4df0563c01052fbb13176675c854', # AUGUSTUS-3.4.0_fix-hardcoding.patch + 'e74023f28ee3e76590f4534d195c313b88b66a92ec779da184d30d056fc8e052', # AUGUSTUS-3.4.0_fix-hardcoding.patch ] dependencies = [ From 158ac255b0cd1bdfe22cb5284d80a65ac320b473 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 16:20:33 +0100 Subject: [PATCH 0329/2365] add Biopython 1.78 easyconfig using foss/2020b (dep for BUSCO 5.0.0) --- .../b/Biopython/Biopython-1.78-foss-2020b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb new file mode 100644 index 0000000000..e3d678f0ed --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.78' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From c49ca80cd7f49af690294c785e86e789976bce9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 16:29:46 +0100 Subject: [PATCH 0330/2365] adding easyconfigs: HMMER-3.3.2-gompi-2020b.eb --- .../h/HMMER/HMMER-3.3.2-gompi-2020b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb new file mode 100644 index 0000000000..116dc59a97 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb @@ -0,0 +1,66 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] + +configopts = '--enable-mpi' + +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From b907c06af10e2ac812392dfbbfc872af509b3815 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 16:30:31 +0100 Subject: [PATCH 0331/2365] adding easyconfigs: Biopython-1.78-foss-2020b.eb --- .../b/Biopython/Biopython-1.78-foss-2020b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb new file mode 100644 index 0000000000..e3d678f0ed --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.78' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From 1365a9060b2fac35a9c46a1ddaecd85314b52490 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 16:37:30 +0100 Subject: [PATCH 0332/2365] use https for homepage in AUGUSTUS 3.4.0 easyconfig --- easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb index 0a43f6938b..0377e4b9b7 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb @@ -6,8 +6,7 @@ easyblock = 'ConfigureMake' name = 'AUGUSTUS' version = '3.4.0' -# HTTPS doesn't work -homepage = 'http://bioinf.uni-greifswald.de/augustus/' +homepage = 'https://bioinf.uni-greifswald.de/augustus/' description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" toolchain = {'name': 'foss', 'version': '2020b'} From cd577707dc978d5edcb9ece46d73b167f10b6d76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 16:51:02 +0100 Subject: [PATCH 0333/2365] adding easyconfigs: prodigal-2.6.3-GCCcore-10.2.0.eb --- .../prodigal/prodigal-2.6.3-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2f72278b36 --- /dev/null +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Updated: Pavel Grochal (INUITS) +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.3' + +homepage = 'https://github.com/hyattpd/Prodigal/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] + +builddependencies = [('binutils', '2.35')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +sanity_check_commands = ["prodigal -h"] + +moduleclass = 'bio' From fc6c5b032c33c3d2824342e2491cf71c9b291e46 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Feb 2021 18:40:48 +0000 Subject: [PATCH 0334/2365] adding easyconfigs: gomkl-2020b.eb, HPL-2.3-gomkl-2020b.eb, imkl-2020.4.304-gompi-2020b.eb --- easybuild/easyconfigs/g/gomkl/gomkl-2020b.eb | 19 +++++++++ .../easyconfigs/h/HPL/HPL-2.3-gomkl-2020b.eb | 21 ++++++++++ .../i/imkl/imkl-2020.4.304-gompi-2020b.eb | 39 +++++++++++++++++++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2020b.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2020b.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2020b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2020b.eb new file mode 100644 index 0000000000..d2743a6546 --- /dev/null +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2020b.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gomkl' +version = '2020b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" + +toolchain = SYSTEM + +local_comp = ('GCC', '10.2.0') + +dependencies = [ + local_comp, + ('OpenMPI', '4.0.5', '', local_comp), + ('imkl', '2020.4.304', '', ('gompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2020b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2020b.eb new file mode 100644 index 0000000000..5d936a2b33 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2020b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gomkl', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb new file mode 100644 index 0000000000..d292d071b1 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.4.304' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' From a886a87d6875d9b61d1415a67d64a38366882961 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Feb 2021 18:51:00 +0000 Subject: [PATCH 0335/2365] updating easyconfig: HPL-2.3-gomkl-2020b.eb --- easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2020b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2020b.eb index 5d936a2b33..5e2c0185cc 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2020b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2020b.eb @@ -1,7 +1,7 @@ name = 'HPL' version = '2.3' -homepage = 'http://www.netlib.org/benchmark/hpl/' +homepage = 'https://www.netlib.org/benchmark/hpl/' description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" @@ -9,7 +9,7 @@ description = """HPL is a software package that solves a (random) dense linear s toolchain = {'name': 'gomkl', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] sources = [SOURCELOWER_TAR_GZ] # fix Make dependencies, so parallel build also works patches = ['HPL_parallel-make.patch'] From 204fdfd6af060a00de7325f4333189c7ab3b8255 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 20:18:07 +0100 Subject: [PATCH 0336/2365] update to 2021.1.2 version of Intel oneAPI compilers --- .../intel-compilers-2021.1.2.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb new file mode 100644 index 0000000000..f087116721 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb @@ -0,0 +1,40 @@ +name = 'intel-compilers' +version = '2021.1.2' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit/download.html +# installing 2021.1.2 patch release of Intel oneAPI compilers requires installing HPC Toolkit 2021.1.0 first +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17427/'], + 'filename': 'l_HPCKit_p_%(version_major_minor)s.0.2684_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17513/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.63_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17508/'], + 'filename': 'l_fortran-compiler_p_%(version)s.62_offline.sh', + }, +] +checksums = [ + '666b1002de3eab4b6f3770c42bcf708743ac74efeba4c05b0834095ef27a11b9', # l_HPCKit_p_2021.1.0.2684_offline.sh + '68d6cb638091990e578e358131c859f3bbbbfbf975c581fd0b4b4d36476d6f0a', # l_dpcpp-cpp-compiler_p_2021.1.2.63_offline.sh + '29345145268d08a59fa7eb6e58c7522768466dd98f6d9754540d1a0803596829', # l_fortran-compiler_p_2021.1.2.62_offline.sh +] + +local_gccver = '10.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.35', '', ('GCCcore', local_gccver)), +] + +# remove parts we don't want (it seems like the Intel installer doesn't really honor --components...) +postinstallcmds = ["rm -rf %(installdir)s/{conda_channel,mpi}"] + +moduleclass = 'compiler' From a95c8571259b36007fa31f08c9206cd66ea26ed8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2021 20:23:04 +0100 Subject: [PATCH 0337/2365] no need to install HPC Toolkit first, we only want the Intel oneAPI compilers anyway... --- .../i/intel-compilers/intel-compilers-2021.1.2.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb index f087116721..1c6c4860ff 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb @@ -7,12 +7,7 @@ description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit/download.html -# installing 2021.1.2 patch release of Intel oneAPI compilers requires installing HPC Toolkit 2021.1.0 first sources = [ - { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17427/'], - 'filename': 'l_HPCKit_p_%(version_major_minor)s.0.2684_offline.sh', - }, { 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17513/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.63_offline.sh', @@ -23,7 +18,6 @@ sources = [ }, ] checksums = [ - '666b1002de3eab4b6f3770c42bcf708743ac74efeba4c05b0834095ef27a11b9', # l_HPCKit_p_2021.1.0.2684_offline.sh '68d6cb638091990e578e358131c859f3bbbbfbf975c581fd0b4b4d36476d6f0a', # l_dpcpp-cpp-compiler_p_2021.1.2.63_offline.sh '29345145268d08a59fa7eb6e58c7522768466dd98f6d9754540d1a0803596829', # l_fortran-compiler_p_2021.1.2.62_offline.sh ] @@ -34,7 +28,4 @@ dependencies = [ ('binutils', '2.35', '', ('GCCcore', local_gccver)), ] -# remove parts we don't want (it seems like the Intel installer doesn't really honor --components...) -postinstallcmds = ["rm -rf %(installdir)s/{conda_channel,mpi}"] - moduleclass = 'compiler' From b8883634a48267169e8cd6804f4c463c8923f12c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 17 Feb 2021 22:55:44 +0000 Subject: [PATCH 0338/2365] Update patch for SHAPEIT4 4.2.0 and add sanity_check_command --- .../s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb new file mode 100644 index 0000000000..32fdf1c65d --- /dev/null +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb @@ -0,0 +1,44 @@ +easyblock = "MakeCp" + +name = 'SHAPEIT4' +version = '4.2.0' + +homepage = 'https://odelaneau.github.io/shapeit4/' +description = """ +SHAPEIT4 is a fast and accurate method for estimation of haplotypes +(aka phasing) for SNP array and high coverage sequencing data. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True, 'cstd': 'std=c++11'} + +github_account = 'odelaneau' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] +checksums = [ + '329aa920be49b085c96b420d4f42ade7ba92eae8a202ecb2f71ca32a61955588', # v4.2.0.tar.gz + '790b1b6631123f5777a70786a2b0b23bdcb7b3cd30e1b3e57bfe6d8e9d7283a0', # SHAPEIT4_4.2.0_use_EB_settings.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('Boost', '1.74.0'), + ('HTSlib', '1.11'), +] + +buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts ' +buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options' + +files_to_copy = [(['bin/shapeit4.2'], 'bin'), 'maps'] + +sanity_check_paths = { + 'files': ["bin/shapeit4.2"], + 'dirs': ['maps'] +} + +sanity_check_commands = ['shapeit4.2 --help'] + +moduleclass = 'bio' From 0aee8d4e563873494b73b28bf2e52cd8905d84ae Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 18 Feb 2021 08:33:49 +0100 Subject: [PATCH 0339/2365] adding easyconfigs: Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb, torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb --- .../Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ ...sion-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb | 34 ++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..712cf054a0 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '7.1.2' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.1.0'), + ('freetype', '2.10.3') +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..bbec243ce6 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'torchvision' +version = '0.8.2' +local_pytorch_version = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9a866c3c8feb23b3221ce261e6153fc65a98ce9ceaa71ccad017016945c178bf'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('PyTorch', local_pytorch_version), +] + +use_pip = True +download_dep_fail = True + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] +preinstallopts = 'export TORCH_CUDA_ARCH_LIST="%(cuda_cc_semicolon_sep)s" && ' + +sanity_pip_check = True + +moduleclass = 'vis' From 226b66a61308e9fb917736a1bbc618a7a04909e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2021 10:09:36 +0100 Subject: [PATCH 0340/2365] use better URL for version info of individual oneAPI components --- .../easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb index 1c6c4860ff..820a237e44 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb @@ -6,7 +6,7 @@ description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" toolchain = SYSTEM -# see https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit/download.html +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17513/'], From 3f5fadc8660371c70efacf9e49f1466970b1f803 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 18 Feb 2021 16:53:10 +0000 Subject: [PATCH 0341/2365] Update patch checksum --- easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb index 32fdf1c65d..9c801d1f6f 100644 --- a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] checksums = [ '329aa920be49b085c96b420d4f42ade7ba92eae8a202ecb2f71ca32a61955588', # v4.2.0.tar.gz - '790b1b6631123f5777a70786a2b0b23bdcb7b3cd30e1b3e57bfe6d8e9d7283a0', # SHAPEIT4_4.2.0_use_EB_settings.patch + '2d34bef954aa38dfe5b352dd44c0b8ccc778b430dbd4a81f14520eb5a1714cd8', # SHAPEIT4_4.2.0_use_EB_settings.patch ] dependencies = [ From 1c84f19b3dff71e7d893e0d85a6423338ef89037 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2021 19:58:12 +0100 Subject: [PATCH 0342/2365] fix impi 2021.1.1 version --- .../impi/impi-2021.1.1-intel-compilers-2021.1.2.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb diff --git a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb new file mode 100644 index 0000000000..9f36c8608a --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb @@ -0,0 +1,14 @@ +name = 'impi' +version = '2021.1.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2021.1.2'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17397/'] +sources = ['l_mpi_oneapi_p_%(version)s.76_offline.sh'] +checksums = ['8b7693a156c6fc6269637bef586a8fd3ea6610cac2aae4e7f48c1fbb601625fe'] + +moduleclass = 'compiler' From 826f6a70dcae4ceecbcfa7fe9df677e9b255b922 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2021 09:31:14 +0000 Subject: [PATCH 0343/2365] Fix lack of optimisation --- easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb index 9c801d1f6f..40dbf8ee9f 100644 --- a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] checksums = [ '329aa920be49b085c96b420d4f42ade7ba92eae8a202ecb2f71ca32a61955588', # v4.2.0.tar.gz - '2d34bef954aa38dfe5b352dd44c0b8ccc778b430dbd4a81f14520eb5a1714cd8', # SHAPEIT4_4.2.0_use_EB_settings.patch + 'ff68a0a3621c7b3d6f0ca8140774851659251d5cfee374f92a6b01683649775a', # SHAPEIT4_4.2.0_use_EB_settings.patch ] dependencies = [ From dd94b7d1f7f923276f7f376d5886c49107092c03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Feb 2021 14:03:33 +0100 Subject: [PATCH 0344/2365] add missing gnuplot dependency for OpenFOAM 8 with foss/2020b --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb index 58ae8e587c..5129ca3258 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb @@ -28,6 +28,7 @@ dependencies = [ ('SCOTCH', '6.1.0'), ('CGAL', '5.2'), ('ParaView', '5.8.1', '-mpi'), + ('gnuplot', '5.4.1'), ] builddependencies = [ From 4ea73d44ba71e63dda45641979337d6dfc88be0a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2021 17:29:05 +0000 Subject: [PATCH 0345/2365] Set CXXFLAGS and LDFLAG properly, using variables --- easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb index 40dbf8ee9f..f6996f172e 100644 --- a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb @@ -10,7 +10,7 @@ SHAPEIT4 is a fast and accurate method for estimation of haplotypes """ toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'opt': True, 'cstd': 'std=c++11'} +toolchainopts = {'opt': True, 'cstd': 'c++11'} github_account = 'odelaneau' source_urls = [GITHUB_SOURCE] @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] checksums = [ '329aa920be49b085c96b420d4f42ade7ba92eae8a202ecb2f71ca32a61955588', # v4.2.0.tar.gz - 'ff68a0a3621c7b3d6f0ca8140774851659251d5cfee374f92a6b01683649775a', # SHAPEIT4_4.2.0_use_EB_settings.patch + 'd666e5ec65ab0a77e5f72ed9a95a47ceedc98734c9cfdb9cd0b344e41516d3de', # SHAPEIT4_4.2.0_use_EB_settings.patch ] dependencies = [ From 130d4e4d3845d027ac23e932d26359eb24822c99 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2021 17:33:05 +0000 Subject: [PATCH 0346/2365] Set flags properly properly, using buildopts --- easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb index f6996f172e..00b01b7846 100644 --- a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] checksums = [ '329aa920be49b085c96b420d4f42ade7ba92eae8a202ecb2f71ca32a61955588', # v4.2.0.tar.gz - 'd666e5ec65ab0a77e5f72ed9a95a47ceedc98734c9cfdb9cd0b344e41516d3de', # SHAPEIT4_4.2.0_use_EB_settings.patch + '852c8fd32cd8dd2dbff82277074e4a86e45c296bf2ce75e6c8e598d9906472ce', # SHAPEIT4_4.2.0_use_EB_settings.patch ] dependencies = [ @@ -31,6 +31,7 @@ dependencies = [ buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts ' buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options' +buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS"' files_to_copy = [(['bin/shapeit4.2'], 'bin'), 'maps'] From 46f67dabae590fde8593ab4c478fe1decea9b7ba Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2021 18:01:42 +0000 Subject: [PATCH 0347/2365] Re-add patch explanation --- easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb index 00b01b7846..a590ddc67a 100644 --- a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] checksums = [ '329aa920be49b085c96b420d4f42ade7ba92eae8a202ecb2f71ca32a61955588', # v4.2.0.tar.gz - '852c8fd32cd8dd2dbff82277074e4a86e45c296bf2ce75e6c8e598d9906472ce', # SHAPEIT4_4.2.0_use_EB_settings.patch + 'c4a5a5d280463a7e39435239284702e0d13feb2eb10f902434874176c884516e', # SHAPEIT4_4.2.0_use_EB_settings.patch ] dependencies = [ From 920a659bf894a59fa57ce7f0f9a70a14dcc66ada Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2021 18:28:31 +0000 Subject: [PATCH 0348/2365] Add missing spaces in buildopts --- easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb index a590ddc67a..738044390d 100644 --- a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb @@ -30,8 +30,8 @@ dependencies = [ ] buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts ' -buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options' -buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS"' +buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options ' +buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS" ' files_to_copy = [(['bin/shapeit4.2'], 'bin'), 'maps'] From 60a644ca168d677447f036bdf5c0da144e3728e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 20 Feb 2021 11:47:13 +0100 Subject: [PATCH 0349/2365] fix checksum for patch file in PyTorch 1.7.1 easyconfig using foss/2020b --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index 7b29d606cb..d270180023 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -286,7 +286,7 @@ checksums = [ '97febb91ae2d051db9541e1e4c5924c77555ab73ee49ad7d62ef3e4714110297', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch # PyTorch-1.7.0_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch ] From afca39320967cdea5a5384f81c1c4ba5c4690fa4 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 20 Feb 2021 15:31:04 +0100 Subject: [PATCH 0350/2365] rename SNAP to SNAP-HMM and update easyconfig --- .../SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb new file mode 100644 index 0000000000..6767efd60c --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'SNAP-HMM' +version = '20190603' +_commit = 'daf76ba' + +homepage = 'https://korflab.github.io/' +description = """SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. +SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/KorfLab/SNAP/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = ['%(name)s-%(version)s_makefile_correction.patch'] +checksums = [ + '8222e49160c9c1199664c29f9c2490f57243c896f23676dea846d34129a1638f', # 20190603.tar.gz + 'd518750d4cf01278ba5403ab5717cfcd65b75b5a7c6573ae140f1cdb56b9e655', # SNAP-HMM-20190603_makefile_correction.patch +] + +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' + +files_to_copy = [ + (['hmm-assembler.pl', 'zff2gff3.pl', 'fathom', 'forge', 'snap', 'Zoe/zoe-loop'], 'bin'), + 'DNA', + 'HMM', + 'Zoe' +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/forge', 'bin/zoe-loop'], + 'dirs': ['Zoe'], +} + +sanity_check_commands = [ + 'snap 2>&1 | grep "^usage:"', + 'zoe-loop | grep "^usage:"', +] + +modextrapaths = {'ZOE': 'Zoe'} + +moduleclass = 'bio' From 7ed2f977e1c24126acbc6d3bc84df0dd5c3b43ec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 Feb 2021 01:34:14 +0200 Subject: [PATCH 0351/2365] Fix errors --- .../p/PyAMG/PyAMG-4.0.0-foss-2020b.eb | 24 +++++++++++++++++++ .../p/PyAMG/PyAMG-4.0.0-intel-2020b.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb new file mode 100644 index 0000000000..d3cadf55f0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'PyAMG' +version = '4.0.0' + +homepage = 'https://pyamg.github.io' +description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ceb38ffd86e29774e759486f2961599c8ed847459c68727493cadeaf115a38a'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +options = {'modulename': 'pyamg'} + +use_pip = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb new file mode 100644 index 0000000000..310dc221a6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'PyAMG' +version = '4.0.0' + +homepage = 'https://pyamg.github.io' +description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ceb38ffd86e29774e759486f2961599c8ed847459c68727493cadeaf115a38a'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +options = {'modulename': 'pyamg'} + +use_pip = True + +moduleclass = 'math' From eba71e9f7535eedf25e89a6892cfb51d68d93176 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 22 Feb 2021 10:55:18 +0200 Subject: [PATCH 0352/2365] Drop duplicate, add download_dep_fail --- easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb | 1 + easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb index d3cadf55f0..f61b83a63f 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb @@ -20,5 +20,6 @@ dependencies = [ options = {'modulename': 'pyamg'} use_pip = True +download_dep_fail = True moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb index 310dc221a6..4a5fb84393 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb @@ -20,5 +20,6 @@ dependencies = [ options = {'modulename': 'pyamg'} use_pip = True +download_dep_fail = True moduleclass = 'math' From 3154e58a6c62dd6868258fe16a34e05c0a464e22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 22 Feb 2021 11:07:59 +0200 Subject: [PATCH 0353/2365] Add sanity_pip_check --- easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb | 1 + easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb index f61b83a63f..c472741ff9 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb @@ -21,5 +21,6 @@ options = {'modulename': 'pyamg'} use_pip = True download_dep_fail = True +sanity_pip_check = True moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb index 4a5fb84393..94bfa61bf5 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb @@ -21,5 +21,6 @@ options = {'modulename': 'pyamg'} use_pip = True download_dep_fail = True +sanity_pip_check = True moduleclass = 'math' From 784a90ce6ce90b73ec52201a7e003ab6cc0cc4e9 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 22 Feb 2021 10:53:20 +0000 Subject: [PATCH 0354/2365] adding easyconfigs: TensorFlow-2.4.1-foss-2020b.eb --- .../TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 229 ++++++++++++++++++ 1 file changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb new file mode 100644 index 0000000000..bc90bd7090 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -0,0 +1,229 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.4.1' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('Python', '3.8.6'), + # Next 2 are for h5py + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} +use_pip = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + # TF 2.4 needs h5py 2.10, later versions allow 3.x + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch + ], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + }), + ('Markdown', '3.3.3', { + 'checksums': ['5d9f2b5ca24bc4c7a390d22323ca4bad200368612b5aaa7796babf971d2b2f18'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7', { + 'checksums': ['69805d6b69f56eb05b62daea3a7dbd7aa44324ad1306445e05da8060232d00f4'], + }), + ('cachetools', '4.2.0', { + 'checksums': ['3796e1de094f0eaca982441c92ce96c68c89cced4cd97721ab297ea4b16db90e'], + }), + ('google-auth', '1.24.0', { + 'modulename': 'google.auth', + 'checksums': ['0b0e026b412a0ad096e753907559e4bdb180d9ba9f68dd9036164db4fdc4ad2e'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.2', { + 'checksums': ['65b65bc39ad8cab15039b35e5898455d3d66296d0584d96fe0e79d67d04c51d9'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('absl-py', '0.10.0', { + 'modulename': 'absl', + 'checksums': ['b20f504a7871a580be5268a18fbad48af4203df5d33dbc9272426cb806245a45'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.32.0', { + 'modulename': 'grpc', + 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard', version, { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['7b8c53c396069b618f6f276ec94fc45d17e3282d668979216e5d30be472115e4'], + }), + ('tensorboard-plugin-wit', '1.8.0', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard-plugin-profile', '2.4.0', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', '2.4.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['5b7b7bf2debe19a8794adacc43e8ba6459daa4efaf54d3302623994a359b17f0'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.3.1_disable-float128-on-power.patch', + 'TensorFlow-2.4.0_add-default-shell-env.patch', + 'TensorFlow-2.4.0_fix-eigen-on-power.patch', + 'TensorFlow-2.4.0_downgrade-required-versions.patch', + 'TensorFlow-2.4.0_add-protobuf-deps.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', + 'TensorFlow-2.4.0_fix-absl-on-power.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Requires access to CUPTI (privileged!) + '-//tensorflow/core/profiler/internal/gpu:device_tracer_test', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Invalid alignment: https://github.com/tensorflow/tensorflow/issues/46460 + '-//tensorflow/core/kernels:sparse_matmul_op_test', + '-//tensorflow/core/kernels:sparse_matmul_op_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'with_xla': True, + 'checksums': [ + 'f681331f8fc0800883761c7709d13cda11942d4ad5ff9f44ad855e9dc78387e0', # v2.4.1.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + # TensorFlow-2.3.1_disable-float128-on-power.patch + 'a8369e92559cce4566ff831e615420fd98b83106c73ee3af7fbd5335c5fcd569', + # TensorFlow-2.4.0_add-default-shell-env.patch + '033a870b458406f4cabab878c4183cdf54cd7627648f24c8cc9f1964ff24d292', + # TensorFlow-2.4.0_fix-eigen-on-power.patch + '761303a9d5a0e78b833610891194e497a45f1218cfcb0ac4854a0d31d3156c2b', + # TensorFlow-2.4.0_downgrade-required-versions.patch + 'ac8f53662ad0bb660089c17bb433faf1ce3c2238234a2c3be7d92c8e02c1a8d6', + # TensorFlow-2.4.0_add-protobuf-deps.patch + '0ae2f4f1f1dc5b85f61edbe8a4a91dcffd5cf7588fa46c6a143455e4bc41a64e', + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_add-missing-llvm-deps.patch + 'ce8c41e75f9854e547d03de99ae72cf41afa967b20439e864bc4af3dd4f565c7', + # TensorFlow-2.4.0_fix-absl-on-power.patch + 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch + 'f384cd97e004673ae530b6e5cc826f8fddb46646991f1a228fc07b2aac87ee80', + ], + }), +] + +moduleclass = 'lib' From dae923281fa41409b3b9d64cd337fb007f453413 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2021 16:42:12 +0100 Subject: [PATCH 0355/2365] {compiler}[GCCcore/10.2.0] Clang v11.0.1 --- .../c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb | 71 +++++++++++++++++++ .../z/Z3/Z3-4.8.10-GCCcore-10.2.0.eb | 33 +++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6a528a4897 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,71 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '11.0.1' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', + 'clang-tools-extra-%(version)s.src.tar.xz', +] +checksums = [ + 'ccd87c254b6aebc5077e4e6977d08d4be888e7eb672c6630a26a15d58b59b528', # llvm-11.0.1.src.tar.xz + '73f572c2eefc5a155e01bcd84815751d722a4d3925f53c144acfb93eeb274b4d', # clang-11.0.1.src.tar.xz + '087be3f1116e861cd969c9b0b0903c27028b52eaf45157276f50a9c2500687fc', # compiler-rt-11.0.1.src.tar.xz + '08dfce0e7b168d621f6c64b6b60a25300acb9337345ab0014c4f64a053c5b9ea', # polly-11.0.1.src.tar.xz + '4d15a21b90e7de2f01296503f6e4b16c50197fbe9c82e7e81f9c07e28bd82ca7', # openmp-11.0.1.src.tar.xz + '60ba0da01a391078dcc437fee629f3bf7e30e06467a3a060b4a2a3aa661308b7', # lld-11.0.1.src.tar.xz + '9fd5f669621ffea88a2b93e3d99f3a958b5defb954f71bf754709b63275f5e3d', # libcxx-11.0.1.src.tar.xz + '4a697056a5c08621a8380dcaf3836525835aa76b3008d9e8f27abf9270bf683f', # libcxxabi-11.0.1.src.tar.xz + '2ca211dd8cc396a919709a9bc35af11b7d425df0c608d85ba6629242893516c9', # clang-tools-extra-11.0.1.src.tar.xz +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.35'), + ('hwloc', '2.2.0'), + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), + ('GMP', '6.2.0'), + ('Z3', '4.8.10'), +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Python', '3.8.6'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True +build_extra_clang_tools = True + +skip_all_tests = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..90cab60b94 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Z3' +version = '4.8.10' + +homepage = 'https://github.com/Z3Prover/z3' +description = """ + Z3 is a theorem prover from Microsoft Research. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/Z3Prover/z3/archive/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['12cce6392b613d3133909ce7f93985d2470f0d00138837de06cf7eb2992886b4'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('GMP', '6.2.0'), +] + +configopts = '-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON ' + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From 4053de02144c94cf5c4ae69017828db5354d6ce0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 22 Feb 2021 10:53:20 +0000 Subject: [PATCH 0356/2365] adding easyconfigs: TensorFlow-2.4.1-foss-2020b.eb --- .../TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 229 ++++++++++++++++++ 1 file changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb new file mode 100644 index 0000000000..bc90bd7090 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -0,0 +1,229 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.4.1' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('Python', '3.8.6'), + # Next 2 are for h5py + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} +use_pip = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + # TF 2.4 needs h5py 2.10, later versions allow 3.x + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch + ], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + }), + ('Markdown', '3.3.3', { + 'checksums': ['5d9f2b5ca24bc4c7a390d22323ca4bad200368612b5aaa7796babf971d2b2f18'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7', { + 'checksums': ['69805d6b69f56eb05b62daea3a7dbd7aa44324ad1306445e05da8060232d00f4'], + }), + ('cachetools', '4.2.0', { + 'checksums': ['3796e1de094f0eaca982441c92ce96c68c89cced4cd97721ab297ea4b16db90e'], + }), + ('google-auth', '1.24.0', { + 'modulename': 'google.auth', + 'checksums': ['0b0e026b412a0ad096e753907559e4bdb180d9ba9f68dd9036164db4fdc4ad2e'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.2', { + 'checksums': ['65b65bc39ad8cab15039b35e5898455d3d66296d0584d96fe0e79d67d04c51d9'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('absl-py', '0.10.0', { + 'modulename': 'absl', + 'checksums': ['b20f504a7871a580be5268a18fbad48af4203df5d33dbc9272426cb806245a45'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.32.0', { + 'modulename': 'grpc', + 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard', version, { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['7b8c53c396069b618f6f276ec94fc45d17e3282d668979216e5d30be472115e4'], + }), + ('tensorboard-plugin-wit', '1.8.0', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard-plugin-profile', '2.4.0', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', '2.4.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['5b7b7bf2debe19a8794adacc43e8ba6459daa4efaf54d3302623994a359b17f0'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.3.1_disable-float128-on-power.patch', + 'TensorFlow-2.4.0_add-default-shell-env.patch', + 'TensorFlow-2.4.0_fix-eigen-on-power.patch', + 'TensorFlow-2.4.0_downgrade-required-versions.patch', + 'TensorFlow-2.4.0_add-protobuf-deps.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', + 'TensorFlow-2.4.0_fix-absl-on-power.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Requires access to CUPTI (privileged!) + '-//tensorflow/core/profiler/internal/gpu:device_tracer_test', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Invalid alignment: https://github.com/tensorflow/tensorflow/issues/46460 + '-//tensorflow/core/kernels:sparse_matmul_op_test', + '-//tensorflow/core/kernels:sparse_matmul_op_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'with_xla': True, + 'checksums': [ + 'f681331f8fc0800883761c7709d13cda11942d4ad5ff9f44ad855e9dc78387e0', # v2.4.1.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + # TensorFlow-2.3.1_disable-float128-on-power.patch + 'a8369e92559cce4566ff831e615420fd98b83106c73ee3af7fbd5335c5fcd569', + # TensorFlow-2.4.0_add-default-shell-env.patch + '033a870b458406f4cabab878c4183cdf54cd7627648f24c8cc9f1964ff24d292', + # TensorFlow-2.4.0_fix-eigen-on-power.patch + '761303a9d5a0e78b833610891194e497a45f1218cfcb0ac4854a0d31d3156c2b', + # TensorFlow-2.4.0_downgrade-required-versions.patch + 'ac8f53662ad0bb660089c17bb433faf1ce3c2238234a2c3be7d92c8e02c1a8d6', + # TensorFlow-2.4.0_add-protobuf-deps.patch + '0ae2f4f1f1dc5b85f61edbe8a4a91dcffd5cf7588fa46c6a143455e4bc41a64e', + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_add-missing-llvm-deps.patch + 'ce8c41e75f9854e547d03de99ae72cf41afa967b20439e864bc4af3dd4f565c7', + # TensorFlow-2.4.0_fix-absl-on-power.patch + 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch + 'f384cd97e004673ae530b6e5cc826f8fddb46646991f1a228fc07b2aac87ee80', + ], + }), +] + +moduleclass = 'lib' From b885b0d15fcf5bec2c9dd9f3182e6d04dcad7950 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2021 17:00:03 +0100 Subject: [PATCH 0357/2365] {vis}[foss/2020b] PyOpenCL v2021.1.2 + pocl v1.6 w/ Python 3.8.6 --- .../PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb | 35 ++++++++++++++++ .../easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb | 40 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb new file mode 100644 index 0000000000..ba1007e107 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2021.1.2' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('pocl', '1.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.1', { + 'checksums': ['073ae22a0ae946e2db97164f2eb24a599cd3a51430384aa40859dffd73056c40'], + }), + ('pyopencl', version, { + 'checksums': ['18871bc80c5a94869521189cf2c04d72c88367a441a9a033f72f66792ac33d29'], + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb new file mode 100644 index 0000000000..7f2991f31f --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '1.6' + +homepage = 'https://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b0a4c0c056371b6f0db726b88fbb76bbee94948fb2abd4dbc8d958f7c42f766c'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Clang', '11.0.1'), + ('hwloc', '2.2.0'), + ('libtool', '2.4.6'), + ('libxml2', '2.9.10'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 74f1ab5bdbc5728093d4d7e64d55fd72dbab4048 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2021 17:02:17 +0100 Subject: [PATCH 0358/2365] adding easyconfigs: pymca-5.6.3-foss-2020b.eb, silx-0.14.0-foss-2020b.eb, PyOpenGL-3.1.5-GCCcore-10.2.0.eb, FabIO-0.11.0-foss-2020b.eb, Qtconsole-5.0.2-foss-2020b.eb, QtPy-1.9.0-GCCcore-10.2.0.eb --- .../f/FabIO/FabIO-0.11.0-foss-2020b.eb | 27 ++++++++++++ .../PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb | 43 +++++++++++++++++++ .../p/pymca/pymca-5.6.3-foss-2020b.eb | 39 +++++++++++++++++ .../q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb | 27 ++++++++++++ .../s/silx/silx-0.14.0-foss-2020b.eb | 43 +++++++++++++++++++ 5 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pymca/pymca-5.6.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb new file mode 100644 index 0000000000..56e8729639 --- /dev/null +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'FabIO' +version = '0.11.0' + +homepage = 'http://www.silx.org' +description = """FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. +FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), +for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers +(as a python dictionary) and datasets (as a numpy ndarray of integers or floats).""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1d2fcf58006c82548a16004e607d4518613d49e4a2f02a3797703eee2b39c6d8'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f51c02e2fa --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'PyOpenGL' +version = '3.1.5' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4107ba0d0390da5766a08c242cf0cf3404c377ed293c5f6d701e457c57ba3424'] + +builddependencies = [ + ('binutils', '2.35'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('Mesa', '20.2.1'), + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'OpenGL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pymca/pymca-5.6.3-foss-2020b.eb b/easybuild/easyconfigs/p/pymca/pymca-5.6.3-foss-2020b.eb new file mode 100644 index 0000000000..a36cfe17e6 --- /dev/null +++ b/easybuild/easyconfigs/p/pymca/pymca-5.6.3-foss-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'pymca' +version = '5.6.3' + +github_account = 'vasole' +homepage = "https://github.com/%(github_account)s/pymca" +description = """The PyMca X-Ray Fluorescence Toolkit, including PyMca5 and fisx.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('matplotlib', '3.3.3'), + ('PyQt5', '5.15.1'), + ('silx', '0.14.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = { + 'source_urls': [GITHUB_SOURCE], + 'sources': ['v%(version)s.tar.gz'], +} + +exts_list = [ + ('fisx', '1.2.0', { + 'checksums': ['868642045725552126d43331cdec7d7a6a85251d54011b4a0360fc90b02041e4'], + }), + (name, version, { + 'checksums': ['36b37f51a550b1262346e853ec8d3f1e8dd45adfc1a80e3626dc35e197eadb8c'], + 'modulename': 'PyMca5', + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6dd7277e0d --- /dev/null +++ b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'QtPy' +version = '1.9.0' + +homepage = "https://github.com/spyder-ide/qtpy" +description = """QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. +It provides support for PyQt5, PyQt4, PySide2 and PySide.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2db72c44b55d0fe1407be8fba35c838ad0d6d3bb81f23007886dc1fc0f459c8d'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('PyQt5', '5.15.1') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb new file mode 100644 index 0000000000..350f3a7677 --- /dev/null +++ b/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'silx' +version = '0.14.0' + +homepage = "http://www.silx.org/" +description = """The silx project provides a collection of Python packages to support the +development of data assessment, reduction and analysis applications at synchrotron radiation facilities.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('PyOpenGL', '3.1.5'), + ('matplotlib', '3.3.3'), + ('Mako', '1.1.3'), + ('Pillow', '8.0.1'), + ('FabIO', '0.11.0'), + ('Qtconsole', '5.0.2'), + ('PyOpenCL', '2021.1.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('hdf5plugin', '2.3.1', { + 'checksums': ['2f6d886012c37bf7e8e002173dd6b16e6879b8e0e9f7d2f2ef9f79db97ed28d2'], + }), + (name, version, { + 'checksums': ['17c595fe18c9eb3403a9d1f0ee6ea7b523607043c46c944573ecf406f6997866'], + }), +] + +modextrapaths = { + 'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins', +} + +moduleclass = 'vis' From ee87ed71e8224d7bf6e02161864d2f88b3bd5eab Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Mon, 22 Feb 2021 17:06:11 +0100 Subject: [PATCH 0359/2365] Update ABySS-2.2.5-foss-2020b.eb add deprecated-copy option --- easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb index f201e60805..71ce82f694 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb @@ -19,6 +19,8 @@ dependencies = [ ('SQLite', '3.33.0'), ] +configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error=deprecated-copy"' + sanity_check_paths = { 'files': ["bin/ABYSS", "bin/ABYSS-P"], 'dirs': [] From 01769062419ad0456a285be1bbf1401d3237cd27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2021 17:43:19 +0100 Subject: [PATCH 0360/2365] {bio}[gompi/2020b] HISAT2 v2.2.1, NGS v2.10.9, ncbi-vdb v2.10.9 --- .../f/file/file-5.39-GCCcore-10.2.0.eb | 33 ++++++++++++ .../h/HISAT2/HISAT2-2.2.1-gompi-2020b.eb | 52 +++++++++++++++++++ .../n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb | 45 ++++++++++++++++ .../n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb | 49 +++++++++++++++++ 4 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb diff --git a/easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1e5eec58ab --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.39' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f05d286a76d9556243d0cb05814929c2ecf3a5ba07963f8f70bfaaa70517fad1'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2020b.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2020b.eb new file mode 100644 index 0000000000..71d572cce9 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2020b.eb @@ -0,0 +1,52 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +# 2.2.1 - changes from Adam Huffman +## + +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.2.1' + +homepage = 'https://daehwankimlab.github.io/hisat2' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +sources = [{ + 'source_urls': ['https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi'], + 'download_filename': 'download', + 'filename': '%(namelower)s-%(version)s-source.zip', +}] +checksums = ['48e933330d4d8470d2b3dfe7ec3918f2e98a75f7381891e23b7df1fb4f135eb1'] + +dependencies = [ + ('NGS', '2.10.9'), + ('ncbi-vdb', '2.10.9'), +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +local_executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l', 'hisat2-repeat', 'extract_exons.py', + 'extract_splice_sites.py', 'hisat2_extract_exons.py', 'hisat2_extract_snps_haplotypes_UCSC.py', + 'hisat2_extract_snps_haplotypes_VCF.py', 'hisat2_extract_splice_sites.py', + 'hisat2_read_statistics.py', 'hisat2_simulate_reads.py'] +files_to_copy = [(local_executables, 'bin'), 'scripts', 'example'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': ['scripts', 'example'], +} + +sanity_check_commands = ["hisat2 --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3ca4af87ce --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'NGS' +version = '2.10.9' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups +produced from Next Generation Sequencing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), + ('Perl', '5.32.0'), +] + +dependencies = [('Java', '11', '', True)] + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://github.com/ncbi/ngs/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['1372695af5ac2599c9dad0b8cdce857c95c7827ff831a6709343276a29438b1e'], +} + +components = [ + ('NGS-SDK', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), + ('NGS-Java', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), +] + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb new file mode 100644 index 0000000000..f46954badf --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.10.9' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch'] +checksums = [ + '3707f81412dbf6ce2b29d3e65e364116c86acc534543e5a084cf8a666b81960d', # ncbi-vdb-2.10.9.tar.gz + 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch +] + +builddependencies = [('Perl', '5.32.0')] + +dependencies = [ + ('NGS', '2.10.9'), + ('file', '5.39'), # provides libmagic + ('HDF5', '1.10.7'), + ('libxml2', '2.9.10'), + ('bzip2', '1.0.8'), +] + +# add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl &&" + +configopts = "--build-prefix=%(builddir)s " # change default build directory +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS/jar/ngs-java.jar " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +# replace hardcoded optimization flags with EB settings +prebuildopts = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + + [('lib/libncbi-%s.%s' % (l, e), 'lib64/libncbi-%s.%s' % (l, e)) + for l in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' From ea389c7ccdb0b8c8f6baece81ce30cc521fa12a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2021 18:45:58 +0100 Subject: [PATCH 0361/2365] adding easyconfigs: DIAMOND-2.0.7-GCC-10.2.0.eb --- .../d/DIAMOND/DIAMOND-2.0.7-GCC-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.7-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.7-GCC-10.2.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.7-GCC-10.2.0.eb new file mode 100644 index 0000000000..e8a87219c1 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.7-GCC-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.0.7' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/bbuchfink/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ece969b38620e3540e8510496212149030a9918bd32f7f68aee628b788acb3e6'] + +separate_build_dir = True + +builddependencies = [ + ('CMake', '3.18.4') +] +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["diamond help"] + +moduleclass = 'bio' From b0149a26474a60d4ce4b8d63bc8a9460a0f2d404 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2021 18:50:58 +0100 Subject: [PATCH 0362/2365] adding easyconfigs: CD-HIT-4.8.1-GCC-10.2.0.eb --- .../c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..4783f6bad6 --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.32.0'), + ('zlib', '1.2.11'), +] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + +moduleclass = 'bio' From f0befbf88c0ae3faaabef412848a6f68d1a1ceed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2021 19:40:50 +0100 Subject: [PATCH 0363/2365] adding easyconfigs: Ruby-2.7.2-GCCcore-10.2.0.eb --- .../r/Ruby/Ruby-2.7.2-GCCcore-10.2.0.eb | 164 ++++++++++++++++++ 1 file changed, 164 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.7.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.7.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.7.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c82b949e90 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.7.2-GCCcore-10.2.0.eb @@ -0,0 +1,164 @@ +name = 'Ruby' +version = '2.7.2' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6e5706d0d4ee4e1e2f883db9d768586b4d06567debea353c796ec45e8321c3d4'] + +builddependencies = [('binutils', '2.35')] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# !! order of packages is important !! +# some packages have dependencies with minimum and maximum version requirements +# each version is picked as high as possible to fullfill all requirements +# packages updated on 22 Feb 2021 +exts_list = [ + ('ffi', '1.14.2', { + 'checksums': ['7dce3fe0f047a6f774d141d4667c9d23ee28c8dc72fbef6194dca398808f0f96'], + }), + ('childprocess', '4.0.0', { + 'checksums': ['72bc4c3e63b88d29e5faebb981e809562ba643c1939b46b465294447451b0d22'], + }), + ('json', '2.5.1', { + 'checksums': ['918d8c41dacb7cfdbe0c7bbd6014a5372f0cf1c454ca150e9f4010fe80cc3153'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.20.2', { + 'checksums': ['3b42e282071c72c6a1e9b3f3a5ff1b2f37e38b78d1adeb8dcffcd9604fa198b2'], + }), + ('arr-pm', '0.0.10', { + 'checksums': ['0fa2d425a84eeeaf8f95268568e826723b41aeefa14511d1f0ed1368c30bdd1f'], + }), + ('clamp', '1.3.2', { + 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], + }), + ('multipart-post', '2.1.1', { + 'checksums': ['d2dd7aa957650e0d99e0513cd388401b069f09528441b87d884609c8e94ffcfd'], + }), + ('ruby2_keywords', '0.0.4', { + 'checksums': ['3ae3189c2e1d2f60204dcceedf890ff49dd28979771e2576016a3ee73b668e97'], + }), + ('faraday-net_http', '1.0.1', { + 'checksums': ['3245ce406ebb77b40e17a77bfa66191dda04be2fd4e13a78d8a4305854d328ba'], + }), + ('faraday', '1.3.0', { + 'checksums': ['7f06817ba823ddeabf4dd85ca5e0f63e234527f564a03f09f6c7127951d3bac2'], + }), + ('faraday_middleware', '1.0.0', { + 'checksums': ['19e808539681bbf2e65df30dfbe27bb402bde916a1dceb4c7496dbe8de14334a'], + }), + ('highline', '2.0.3', { + 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.2.3', { + 'checksums': ['8e5bf44b6bfa96f5c94a5c30ae2447fce3dbcc0828a855a6c513fdb015a133e2'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.15.0', { + 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], + }), + ('public_suffix', '4.0.6', { + 'checksums': ['a99967c7b2d1d2eb00e1142e60de06a1a6471e82af574b330e9af375e87c0cf7'], + }), + ('addressable', '2.7.0', { + 'checksums': ['5e9b62fe1239091ea9b2893cd00ffe1bcbdd9371f4e1d35fac595c98c5856cbb'], + }), + ('concurrent-ruby', '1.1.8', { + 'checksums': ['e35169e8e01c33cddc9d322e4e793a9bc8c3c00c967d206d17457e0d301f2257'], + }), + ('i18n', '1.8.9', { + 'checksums': ['62a877ff6b5fdb4c20ca614c6bfcd6abd7b426d883069e59ce41a6744758e622'], + }), + ('minitest', '5.14.3', { + 'checksums': ['b2f80910d5ae04615c1f94645882b87cf22c17123c0ebd0e4cd8e8867883f246'], + }), + ('thread_safe', '0.3.6', { + 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], + }), + ('tzinfo', '1.2.9', { + 'checksums': ['725b865cc72ac00ef21f1413fe55e01400dfb95f6e7317c45848a3110cc4987f'], + }), + ('zeitwerk', '2.4.2', { + 'checksums': ['f4d6279b0ef0cb35c9e1bddbcecd6b148df82f1cf7b8023ac03d6625f567869c'], + }), + ('activesupport', '5.2.4.5', { + 'checksums': ['8c25759e6c5df1de673e9bfc35e42f4c5e021d47a8dde103a00f17f1467ee43a'], + }), + ('gh', '0.18.0', { + 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], + }), + ('launchy', '2.5.0', { + 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], + }), + ('ethon', '0.12.0', { + 'checksums': ['e99d3095e89f82c5a7e63d9261ddf4a21f28ae5d12a9d3abaa6920cce6cbef3d'], + }), + ('typhoeus', '1.4.0', { + 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], + }), + ('websocket', '1.2.9', { + 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.4.4', { + 'checksums': ['bf3a658875f70c1467fe7a3b302b795f074c84b28db6e4a2bd6b1ad6d12a2255'], + }), + ('rspec-support', '3.10.2', { + 'checksums': ['74315f89069fbaf2a710e2117340373b77ee45eceb026de87e0cad9dd5154596'], + }), + ('rspec-mocks', '3.10.2', { + 'checksums': ['93fc76e312c3d19cacc1cb2eb64bf82731de2e216295cf2b4d0ce31ba77923b4'], + }), + ('rspec-expectations', '3.10.1', { + 'checksums': ['27acf5d5df13f8cc8f7158001ebf572513bcec3d45404ba76e0a8998895ce9eb'], + }), + ('rspec-core', '3.10.1', { + 'checksums': ['ac9abdc9577a3a34e9e92815603da8343931055ab4fba1c2a49de6dd3b749673'], + }), + ('rspec', '3.10.0', { + 'checksums': ['b870b43d49ae4a4e063b94976d2742b0854ec10458c425d569b5556ee5898ab7'], + }), + ('rack', '2.2.3', { + 'checksums': ['2638e7eb6689a5725c7e16f30cc4aa4e31694dc3ca30d790952526781bd0bb44'], + }), + ('rack-protection', '2.1.0', { + 'checksums': ['1f523c16e5b32f139c8f6f1e3b3eb53aaa7a69bc79a30f3e80f8a93c89242a95'], + }), + ('tilt', '2.0.10', { + 'checksums': ['9b664f0e9ae2b500cfa00f9c65c34abc6ff1799cf0034a8c0a0412d520fac866'], + }), + ('mustermann', '1.1.1', { + 'checksums': ['0a21cfe505869cce9ce17998db5260344e78df81ae857c07a62143fd30299531'], + }), + ('sinatra', '2.1.0', { + 'checksums': ['f323e4446f3e2a132dcaaa134f89caddb29dd88370317f4f32faf5797f1ea535'], + }), + ('rack-test', '1.1.0', { + 'checksums': ['154161f40f162b1c009a655b7b0c5de3a3102cc6d7d2e94b64e1f46ace800866'], + }), + ('bundler', '2.2.11', { + 'checksums': ['4ea2e025ced4c8487ab5e25a80978e3973b870f9e1bfaffab2d5d4263537fdc7'], + }), +] + +moduleclass = 'lang' From 37e96ba93aafe1791033f1f760d78867af41fd75 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 22 Feb 2021 13:03:12 -0800 Subject: [PATCH 0364/2365] revenge of VCF tools --- .../d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0b79bde69a --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.855' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['d9ffe2a25be6cdfee7a34d64235cdc899e99ba8b3fb8de8a9e7f4af20e4ca960'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Perl', '5.32.0'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' From e7d42b060829f246236704ab8a289f03b889a39e Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 22 Feb 2021 19:53:15 -0800 Subject: [PATCH 0365/2365] {bio}[GCC/10.2.0] VCFtools 0.1.16 --- .../v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb new file mode 100644 index 0000000000..703544de6d --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.35'), +] + +dependencies = [ + ('Perl', '5.32.0'), + ('HTSlib', '1.11'), + ('zlib', '1.2.11'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' From df18a73851dff5aabdcee434e4deb0e62f5480c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 15:18:15 +0100 Subject: [PATCH 0366/2365] {lib}[foss/2020b] GDAL v3.2.1, GEOS v3.9.1, PROJ v7.2.1, libgeotiff 1.6.0 w/ Python 3.8.6 --- .../g/GDAL/GDAL-3.2.1-foss-2020b.eb | 60 +++++++++++++++++++ .../g/GEOS/GEOS-3.9.1-GCC-10.2.0.eb | 20 +++++++ .../libgeotiff-1.6.0-GCCcore-10.2.0.eb | 36 +++++++++++ .../p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb | 42 +++++++++++++ 4 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.6.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb new file mode 100644 index 0000000000..f17634b9d7 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -0,0 +1,60 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.2.1' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + '6c588b58fcb63ff3f288eb9f02d76791c0955ba9210d98c3abd879c770ae28ea', # gdal-3.2.1.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('netCDF', '4.7.4'), + ('expat', '2.2.9'), + ('GEOS', '3.9.1'), + ('SQLite', '3.33.0'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.1.0'), + ('zlib', '1.2.11'), + ('cURL', '7.72.0'), + ('PCRE2', '10.35'), + ('PROJ', '7.2.1'), + ('libgeotiff', '1.6.0'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --without-hdf4 --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..70f364a942 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-10.2.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.9.1' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7e630507dcac9dc07565d249a26f06a15c9f5b0c52dd29129a0e3d381d7e382a'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a739034a87 --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.6.0' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['9311017e5284cffb86f2c7b7a9df1fb5ebcdc61c30468fb2e6bca36e4272ebca'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('PROJ', '7.2.1'), + ('libjpeg-turbo', '2.0.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('LibTIFF', '4.1.0'), + ('cURL', '7.72.0'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cb19aeb08e --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '7.2.1' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b384f42e5fb9c6d01fe5fa4d31da2e91329668863a684f97be5d4760dbbf0a14'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.35'), +] + +dependencies = [ + ('SQLite', '3.33.0'), + ('LibTIFF', '4.1.0'), + ('cURL', '7.72.0'), +] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 8b65a932411c969e01a097b9680d642f322b46f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 15:22:03 +0100 Subject: [PATCH 0367/2365] {bio}[foss/2020b] cicero v1.3.4.11, Monocle3 v0.2.3 w/ R 4.0.3 --- ...ro-1.3.4.11-foss-2020b-R-4.0.3-Monocle3.eb | 30 ++++++ .../Monocle3-0.2.3-foss-2020b-R-4.0.3.eb | 91 +++++++++++++++++++ 2 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/c/cicero/cicero-1.3.4.11-foss-2020b-R-4.0.3-Monocle3.eb create mode 100644 easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/c/cicero/cicero-1.3.4.11-foss-2020b-R-4.0.3-Monocle3.eb b/easybuild/easyconfigs/c/cicero/cicero-1.3.4.11-foss-2020b-R-4.0.3-Monocle3.eb new file mode 100644 index 0000000000..1ff6a618d8 --- /dev/null +++ b/easybuild/easyconfigs/c/cicero/cicero-1.3.4.11-foss-2020b-R-4.0.3-Monocle3.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'cicero' +# see https://github.com/cole-trapnell-lab/cicero-release/tree/monocle3 +local_commit = '39aa789' +version = '1.3.4.11' +versionsuffix = '-R-%(rver)s-Monocle3' + +homepage = 'https://cole-trapnell-lab.github.io/cicero-release' +description = """Cicero is an R package that provides tools for analyzing single-cell chromatin accessibility + experiments.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/cole-trapnell-lab/cicero-release/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'cicero-%(version)s-monocle3.tar.gz'}] +checksums = ['7be8a11d0d6c5fbb0153d013d28dac7b96488e22adf02ddac75c6ccbec598a57'] + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), + ('Monocle3', '0.2.3', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..a7fe1aedf2 --- /dev/null +++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb @@ -0,0 +1,91 @@ +easyblock = 'Bundle' + +name = 'Monocle3' +local_commit = '4c01d89' +version = '0.2.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cole-trapnell-lab.github.io/monocle3/' +description = """ An analysis toolkit for single-cell RNA-seq. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('R', '4.0.3'), + ('Python', '3.8.6'), + ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), + ('GDAL', '3.2.1'), +] + +github_account = 'cole-trapnell-lab' +exts_defaultclass = 'RPackage' +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('grr', '0.9.5', { + 'checksums': ['292606de2983ac5840c90d3e0977441b482c9e73c1674b662f8b4fb8f3632b2b'], + }), + ('Matrix.utils', '0.9.8', { + 'checksums': ['ebc59d3ef751775515586ff1f2396e429a1e9d91a10099d804134fcf74c0ae28'], + }), + ('pbmcapply', '1.5.0', { + 'checksums': ['df52ed585c0b32ac6180616efd94cd75dd7c5621f5398c0861db2f7b317ba844'], + }), + ('furrr', '0.2.2', { + 'checksums': ['e5c10353dc47416eda870d16cf810c576f11bdc9e4c7277f7755581f3824cd4d'], + }), + ('warp', '0.2.0', { + 'checksums': ['0e0de344f3d711d58e6be2ab47ade1db3b703bf3ca85080b1124c0c25a630a68'], + }), + ('slider', '0.1.5', { + 'checksums': ['93f5801ad81a6e4f7e710666a2ca1530709767d10d171dd6749f91aabae392f4'], + }), + ('rlang', '0.4.10', { + 'checksums': ['07530270c4c199f2b7efc5d57a476d99babd9d0c3388a02bb7d57fe312da3576'], + }), + ('rsample', '0.0.9', { + 'checksums': ['4cb4bc9708c9314aecaad703bae5aeffdd533af0bf1273a05042d647fdd61c0f'], + }), + ('RhpcBLASctl', '0.20-137', { + 'checksums': ['db02cbdad32fc54bc60bb27baf0799e919c09c09710c33bf72c741f93421616f'], + }), + ('sf', '0.9-7', { + 'checksums': ['4acac2f78badf9d252da5bf377975f984927c14a56a72d9f83d285c0adadae9c'], + }), + ('spdep', '1.1-5', { + 'checksums': ['47cb46cf5cf1f4386eb1b5e4d8541d577d7f2939e74addbdb884ecf2323f6d5d'], + }), + ('speedglm', '0.3-3', { + 'checksums': ['d065d0ee42fb772760fca8d97ad2aa56cd76b1d9ecb4e97478ec362429e16738'], + }), + ('uwot', '0.1.10', { + 'checksums': ['6ee1b6027bce679cd5a35f647f516a5b327632234bcf323c7f3d5b5e10807d23'], + }), + ('leidenbase', '0.1.2', { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '8c52ebc.tar.gz', 'filename': 'leidenbase-0.1.2.tar.gz'}], + 'checksums': ['d7b246ff103e257b137481e2a94d1bfb56eef29d935999e0c981d0ed638f23d6'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '4c01d89.tar.gz', 'filename': 'Monocle3-%(version)s.tar.gz'}], + 'checksums': ['022263ed59c7d42767759e9a53e4a7184cee38c252ce0b45a626aa38496ee7e0'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['leidenbase', '%(namelower)s'], +} + +moduleclass = 'bio' From 48cc3c6b3e86c66ced67f6735b47b0a55f52a422 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Feb 2021 09:07:24 +0100 Subject: [PATCH 0368/2365] Drop Python suffix on foss/2020b version. --- .../g/GROMACS/GROMACS-2021-foss-2020b.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb new file mode 100644 index 0000000000..5e4aad028e --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb @@ -0,0 +1,88 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI builds +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', +] +checksums = [ + 'efa78ab8409b0f5bf0fbca174fb8fbcf012815326b5c71a9d7c385cde9a8f87b', # gromacs-2021.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch + '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 6b5a146d79554a881583817ea2207c46a69e6ce2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 14:05:47 +0100 Subject: [PATCH 0369/2365] adding easyconfigs: SUNDIALS-5.7.0-foss-2020b.eb, SUNDIALS-5.7.0-intel-2020b.eb --- .../s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb | 35 +++++++++++++++++++ .../s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb new file mode 100644 index 0000000000..cf95385b96 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '5.7.0' + +homepage = 'https://computation.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] + +builddependencies = [('CMake', '3.18.4')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb new file mode 100644 index 0000000000..218050a770 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '5.7.0' + +homepage = 'https://computation.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] + +builddependencies = [('CMake', '3.18.4')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From e9c72ab90dc54b949022204b094333aedf251756 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 14:16:16 +0100 Subject: [PATCH 0370/2365] adding easyconfigs: lxml-4.6.2-GCCcore-10.2.0.eb, libxslt-1.1.34-GCCcore-10.2.0.eb --- .../libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ .../l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb | 27 ++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..764ee9417e --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.34' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..31000e33a4 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '4.6.2' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['cd11c7e8d21af997ee8079037fff88f16fda188a9776eb4b81c7e4c9c0a7d7fc'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From ddd2519b1a15c56151b7b8b30f86f3483668720b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 14:21:34 +0100 Subject: [PATCH 0371/2365] adding easyconfigs: Myokit-1.32.0-foss-2020b.eb --- .../m/Myokit/Myokit-1.32.0-foss-2020b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb new file mode 100644 index 0000000000..7ab29cb620 --- /dev/null +++ b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'Myokit' +version = '1.32.0' + +homepage = 'http://myokit.org' +description = """Myokit is an open-source Python-based toolkit that facilitates modeling and simulation of cardiac +cellular electrophysiology.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['393ebc85413bd1b573909736caeadd9d7757f41cceb7bd29f3b30f5107237cba'] + +use_pip = True + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Pillow', '8.0.1'), + ('lxml', '4.6.2'), + ('PyQt5', '5.15.1'), + ('SUNDIALS', '5.7.0'), + ('pocl', '1.6'), +] + +# configparser is part of stdlib in Python 3 +preinstallopts = "sed -i 's/.*configparser.*//g' setup.py && " + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/myokit'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "myokit -h", + "myokit system", + "myokit opencl", # make sure OpenCL features work (requires pocl or other dependency providing OpenCL runtime) + "myokit run example", +] + +moduleclass = 'bio' From 936fa44e5ebce929271767fe60bc429426cb0814 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 14:30:04 +0100 Subject: [PATCH 0372/2365] adding easyconfigs: PyOpenCL-2021.1.2-intel-2020b.eb, pocl-1.6-iccifort-2020.4.304.eb --- .../PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb | 35 ++++++++++++++++ .../p/pocl/pocl-1.6-iccifort-2020.4.304.eb | 40 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb new file mode 100644 index 0000000000..0e233b347c --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2021.1.2' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('pocl', '1.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.1', { + 'checksums': ['073ae22a0ae946e2db97164f2eb24a599cd3a51430384aa40859dffd73056c40'], + }), + ('pyopencl', version, { + 'checksums': ['18871bc80c5a94869521189cf2c04d72c88367a441a9a033f72f66792ac33d29'], + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..4dc3a0dc23 --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '1.6' + +homepage = 'https://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b0a4c0c056371b6f0db726b88fbb76bbee94948fb2abd4dbc8d958f7c42f766c'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Clang', '11.0.1'), + ('hwloc', '2.2.0'), + ('libtool', '2.4.6'), + ('libxml2', '2.9.10'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From ea6fedb750f2a72768be345731273ad84eebc775 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 15:13:59 +0100 Subject: [PATCH 0373/2365] {math}[foss/2020b] sympy v1.7.1, gmpy2 v2.1.0b5 w/ Python 3.8.6 --- .../g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb | 26 ++++++++++++ .../s/sympy/sympy-1.7.1-foss-2020b.eb | 40 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb new file mode 100644 index 0000000000..dad396aedb --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.0b5' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8951bcfc61c0f40102b92a4777daf9eb85445b537c4d09086deb0e097190bef0'] + +dependencies = [ + ('Python', '3.8.6'), + ('GMP', '6.2.0'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb new file mode 100644 index 0000000000..0ebb8c13cf --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.7.1' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['sympy-1.6.2_allpython.patch'] +checksums = [ + 'a3de9261e97535b83bb8607b0da2c7d03126650fafea2b2789657b229c246b2e', # sympy-1.7.1.tar.gz + '605f4f1aadbbfd3d44f1cfeae34ed920323a408efb5b43737b0458e9a90e447f', # sympy-1.6.2_allpython.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('gmpy2', '2.1.0b5'), +] + +download_dep_fail = True +use_pip = True + +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +moduleclass = 'math' From b01658f9ff3f10db819f3193ba7a977c3a4a4f6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 15:33:18 +0100 Subject: [PATCH 0374/2365] remove patch for sympy 1.7.1, no longer needed --- easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb index 0ebb8c13cf..35b84aecb0 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb @@ -13,11 +13,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['sympy-1.6.2_allpython.patch'] -checksums = [ - 'a3de9261e97535b83bb8607b0da2c7d03126650fafea2b2789657b229c246b2e', # sympy-1.7.1.tar.gz - '605f4f1aadbbfd3d44f1cfeae34ed920323a408efb5b43737b0458e9a90e447f', # sympy-1.6.2_allpython.patch -] +checksums = ['a3de9261e97535b83bb8607b0da2c7d03126650fafea2b2789657b229c246b2e'] dependencies = [ ('Python', '3.8.6'), From 28efcec0f971d607f40a63d59505304ca979f23f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 16:57:41 +0100 Subject: [PATCH 0375/2365] {vis}[foss/2020b] OpenCV v4.5.1 (incl. opencv-contrib) --- .../o/OpenEXR/OpenEXR-2.5.5-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.5.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.5.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..179dd3fa79 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.5.5-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '2.5.5' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/openexr/openexr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['59e98361cb31456a9634378d0f653a2b9554b8900f233450f2396ff495ea76b3'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +sanity_check_paths = { + 'files': ['lib/lib%s-%%(version_major)s_%%(version_minor)s.%s' % (x, SHLIB_EXT) for x in + ['Half', 'Iex', 'IexMath', 'IlmImf', 'IlmImfUtil', 'IlmThread', 'Imath']] + + ['bin/exr%s' % x for x in + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']], + 'dirs': ['include/OpenEXR', 'share'], +} + +moduleclass = 'vis' From 5fb61c52e438f45e563b50d851961cbff356641e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 17:10:36 +0100 Subject: [PATCH 0376/2365] drop Python from versionsuffix for OpenCV 4.5.1 with foss/2020b --- .../OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb new file mode 100644 index 0000000000..82699bcc1e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb @@ -0,0 +1,69 @@ +name = 'OpenCV' +version = '4.5.1' +versionsuffix = '-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [ + {'source_urls': ['https://github.com/opencv/opencv/archive/'], + 'download_filename': '%(version)s.zip', 'filename': SOURCELOWER_ZIP}, + {'source_urls': ['https://github.com/opencv/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', 'filename': '%(namelower)s_contrib-%(version)s.zip'}, + {'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '5fbc26ee09e148a4d494b225d04217f7c913ca1a4d46115b70cca3565d7bbe05', # opencv-4.5.1.zip + 'fdbd851985fd79797a04e16bdd672aff698aee89086b944295c90265f3cfffda', # opencv_contrib-4.5.1.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.1'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('libwebp', '1.1.0'), + ('OpenEXR', '2.5.5'), + ('JasPer', '2.0.24'), + ('Java', '11', '', True), + ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('GLib', '2.66.1'), + ('GTK+', '3.24.23'), + ('HDF5', '1.10.7'), # needed by hdf from contrib +] + +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules' + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' From 583e75b6388fcecfb16c90d06b7f2d1049c01934 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 17:25:26 +0100 Subject: [PATCH 0377/2365] adding easyconfigs: tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb --- ...boardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..c41886f626 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'tensorboardX' +version = '2.1' +local_pytorch_ver = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_ver + +homepage = 'https://github.com/lanpa/tensorboardX' +description = "Tensorboard for PyTorch." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +github_account = 'lanpa' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2556d5601eab25b8fafa20aa0ea36c9c307be225122e68d6047b558edc302fa3'] + +# tensorboardX v2.x works with tensorboards generated with TensorFlow 2, +# but TensorFlow is not needed to use tensorboardX +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('protobuf-python', '3.14.0'), + ('PyTorch', local_pytorch_ver), + ('torchvision', '0.8.2', versionsuffix), +] + +options = {'modulename': '%(name)s'} + +use_pip = True +download_dep_fail = True + +postinstallcmds = ["cp -r %s %%(installdir)s" % d for d in ['docs', 'examples', 'tests']] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'docs', 'examples', 'tests'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From 6967f61ccf5c36064060974a6bee1e35dd950a8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 18:36:43 +0100 Subject: [PATCH 0378/2365] adding easyconfigs: scikit-image-0.18.1-foss-2020b.eb, dask-2021.2.0-foss-2020b.eb, bokeh-2.2.3-foss-2020b.eb --- .../b/bokeh/bokeh-2.2.3-foss-2020b.eb | 41 +++++++++ .../d/dask/dask-2021.2.0-foss-2020b.eb | 83 +++++++++++++++++++ .../scikit-image-0.18.1-foss-2020b.eb | 47 +++++++++++ 3 files changed, 171 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb new file mode 100644 index 0000000000..99b3dce72e --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.2.3' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('Pillow', '8.0.1'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + (name, version, { + 'checksums': ['c4a3f97afe5f525019dd58ee8c4e3d43f53fe1b1ac264ccaae9b02c07b2abc17'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb new file mode 100644 index 0000000000..99c555e431 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb @@ -0,0 +1,83 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2021.2.0' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('SciPy-bundle', '2020.11'), + ('bokeh', '2.2.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('fsspec', '0.8.7', { + 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('locket', '0.2.1', { + 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + }), + ('partd', '1.1.0', { + 'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.0.0', { + 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + (name, version, { + 'checksums': ['e7054b8d685205e95c789900ae87d6174550180cbe38a3cb1142e10c73004c22'], + }), + ('distributed', version, { + 'checksums': ['9150b99b2c28e7c238c486b117154abd545c6990080d084aaff02f803f86f75e'], + }), + ('dask-mpi', '2.21.0', { + 'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'], + }), + ('immutables', '0.15', { + 'checksums': ['3713ab1ebbb6946b7ce1387bb9d1d7f5e09c45add58c2a2ee65f963c171e746b'], + }), + ('contextvars', '2.4', { + 'checksums': ['f38c908aaa59c14335eeea12abea5f443646216c4e29380d7bf34d2018e2c39e'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.7.2', { + 'checksums': ['1767f4146b2663d9d2eaef62b882a86e1df0bccdb8ae68ae3e5e546aa6796d35'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb new file mode 100644 index 0000000000..72cd0579e4 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.18.1' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('Pillow', '8.0.1'), + ('networkx', '2.5'), + ('dask', '2021.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imageio', '2.9.0', { + 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.3.0', { + 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], + }), + ('tifffile', '2021.2.1', { + 'checksums': ['6793787742e18cf2116bc65e17c51cd9c14cd27a4a6033a8ddd5bf801a637615'], + }), + (name, version, { + 'modulename': 'skimage', + 'checksums': ['fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171'], + }), +] + +moduleclass = 'vis' From 17522852a6d34233c3a52a6698536393c930a7e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Feb 2021 18:41:02 +0100 Subject: [PATCH 0379/2365] {lang}[foss/2020b] numba v0.52.0 (+ LLVM v10.0.1) --- .../l/LLVM/LLVM-10.0.1-GCCcore-10.2.0.eb | 38 ++++++++++++++ .../n/numba/numba-0.52.0-foss-2020b.eb | 51 +++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-10.0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-10.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-10.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fd3c955057 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-10.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +name = 'LLVM' +version = '10.0.1' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['c5d8e30b57cbded7128d78e5e8dad811bff97a8d471896812f57fa99ee82cdf3'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb new file mode 100644 index 0000000000..15e646e2da --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.52.0' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('LLVM', '10.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('llvmlite', '0.35.0', { + 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", + 'checksums': [ + '80e51d5aa02ad72da9870e89d21f9b152b0220ca551b4596a6c0614bcde336fc', # llvmlite-0.35.0.tar.gz + # llvmlite-0.31.0_fix-ffi-Makefile.patch + '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', + ], + }), + (name, version, { + 'checksums': ['44661c5bd85e3d3619be0a40eedee34e397e9ccb3d4c458b70e10bf95d1ce933'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' From d7362bbcbc71461af3f579ebe88b36686ad0aa40 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 24 Feb 2021 17:35:51 -0800 Subject: [PATCH 0380/2365] {system}[GCC/10.2.0] file 5.39 --- .../f/file/file-5.39-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1e5eec58ab --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.39' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f05d286a76d9556243d0cb05814929c2ecf3a5ba07963f8f70bfaaa70517fad1'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From 7b11dc1b236c1f05cb1730eba4bf2350f7c466a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 09:14:35 +0100 Subject: [PATCH 0381/2365] adding easyconfigs: PETSc-3.14.4-foss-2020b.eb, MUMPS-5.3.5-foss-2020b-metis.eb, Hypre-2.20.0-foss-2020b.eb --- .../h/Hypre/Hypre-2.20.0-foss-2020b.eb | 18 +++++++ .../m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb | 27 +++++++++++ .../p/PETSc/PETSc-3.14.4-foss-2020b.eb | 48 +++++++++++++++++++ 3 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-foss-2020b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-foss-2020b.eb new file mode 100644 index 0000000000..666f85cc71 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-foss-2020b.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.20.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5be77b28ddf945c92cde4b52a272d16fb5e9a7dc05e714fc5765948cba802c01'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb new file mode 100644 index 0000000000..ef32bdb818 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb @@ -0,0 +1,27 @@ +name = 'MUMPS' +version = '5.3.5' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4'] + +dependencies = [ + ('SCOTCH', '6.1.0'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-foss-2020b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-foss-2020b.eb new file mode 100644 index 0000000000..1ae2d86cc8 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-foss-2020b.eb @@ -0,0 +1,48 @@ +name = 'PETSc' +version = '3.14.4' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +# https:// does not work here +source_urls = [ + 'http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + '2fb431434b91e054cc3a176f7cb008951088243b5dcb3efc8eec8ce589a2658e', # petsc-3.14.4.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('MUMPS', '5.3.5', '-metis'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('Hypre', '2.20.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' From 736c6d402449d36ea9b1d535c4f878622924ee80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 09:30:25 +0100 Subject: [PATCH 0382/2365] use https in source URL for PETSc 3.14.4 --- easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-foss-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-foss-2020b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-foss-2020b.eb index 1ae2d86cc8..ec7ec7d65c 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-foss-2020b.eb @@ -8,9 +8,8 @@ description = """PETSc, pronounced PET-see (the S is silent), is a suite of data toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} -# https:// does not work here source_urls = [ - 'http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', ] sources = [SOURCELOWER_TAR_GZ] From 08e29eee5790450d13784dc71bcf8608dea0c257 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 10:46:49 +0100 Subject: [PATCH 0383/2365] leverage existing easyconfigs as dependencies, enhance sanity check + small extension updates for bokeh, dask and scikit-image easyconfigs using intel/2020b --- .../b/bokeh/bokeh-2.2.3-intel-2020b.eb | 14 +++++--------- .../d/dask/dask-2021.2.0-foss-2020b.eb | 6 ------ .../d/dask/dask-2021.2.0-intel-2020b.eb | 17 ++++++++--------- .../scikit-image-0.18.1-intel-2020b.eb | 9 +-------- 4 files changed, 14 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb index aa1444c33a..eb38b5693d 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb @@ -13,14 +13,10 @@ dependencies = [ ('PyYAML', '5.3.1'), ('Pillow', '8.0.1'), ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), ] use_pip = True -sanity_pip_check = True - -# required because we're building Python packages (tornado) -# using Intel compilers on top of Python built with GCC. -check_ldshared = True exts_default_options = {'source_urls': [PYPI_SOURCE]} @@ -28,10 +24,6 @@ exts_list = [ ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], }), - ('typing-extensions', '3.7.4.3', { - 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', - 'checksums': ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'], - }), (name, version, { 'checksums': ['c4a3f97afe5f525019dd58ee8c4e3d43f53fe1b1ac264ccaae9b02c07b2abc17'], }), @@ -42,4 +34,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb index 99c555e431..bd28417815 100644 --- a/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb @@ -57,12 +57,6 @@ exts_list = [ ('dask-mpi', '2.21.0', { 'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'], }), - ('immutables', '0.15', { - 'checksums': ['3713ab1ebbb6946b7ce1387bb9d1d7f5e09c45add58c2a2ee65f963c171e746b'], - }), - ('contextvars', '2.4', { - 'checksums': ['f38c908aaa59c14335eeea12abea5f443646216c4e29380d7bf34d2018e2c39e'], - }), ('docrep', '0.3.2', { 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], }), diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb index 50775be1d6..da0afcc593 100644 --- a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb @@ -17,17 +17,12 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True - -# required because we're building Python packages (msgpack) -# using Intel compilers on top of Python built with GCC. -check_ldshared = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ - ('fsspec', '0.8.5', { - 'checksums': ['890c6ce9325030f03bd2eae81389ddcbcee53bdd475334ca064595e1e45f92a6'], + ('fsspec', '0.8.7', { + 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], }), ('toolz', '0.11.1', { 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], @@ -62,8 +57,8 @@ exts_list = [ ('dask-mpi', '2.21.0', { 'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'], }), - ('docrep', '0.3.1', { - 'checksums': ['ef6e7433716c0d2c59889aae8bff800b48e82d7e759dfd934b93100dc7bccaa1'], + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], }), ('dask-jobqueue', '0.7.2', { 'checksums': ['1767f4146b2663d9d2eaef62b882a86e1df0bccdb8ae68ae3e5e546aa6796d35'], @@ -75,4 +70,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb index 1e623b7aae..c2d38297e8 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb @@ -12,22 +12,16 @@ dependencies = [ ('Python', '3.8.6'), ('matplotlib', '3.3.3'), ('Pillow', '8.0.1'), + ('networkx', '2.5'), ('dask', '2021.2.0'), ] use_pip = True sanity_pip_check = True -# required because we're building Python packages -# using Intel compilers on top of Python built with GCC. -check_ldshared = True - exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ - ('networkx', '2.5', { - 'checksums': ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'], - }), ('PyWavelets', '1.1.1', { 'modulename': 'pywt', 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], @@ -50,7 +44,6 @@ exts_list = [ # avoid building with OpenMP support, since that triggers a nasty internal compiler error with # icpc 19.0.5.281 and 19.1.3.304: Segmentation violation 'preinstallopts': "sed -i 's/-fopenmp//g' setup.py && " - }), ] From a1279bd03fec84acc98fda64870a57ca1cb25c72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 10:53:51 +0100 Subject: [PATCH 0384/2365] add patch for scikit-image 0.18.1 to avoid 'Permission denied' error on 'import skimage' --- .../s/scikit-image/scikit-image-0.18.1-foss-2020b.eb | 7 ++++++- .../s/scikit-image/scikit-image-0.18.1-intel-2020b.eb | 11 +++++++---- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb index 72cd0579e4..e922ae4b1e 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb @@ -40,7 +40,12 @@ exts_list = [ }), (name, version, { 'modulename': 'skimage', - 'checksums': ['fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171'], + 'patches': ['scikit-image-%(version)s_fix-README-cache-perms.patch'], + 'checksums': [ + 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], }), ] diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb index c2d38297e8..f1d0c9f2b5 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb @@ -40,10 +40,13 @@ exts_list = [ }), (name, version, { 'modulename': 'skimage', - 'checksums': ['fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171'], - # avoid building with OpenMP support, since that triggers a nasty internal compiler error with - # icpc 19.0.5.281 and 19.1.3.304: Segmentation violation - 'preinstallopts': "sed -i 's/-fopenmp//g' setup.py && " + 'patches': ['scikit-image-%(version)s_fix-README-cache-perms.patch'], + 'preinstallopts': "sed -i 's/-fopenmp//g' setup.py && ", + 'checksums': [ + 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], }), ] From e8af19943437ea9cc2f3b853962baa66ab57d829 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 11:04:34 +0100 Subject: [PATCH 0385/2365] add missing easyconfig for networkx 2.5 with intel/2020b --- .../n/networkx/networkx-2.5-intel-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb new file mode 100644 index 0000000000..bad27695d3 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.5' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 2baf8cb0037787075b288407e840bb9c3975efe9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 11:45:29 +0100 Subject: [PATCH 0386/2365] enable HDF support in GDAL 3.2.1 easyconfig --- .../g/GDAL/GDAL-3.2.1-foss-2020b.eb | 5 +- .../h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb | 58 +++++++++++++++++++ 2 files changed, 61 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb index f17634b9d7..041afc8d3b 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -38,15 +38,16 @@ dependencies = [ ('libgeotiff', '1.6.0'), ('SciPy-bundle', '2020.11'), ('HDF5', '1.10.7'), + ('HDF', '4.2.15'), ] preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' -configopts += ' --without-hdf4 --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6a9f6d507b --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.15' + +homepage = 'https://www.hdfgroup.org/products/hdf4/' + +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '2.0.5'), + ('Szip', '2.1.1'), + ('zlib', '1.2.11'), + ('libtirpc', '1.3.1'), +] + +preconfigopts = "LIBS='-ltirpc' " +local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' +configopts = [ + # -fallow-argument-mismatch is required to compile with GCC 10.x + local_common_configopts + 'FFLAGS="$FFLAGS -fallow-argument-mismatch"', + # Cannot build shared libraries and Fortran... + # https://trac.osgeo.org/gdal/wiki/HDF#IncompatibilitywithNetCDFLibraries + # netcdf must be disabled to allow HDF to be used by GDAL + local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", +] + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', + 'lib/libmfhdf.%s' % SHLIB_EXT], + 'dirs': ['include/hdf'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +moduleclass = 'data' From ed80a7ead677953260d388ac23f24637eec0d898 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 12:03:30 +0100 Subject: [PATCH 0387/2365] bump JasPer version to latest 2.0.24 for 2020b generation of easyconfigs + remove easyconfigs for ancient JasPer 2.0.1.4 with GCCcore/10.2.0 --- easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb | 2 +- .../i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb index f0104f79df..54cb9105d3 100644 --- a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb @@ -19,7 +19,7 @@ builddependencies = [('CMake', '3.18.4')] dependencies = [ ('netCDF', '4.7.4'), - ('JasPer', '2.0.14'), + ('JasPer', '2.0.24'), ('libjpeg-turbo', '2.0.5'), ('libpng', '1.6.37'), ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb index b59eec3649..980874e68b 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('X11', '20201008'), ('Ghostscript', '9.53.3'), - ('JasPer', '2.0.14'), + ('JasPer', '2.0.24'), ('libjpeg-turbo', '2.0.5'), ('LibTIFF', '4.1.0'), ('LittleCMS', '2.11'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb index bde35a1625..0ae73640e1 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb @@ -59,7 +59,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.5'), ('NSS', '3.57'), ('snappy', '1.1.8'), - ('JasPer', '2.0.14'), + ('JasPer', '2.0.24'), ('bzip2', '1.0.8'), # OS dependency should be preferred if the os version is more recent then this version, # it is nice to have an up to date openssl for security reasons From d32b28d6b66153522258d6acf45af11ed65df5a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 13:18:09 +0100 Subject: [PATCH 0388/2365] add patch to fix compilation of Qt5 5.14.2 with JasPer 2.0.24 --- easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb index 0ae73640e1..ad095ebda2 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb @@ -22,6 +22,7 @@ patches = [ 'Qt5-5.14.2_fix-missing-stdint.patch', 'Qt5-5.14.2_fix-webengine-bison.patch', 'Qt5-5.14.2_fix-std-runtime_error.patch', + 'Qt5-5.14.2_fix-include-math.patch', ] checksums = [ 'c6fcd53c744df89e7d3223c02838a33309bd1c291fcb6f9341505fe99f7f19fa', # qt-everywhere-src-5.14.2.tar.xz @@ -31,6 +32,7 @@ checksums = [ '648e2a92d5ea139543db5d01a80aa33d4721e52bb59c785490b64497b0ede4ab', # Qt5-5.14.2_fix-missing-stdint.patch '6ace4735e35dee95d6b6c7eea3a7c46c264589a319d745310282ee724f632861', # Qt5-5.14.2_fix-webengine-bison.patch '290d91efe8fc7c6daedf01f4a055ff30123c987d41b1832a34920ef521579f5c', # Qt5-5.14.2_fix-std-runtime_error.patch + '32c975b4ad12150f872554f1960c7108bc9c994e318988bab27e762a6c666fa2', # Qt5-5.14.2_fix-include-math.patch ] builddependencies = [ From 8b70f9b589371472d298f4540b1c2e29ca1954e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 16:41:46 +0100 Subject: [PATCH 0389/2365] adding easyconfigs: MDTraj-1.9.5-foss-2020b.eb, MDTraj-1.9.5-intel-2020b.eb --- .../m/MDTraj/MDTraj-1.9.5-foss-2020b.eb | 45 +++++++++++++++++++ .../m/MDTraj/MDTraj-1.9.5-intel-2020b.eb | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb new file mode 100644 index 0000000000..b446a9bc9c --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb @@ -0,0 +1,45 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.5' + +homepage = 'http://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('zlib', '1.2.11'), +] + +use_pip = True +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.0.5', { + 'checksums': ['b079a7d0b9fbc8a92850277b664bb582991ef5ac399b3607e695569148f6c784'], + }), + # must be astunparse < 1.6.3 with Python 3.8, see https://github.com/mdtraj/mdtraj/pull/1621 + ('astunparse', '1.6.2', { + 'checksums': ['dab3e426715373fd76cd08bb1abe64b550f5aa494cf1e32384f26fd60961eb67'], + }), + ('mdtraj', version, { + 'checksums': ['f22c28c9dd51aa0f8692078dd3c2c7a338a7ca27cbd9aaeb669a60361e95adc4'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb new file mode 100644 index 0000000000..f348c27f1f --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb @@ -0,0 +1,45 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.5' + +homepage = 'http://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('zlib', '1.2.11'), +] + +use_pip = True +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.0.5', { + 'checksums': ['b079a7d0b9fbc8a92850277b664bb582991ef5ac399b3607e695569148f6c784'], + }), + # must be astunparse < 1.6.3 with Python 3.8, see https://github.com/mdtraj/mdtraj/pull/1621 + ('astunparse', '1.6.2', { + 'checksums': ['dab3e426715373fd76cd08bb1abe64b550f5aa494cf1e32384f26fd60961eb67'], + }), + ('mdtraj', version, { + 'checksums': ['f22c28c9dd51aa0f8692078dd3c2c7a338a7ca27cbd9aaeb669a60361e95adc4'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' From 4637d73dbb55bded756041f62d26bd25e0368b9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 16:42:27 +0100 Subject: [PATCH 0390/2365] {data}[foss/2020b,intel/2020b] PyTables v3.6.1 + Blosc v1.21.0 w/ Python 3.8.6 --- .../b/Blosc/Blosc-1.21.0-GCCcore-10.2.0.eb | 28 +++++++++++ .../p/PyTables/PyTables-3.6.1-foss-2020b.eb | 48 +++++++++++++++++++ .../p/PyTables/PyTables-3.6.1-intel-2020b.eb | 48 +++++++++++++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7ff2a0c648 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.0' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b0ef4fda82a1d9cbd11e0f4b9685abf14372db51703c595ecd4d76001a8b342d'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2020b.eb new file mode 100644 index 0000000000..31070d115f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.6.1' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-libs.patch'] +checksums = [ + '4cea86bab5bcb5423a07c7951b8c65e24b674e0dcec0e448d434829eff5f18d0', # v3.6.1.tar.gz + '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.6.1-fix-libs.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # provides numexpr + ('HDF5', '1.10.7'), + ('LZO', '2.10'), + ('Blosc', '1.21.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020b.eb new file mode 100644 index 0000000000..d2a6ff233d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.6.1' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-libs.patch'] +checksums = [ + '4cea86bab5bcb5423a07c7951b8c65e24b674e0dcec0e448d434829eff5f18d0', # v3.6.1.tar.gz + '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.6.1-fix-libs.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # provides numexpr + ('HDF5', '1.10.7'), + ('LZO', '2.10'), + ('Blosc', '1.21.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'data' From 6dad96fc1f725bbb976a2c4362b480ffd2a82947 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 16:55:51 +0100 Subject: [PATCH 0391/2365] use https for MDTraj homepage --- easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb | 2 +- easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb index b446a9bc9c..279267dba9 100644 --- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb @@ -5,7 +5,7 @@ easyblock = 'PythonBundle' name = 'MDTraj' version = '1.9.5' -homepage = 'http://mdtraj.org' +homepage = 'https://mdtraj.org' description = "Read, write and analyze MD trajectories with only a few lines of Python code." toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb index f348c27f1f..ee69963428 100644 --- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb @@ -5,7 +5,7 @@ easyblock = 'PythonBundle' name = 'MDTraj' version = '1.9.5' -homepage = 'http://mdtraj.org' +homepage = 'https://mdtraj.org' description = "Read, write and analyze MD trajectories with only a few lines of Python code." toolchain = {'name': 'intel', 'version': '2020b'} From 26d3cf1d4b7cf536c9e961ac4f6ede0dcde12bdd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 25 Feb 2021 18:04:25 +0200 Subject: [PATCH 0392/2365] adding easyconfigs: FLAC-1.3.3-GCCcore-10.2.0.eb, libogg-1.3.4-GCCcore-10.2.0.eb --- .../f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ .../l/libogg/libogg-1.3.4-GCCcore-10.2.0.eb | 25 ++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libogg/libogg-1.3.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2f37ef9afa --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.3.3' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['213e82bd716c9de6db2f98bcadbc4c24c7e2efe8c75939a1a84e28539c4e1748'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('libogg', '1.3.4')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libFLAC.a', 'lib/libFLAC++.a', 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b215ccb49f --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.4-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.4' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c163bc12bc300c401b6aa35907ac682671ea376f13ae0969a220f7ddf71893fe'] + +builddependencies = [('binutils', '2.35')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' From 69f6b50fe4c0b3fd3c162898602a10ef0bdc5249 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 25 Feb 2021 18:11:12 +0200 Subject: [PATCH 0393/2365] Include bin/flac in sanity check --- easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb index 2f37ef9afa..42e9d51dd5 100644 --- a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb @@ -19,7 +19,9 @@ dependencies = [('libogg', '1.3.4')] configopts = '--enable-static --enable-shared' sanity_check_paths = { - 'files': ['lib/libFLAC.a', 'lib/libFLAC++.a', 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'files': ['lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT, + 'bin/flac'], 'dirs': ['include/FLAC', 'include/FLAC++'], } From 0271cbda89e148f843241a64f4fa563241878d1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 17:15:47 +0100 Subject: [PATCH 0394/2365] drop Python versionsuffix for PyRETIS with */2020b --- .../p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb | 44 +++++++++++++++++++ .../p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb | 44 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb new file mode 100644 index 0000000000..223cac2960 --- /dev/null +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'PyRETIS' +version = '2.5.0' + +homepage = 'http://www.pyretis.org' +description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based + on transition interface sampling and replica exchange transition interface sampling.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('MDTraj', '1.9.5'), + ('PyTables', '3.6.1'), + ('tqdm', '4.56.2'), +] + +use_pip = True + +exts_list = [ + ('colorama', '0.4.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + (name, version, { + 'source_tmpl': 'pyretis-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyretis'], + 'checksums': ['b4b842a83f39e97a9bbf2d9797f53823b9e741b479b5a6744aeb42daf1c7ad2b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyretisanalyse', 'bin/pyretisrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pyretisanalyse --help", + "pyretisrun --help", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb new file mode 100644 index 0000000000..73df2b8f6b --- /dev/null +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'PyRETIS' +version = '2.5.0' + +homepage = 'http://www.pyretis.org' +description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based + on transition interface sampling and replica exchange transition interface sampling.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('MDTraj', '1.9.5'), + ('PyTables', '3.6.1'), + ('tqdm', '4.56.2'), +] + +use_pip = True + +exts_list = [ + ('colorama', '0.4.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + (name, version, { + 'source_tmpl': 'pyretis-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyretis'], + 'checksums': ['b4b842a83f39e97a9bbf2d9797f53823b9e741b479b5a6744aeb42daf1c7ad2b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyretisanalyse', 'bin/pyretisrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pyretisanalyse --help", + "pyretisrun --help", +] + +moduleclass = 'chem' From 3aef329cbbfbd9b7e37a5254dfb08f74a095a458 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 25 Feb 2021 18:22:49 +0000 Subject: [PATCH 0395/2365] Fix JasPer version in GDAL after 12277 --- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb index 041afc8d3b..ea56b033af 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ ('libxml2', '2.9.10'), ('libpng', '1.6.37'), ('libjpeg-turbo', '2.0.5'), - ('JasPer', '2.0.14'), + ('JasPer', '2.0.24'), ('LibTIFF', '4.1.0'), ('zlib', '1.2.11'), ('cURL', '7.72.0'), From ed1d7a517a1e7439d6ea7fb35fd1e0a0704ee0ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 20:03:00 +0100 Subject: [PATCH 0396/2365] use proper tags for leidenalg 0.1.2 and Monocle3 0.2.3 --- .../m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb index a7fe1aedf2..b73eacbe67 100644 --- a/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb @@ -69,15 +69,15 @@ exts_list = [ 'checksums': ['6ee1b6027bce679cd5a35f647f516a5b327632234bcf323c7f3d5b5e10807d23'], }), ('leidenbase', '0.1.2', { - 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], - 'sources': [{'download_filename': '8c52ebc.tar.gz', 'filename': 'leidenbase-0.1.2.tar.gz'}], - 'checksums': ['d7b246ff103e257b137481e2a94d1bfb56eef29d935999e0c981d0ed638f23d6'], + 'source_urls': ['https://github.com/%(github_account)s/leidenbase/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'leidenbase-%(version)s.tar.gz'}], + 'checksums': ['163f6e8ebc6bd0f6927d1c7e80fe45038eedb07044febb2f8d28459185d367af'], }), (name, version, { 'modulename': '%(namelower)s', - 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], - 'sources': [{'download_filename': '4c01d89.tar.gz', 'filename': 'Monocle3-%(version)s.tar.gz'}], - 'checksums': ['022263ed59c7d42767759e9a53e4a7184cee38c252ce0b45a626aa38496ee7e0'], + 'source_urls': ['https://github.com/%(github_account)s/monocle3/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': 'Monocle3-%(version)s.tar.gz'}], + 'checksums': ['fe95f724ff7a8f35cc4c8152865052c3a6d44332485b0626fbc3e1af09c17738'], }), ] From 517ebf9cae7405e818975a0e2118609895e6f7a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 20:17:45 +0100 Subject: [PATCH 0397/2365] adding easyconfigs: scikit-image-0.18.1-fosscuda-2020b.eb, dask-2021.2.0-fosscuda-2020b.eb, bokeh-2.2.3-fosscuda-2020b.eb --- .../b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb | 41 ++++++++++ .../d/dask/dask-2021.2.0-fosscuda-2020b.eb | 75 +++++++++++++++++++ .../scikit-image-0.18.1-fosscuda-2020b.eb | 52 +++++++++++++ 3 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..a9bd000902 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.2.3' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('Pillow', '8.0.1'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + (name, version, { + 'checksums': ['c4a3f97afe5f525019dd58ee8c4e3d43f53fe1b1ac264ccaae9b02c07b2abc17'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..5294364004 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb @@ -0,0 +1,75 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2021.2.0' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('SciPy-bundle', '2020.11'), + ('bokeh', '2.2.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('fsspec', '0.8.7', { + 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('locket', '0.2.1', { + 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + }), + ('partd', '1.1.0', { + 'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.0.0', { + 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + (name, version, { + 'checksums': ['e7054b8d685205e95c789900ae87d6174550180cbe38a3cb1142e10c73004c22'], + }), + ('distributed', version, { + 'checksums': ['9150b99b2c28e7c238c486b117154abd545c6990080d084aaff02f803f86f75e'], + }), + ('dask-mpi', '2.21.0', { + 'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.7.2', { + 'checksums': ['1767f4146b2663d9d2eaef62b882a86e1df0bccdb8ae68ae3e5e546aa6796d35'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..2eaefc8afe --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.18.1' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('Pillow', '8.0.1'), + ('networkx', '2.5'), + ('dask', '2021.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imageio', '2.9.0', { + 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.3.0', { + 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], + }), + ('tifffile', '2021.2.1', { + 'checksums': ['6793787742e18cf2116bc65e17c51cd9c14cd27a4a6033a8ddd5bf801a637615'], + }), + (name, version, { + 'modulename': 'skimage', + 'patches': ['scikit-image-%(version)s_fix-README-cache-perms.patch'], + 'checksums': [ + 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], + }), +] + +moduleclass = 'vis' From 4869194b15e9054b5a2650f9c16a45892e047f75 Mon Sep 17 00:00:00 2001 From: Alfred Gil Date: Fri, 26 Feb 2021 00:41:36 +0100 Subject: [PATCH 0398/2365] switching back to pip-20.1.1 to fix error in building Python-2.7.18-GCCcore-10.2.0 --- .../easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index 9328a9011b..9c4249515c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -43,9 +43,9 @@ exts_list = [ 'use_pip': False, 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], }), - ('pip', '20.2.3', { + ('pip', '20.1.1', { 'use_pip': False, - 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + 'checksums': ['27f8dc29387dd83249e06e681ce087e6061826582198a425085e0bf4c1cf3a55'], }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], From 8c2db82e005036b58d5442626c38260541917e3e Mon Sep 17 00:00:00 2001 From: Alfred Gil Date: Fri, 26 Feb 2021 02:37:01 +0100 Subject: [PATCH 0399/2365] skipping test_system_interrupt, generally failing (https://github.com/ipython/ipython/issues/12164) --- .../easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb index 0c967ad135..99ddf43c2b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb @@ -141,7 +141,7 @@ sanity_check_paths = { sanity_check_commands = [ "ipython -h", "jupyter notebook --help", - "iptest", + "NOSE_EXCLUDE='system_interrupt' iptest", ] sanity_pip_check = True From 8a679fe35ce5592b99172eff5a718fc8715eefa0 Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 26 Feb 2021 12:37:52 +0000 Subject: [PATCH 0400/2365] Autoconf added --- easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb index 7a1da55ff1..cd2b1ff7c8 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb @@ -23,6 +23,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['f22901582138e3203959c9257cf83eba9929ac41d7be4a42557213a22ebcc7a0'] preconfigopts = 'autoreconf -i && ' +builddependencies = [('Autoconf', '2.69')] sanity_check_paths = { 'files': ['lib/libjansson.%s' % SHLIB_EXT], From edf9c8e76456288a847c7dddfa1b56dac8546c2d Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 26 Feb 2021 14:22:10 +0000 Subject: [PATCH 0401/2365] Swapped Autoconf with Autotools --- easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb index cd2b1ff7c8..ec96079841 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb @@ -23,7 +23,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['f22901582138e3203959c9257cf83eba9929ac41d7be4a42557213a22ebcc7a0'] preconfigopts = 'autoreconf -i && ' -builddependencies = [('Autoconf', '2.69')] +builddependencies = [('Autotools', '20200321')] sanity_check_paths = { 'files': ['lib/libjansson.%s' % SHLIB_EXT], From 9f1978c59dedb3d086e718dd8e6bd44791fa8a50 Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 26 Feb 2021 14:36:24 +0000 Subject: [PATCH 0402/2365] Changed foss-2018b to GCCcore-8.3.0, added GCCcore-10.2.0 as that is latest --- .../t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..442eed6ab0 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# updated to newer toolchain + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] +checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' From 3ff59ef9db8c9b3afeadedf4c5e9855eff18c91b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 26 Feb 2021 17:58:18 +0100 Subject: [PATCH 0403/2365] Update easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb index 42e9d51dd5..c288ef191b 100644 --- a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb @@ -19,10 +19,11 @@ dependencies = [('libogg', '1.3.4')] configopts = '--enable-static --enable-shared' sanity_check_paths = { - 'files': ['lib/libFLAC.a', 'lib/libFLAC++.a', - 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT, - 'bin/flac'], + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], 'dirs': ['include/FLAC', 'include/FLAC++'], } +sanity_check_commands = ["flac --help"] + moduleclass = 'lib' From c70d44007e6eb64634f3a5fdc594cfd974b42688 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 26 Feb 2021 19:12:57 +0200 Subject: [PATCH 0404/2365] Add libvorbis,vorbis-tools and use in libsndfile --- .../libsndfile-1.0.28-GCCcore-10.2.0.eb | 10 ++++++- .../libvorbis-1.3.7-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ .../vorbis-tools-1.4.2-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 3 files changed, 69 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb index 74a8116b7b..ffbc20beb7 100644 --- a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb @@ -13,7 +13,15 @@ source_urls = ['http://www.mega-nerd.com/libsndfile/files/'] sources = [SOURCE_TAR_GZ] checksums = ['1ff33929f042fa333aed1e8923aa628c3ee9e1eb85512686c55092d1e5a9dfa9'] -builddependencies = [('binutils', '2.35')] +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('FLAC', '1.3.3'), + ('libvorbis', '1.3.7'), +] configopts = '--enable-octave=no' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..92bb35e68f --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [('libogg', '1.3.4')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0e3ae44bfb --- /dev/null +++ b/easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'vorbis-tools' +version = '1.4.2' + +homepage = 'https://xiph.org/vorbis/' +description = """Command-line tools for creating and playing Ogg Vorbis files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_GZ] +checksums = ['db7774ec2bf2c939b139452183669be84fda5774d6400fc57fde37f77624f0b0'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libvorbis', '1.3.7'), + ('FLAC', '1.3.3'), +] + +sanity_check_paths = { + 'files': ['bin/oggdec', 'bin/oggenc', 'bin/ogginfo', 'bin/vcut', 'bin/vorbiscomment'], + 'dirs': [], +} + +moduleclass = 'tools' From bb5c4015a79b8d11f871fae956711997d2e436a8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 26 Feb 2021 20:58:31 +0200 Subject: [PATCH 0405/2365] Add missing checksum --- easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb index 818445eea0..1eb3a345b2 100644 --- a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'iccifort', 'version': '2020.4.304'} source_urls = ['https://confluence.slac.stanford.edu/download/attachments/146704476/'] sources = ['libbeef-%(version)s.tar.gz'] +checksums = ['b6af622b74a4e55d637d8cd5027cfa850cf22fec53981c5732de5c40cc0a938a'] configopts = 'CC="$CC"' From b52f10feaf0c6bf169da79fd99f19fcbbc925f4c Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 26 Feb 2021 11:55:18 -0800 Subject: [PATCH 0406/2365] move from GCC to GCCcore --- .../n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3ca4af87ce --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'NGS' +version = '2.10.9' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups +produced from Next Generation Sequencing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), + ('Perl', '5.32.0'), +] + +dependencies = [('Java', '11', '', True)] + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://github.com/ncbi/ngs/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['1372695af5ac2599c9dad0b8cdce857c95c7827ff831a6709343276a29438b1e'], +} + +components = [ + ('NGS-SDK', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), + ('NGS-Java', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), +] + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' From bf7092a9889f4b3ea4fab44378a9a26d8bcb4d14 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 26 Feb 2021 12:00:46 -0800 Subject: [PATCH 0407/2365] remove binutils --- easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb index 703544de6d..04dec16e82 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb @@ -16,7 +16,6 @@ checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] builddependencies = [ ('pkg-config', '0.29.2'), - ('binutils', '2.35'), ] dependencies = [ From 2aa6118b7c2c7c76f880d668ce8c6a92c2972053 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 26 Feb 2021 12:12:08 -0800 Subject: [PATCH 0408/2365] move to GCCcore --- .../XML-LibXML-2.0206-GCCcore-10.2.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ee314c18f7 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0206' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.35'), +] + +dependencies = [ + ('Perl', '5.32.0'), + ('libxml2', '2.9.10'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1010', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['efc121f40bd7a0f62f8ec9b8bc70f7f5409d81cd705e37008596c8efc4452b01'], + }), + ('Alien::Base', '2.38', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['6bbd4116d1a08f95df669fcba16acd6a7e94329843abc8cb7c4b038d1778bded'], + }), + ('Alien::Libxml2', '0.17', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['73b45244f0b5c36e5332c33569b82a1ab2c33e263f1d00785d2003bcaec68db3'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['010ba395c38711f9c233ee23d0b0b18b761e6d99a762125f7e6180d068851619'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' From 46d83bd9285621fea87c09c9f5354482c9b4d6f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2021 09:00:21 +0100 Subject: [PATCH 0409/2365] enable download_dep_fail in Myokit easyconfig --- easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb index 7ab29cb620..8b2c592db4 100644 --- a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb @@ -13,6 +13,7 @@ source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['393ebc85413bd1b573909736caeadd9d7757f41cceb7bd29f3b30f5107237cba'] +download_dep_fail = True use_pip = True dependencies = [ From 505efcf5e88c93b83d98c9e96a682d3dad68460e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2021 09:03:37 +0100 Subject: [PATCH 0410/2365] adding easyconfigs: CP2K-8.1-foss-2020b.eb --- .../easyconfigs/c/CP2K/CP2K-8.1-foss-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-8.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-8.1-foss-2020b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-8.1-foss-2020b.eb new file mode 100644 index 0000000000..de7450f83b --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-8.1-foss-2020b.eb @@ -0,0 +1,36 @@ +name = 'CP2K' +version = '8.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7f37aead120730234a60b2989d0547ae5e5498d93b1e9b5eb548c041ee8e7772'] + +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '4.3.4'), + ('libxsmm', '1.16.1'), + ('FFTW', '3.3.8'), + ('PLUMED', '2.6.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.1'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' From 77eaea515f0d0067f8ac797c519f464d57a073d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2021 09:27:13 +0100 Subject: [PATCH 0411/2365] add sanity check commands for vorbis-tools --- .../v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb index 0e3ae44bfb..d3ffd1ef9c 100644 --- a/easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb @@ -22,9 +22,12 @@ dependencies = [ ('FLAC', '1.3.3'), ] +local_bins = ['oggdec', 'oggenc', 'ogginfo', 'vorbiscomment'] sanity_check_paths = { - 'files': ['bin/oggdec', 'bin/oggenc', 'bin/ogginfo', 'bin/vcut', 'bin/vorbiscomment'], + 'files': ['bin/%s' % x for x in local_bins] + ['bin/vcut'], 'dirs': [], } +sanity_check_commands = ["%s --help" % x for x in local_bins] + moduleclass = 'tools' From 9ffaa1dc9d63831b78e59d4218ce99a109e7e65f Mon Sep 17 00:00:00 2001 From: Alfred Gil Date: Sat, 27 Feb 2021 14:24:06 +0100 Subject: [PATCH 0412/2365] switching to latest pip supportin python2 (20.3.4) --- .../easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index 9c4249515c..ac42a9c106 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -43,9 +43,9 @@ exts_list = [ 'use_pip': False, 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], }), - ('pip', '20.1.1', { + ('pip', '20.3.4', { 'use_pip': False, - 'checksums': ['27f8dc29387dd83249e06e681ce087e6061826582198a425085e0bf4c1cf3a55'], + 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], From 9444ea60e878ba7fb9592663d1cd99d28b000224 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2021 18:25:34 +0100 Subject: [PATCH 0413/2365] adding easyconfigs: OpenCV-4.5.1-fosscuda-2020b-contrib.eb --- .../OpenCV-4.5.1-fosscuda-2020b-contrib.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb new file mode 100644 index 0000000000..dd102dc3ae --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb @@ -0,0 +1,69 @@ +name = 'OpenCV' +version = '4.5.1' +versionsuffix = '-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [ + {'source_urls': ['https://github.com/opencv/opencv/archive/'], + 'download_filename': '%(version)s.zip', 'filename': SOURCELOWER_ZIP}, + {'source_urls': ['https://github.com/opencv/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', 'filename': '%(namelower)s_contrib-%(version)s.zip'}, + {'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '5fbc26ee09e148a4d494b225d04217f7c913ca1a4d46115b70cca3565d7bbe05', # opencv-4.5.1.zip + 'fdbd851985fd79797a04e16bdd672aff698aee89086b944295c90265f3cfffda', # opencv_contrib-4.5.1.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.1'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('libwebp', '1.1.0'), + ('OpenEXR', '2.5.5'), + ('JasPer', '2.0.24'), + ('Java', '11', '', True), + ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('GLib', '2.66.1'), + ('GTK+', '3.24.23'), + ('HDF5', '1.10.7'), # needed by hdf from contrib +] + +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules' + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' From 4522f586cae996646f5f3a18656c7d7d1e6d0cdc Mon Sep 17 00:00:00 2001 From: easybuilder Date: Sun, 28 Feb 2021 19:24:39 +0100 Subject: [PATCH 0414/2365] adding easyconfigs: groff-1.22.4-GCCcore-10.2.0.eb, groff-1.22.4-GCCcore-8.3.0.eb --- .../g/groff/groff-1.22.4-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4d08613ba5 --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.22.4' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] + +builddependencies = [ + ('binutils', '2.35'), + ('makeinfo', '6.7'), +] + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' From ba9862eac4f04d057008600c1b40d81c606062ec Mon Sep 17 00:00:00 2001 From: Mormacill <31103546+Mormacill@users.noreply.github.com> Date: Sun, 28 Feb 2021 19:27:33 +0100 Subject: [PATCH 0415/2365] add missing groff build dependency for Perl provides nroff tool requires to install man pages --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index b192f54ba0..76d0b56cf8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -11,7 +11,10 @@ source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] checksums = ['efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'] -builddependencies = [('binutils', '2.35')] +builddependencies = [ + ('binutils', '2.35'), + ('groff', '1.22.4'), +] dependencies = [ ('zlib', '1.2.11'), # for Net::SSLeay From a99ddb7217e492b4cb525e69a919b7f3ab2d74e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 1 Mar 2021 12:09:55 +0200 Subject: [PATCH 0416/2365] adding easyconfigs: buildenv-default-foss-2020a.eb, buildenv-default-foss-2020b.eb, buildenv-default-fosscuda-2019b.eb, buildenv-default-fosscuda-2020a.eb, buildenv-default-fosscuda-2020b.eb, buildenv-default-intel-2020a.eb, buildenv-default-intel-2020b.eb, buildenv-default-intelcuda-2019b.eb, buildenv-default-intelcuda-2020a.eb, buildenv-default-intelcuda-2020b.eb --- .../b/buildenv/buildenv-default-foss-2020b.eb | 13 +++++++++++++ .../b/buildenv/buildenv-default-fosscuda-2020b.eb | 13 +++++++++++++ .../b/buildenv/buildenv-default-intel-2020b.eb | 13 +++++++++++++ .../b/buildenv/buildenv-default-intelcuda-2020b.eb | 13 +++++++++++++ 4 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2020b.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2020b.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2020b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2020b.eb new file mode 100644 index 0000000000..8a480f0a78 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2020b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-fosscuda-2020b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-fosscuda-2020b.eb new file mode 100644 index 0000000000..cf4d4b054b --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-fosscuda-2020b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2020b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2020b.eb new file mode 100644 index 0000000000..227c38508d --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2020b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2020b'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intelcuda-2020b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intelcuda-2020b.eb new file mode 100644 index 0000000000..2670ea6735 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intelcuda-2020b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +moduleclass = 'devel' From d0beaf8e1fac1e9ed389b3b8b0e710f69c9e5f81 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 1 Mar 2021 12:39:23 +0200 Subject: [PATCH 0417/2365] Add missing checksums, add YACS-0.1.8-GCCcore-10.2.0.eb --- .../y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6b8c4dd900 --- /dev/null +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'YACS' +version = '0.1.8' + +homepage = "https://github.com/rbgirshick/yacs" +description = """YACS was created as a lightweight library to define and +manage system configurations, such as those commonly found in software +designed for scientific experimentation. These "configurations" +typically cover concepts like hyperparameters used in training a machine +learning model or configurable model hyperparameters, such as the depth +of a convolutional neural network.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 1555952c2acb996dfdd13ac13706bc1d7b1ab442 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Mon, 1 Mar 2021 11:19:39 +0000 Subject: [PATCH 0418/2365] Create imake-1.0.8-GCCcore-10.2.0.eb As per discussion re imake-1.0.8-foss-2020b.eb. --- .../i/imake/imake-1.0.8-GCCcore-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0b22abed72 --- /dev/null +++ b/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'imake' +version = '1.0.8' + +homepage = 'https://www.x.org/' +description = """imake is a Makefile-generator that is intended to make it +easier to develop software portably for multiple systems.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35', '', ('GCCcore', '10.2.0'))] + +source_urls = ['https://artfiles.org/x.org/pub/individual/util/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8178a09bfef33ad5f61cb5cb62283df7d3a5682f014507d2e7cfd922485a5c00'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ccmakedep', 'cleanlinks', 'imake', + 'makeg', 'mergelib', 'mkdirhier', + 'mkhtmlindex', 'revpath', 'xmkmf']], + 'dirs': [], +} + +moduleclass = 'devel' From 935dd1756ef32cf343a54702473986f3b964ac4d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 1 Mar 2021 13:38:21 +0200 Subject: [PATCH 0419/2365] Remove redundant sanity_check_paths. --- easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb index 6b8c4dd900..91ac3e247d 100644 --- a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb @@ -29,9 +29,4 @@ download_dep_fail = True sanity_pip_check = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' From e86a5bec8a773e2a573361b2ed54033ac5f52a16 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Mon, 1 Mar 2021 11:53:32 +0000 Subject: [PATCH 0420/2365] Update imake-1.0.8-GCCcore-10.2.0.eb --- easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb index 0b22abed72..98c68c4297 100644 --- a/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb @@ -8,12 +8,13 @@ description = """imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -builddependencies = [('binutils', '2.35', '', ('GCCcore', '10.2.0'))] source_urls = ['https://artfiles.org/x.org/pub/individual/util/'] sources = [SOURCE_TAR_GZ] checksums = ['8178a09bfef33ad5f61cb5cb62283df7d3a5682f014507d2e7cfd922485a5c00'] +builddependencies = [('binutils', '2.35')] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ccmakedep', 'cleanlinks', 'imake', 'makeg', 'mergelib', 'mkdirhier', From 922bbd0bed33f2b22f63f43a100c10c49d48efc2 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Thu, 25 Feb 2021 19:01:11 +0100 Subject: [PATCH 0421/2365] adding easyconfigs: LncLOOM-2.0-foss-2020b-Python-3.8.6.eb, MAFFT-7.475-gompi-2020b-with-extensions.eb, Biopython-1.76-foss-2020b-Python-3.8.6.eb and patches: LncLOOM-2.0-environment.patch Squash: LncLOOM: sanity_check -> postinstall LncLOOM: Biopython-1.76-foss-2020b-Python-3.8.6.eb LncLOOM: don't include python suffix LncLOOM: delete LncLOOM-2.0-foss-2020b-Python-3.8.6.eb LncLOOM: use Biopython 1.78, figure out pulptest LncLOOM: Biopython-1.76-foss-2020b.eb LncLOOM: extract gorubipy dependency --- .../g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb | 26 +++++++ .../l/LncLOOM/LncLOOM-2.0-foss-2020b.eb | 71 +++++++++++++++++++ ...MAFFT-7.475-gompi-2020b-with-extensions.eb | 52 ++++++++++++++ 3 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-gompi-2020b-with-extensions.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8885e2b6be --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +name = 'Gurobi' +version = '9.1.1' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +checksums = ['ba57a83656bf6ab481e1114f5596664385a88a35a47ae51aa2ac307f58aaa44a'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb b/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb new file mode 100644 index 0000000000..8d8ba2eedc --- /dev/null +++ b/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'LncLOOM' +version = '2.0' + +homepage = 'https://github.com/lncLOOM/lncLOOMv2/' +description = """LncLOOM is a graph-based framework that uses integer +programming to identify combinations of short motifs that are deeply conserved +in rapidly evolving sequences.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('MAFFT', '7.475', '-with-extensions'), + ('BLAST+', '2.11.0'), + ('Gurobi', '9.1.1'), + ('Biopython', '1.78'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} +exts_list = [ + ('amply', '0.1.4', { + 'checksums': ['cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38'], + }), + ('networkx', '2.5', { + 'checksums': ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'], + }), + ('PuLP', '2.4', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/coin-or/pulp/archive/'], + 'checksums': ['d52d52b6078ea2c503b33814738866902d661cfe60d7a76251d50423e4af3ad0'], + }), + ('pyBigWig', '0.3.18', { + 'modulename': 'pyBigWig', + 'checksums': ['4c2a8c571b4100ad7c4c318c142eb48558646be52aaab28215a70426f5be31bc'], + }), + (name, version, { + 'modulename': 'LncLOOMv2', + 'patches': ['LncLOOM-2.0-config-from-environment.patch'], + 'source_tmpl': '75b82aeb359b65998770577e7516ed54845ba66c.tar.gz', + 'source_urls': ['https://github.com/lncLOOM/LncLOOMv2/archive/'], + 'checksums': [ + # 75b82aeb359b65998770577e7516ed54845ba66c.tar.gz + 'cc00beec1ddfc879c94948d9e7b7736b2b5156617b8724927d7459e6b88d0e59', + # LncLOOM-2.0-config-from-environment.patch + 'bd8f13af556efe062e70ca06805fb0d1a6046bd50a59eaf69fb0014a844f169d', + ], + }), +] + +postinstallcmds = [ + 'chmod +x %(installdir)s/lib/python%(pyshortver)s/site-packages/LncLOOMv2/src/blat', + 'find %(installdir)s/lib/python%(pyshortver)s/site-packages/pulp/' + ' -executable -type f -exec chmod +x {} \\;', +] + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/LncLOOM'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/LncLOOMv2'], +} +sanity_check_commands = [ + 'pulptest', + 'LncLOOM --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-gompi-2020b-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-gompi-2020b-with-extensions.eb new file mode 100644 index 0000000000..6d0bc5ea12 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-gompi-2020b-with-extensions.eb @@ -0,0 +1,52 @@ +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.475' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['bb6973ae089ea18cfbd3861a5b9d2c8b7e1543a1fdc78ac2d7cd8dbe3443f319'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), + ('%s MPI' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/MPI', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft'] + ['libexec/mafft/%s' % x for x in [ + 'mxscarnamod', # installed by MAFFT Extensions + 'mpiscript', 'nodepair_mpi', # installed by MAFFT MPI + ]], + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +modextravars = {'MAFFT_N_THREADS_PER_PROCESS': '1'} +# MAFFT MPI requires other environment variables that depend on job resources +# More information at at https://mafft.cbrc.jp/alignment/software/mpi.html + +moduleclass = 'bio' From e84c8dfca01f29da36ff81351fb79d575ffa0c08 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Mar 2021 18:32:39 +0100 Subject: [PATCH 0422/2365] add linkcomm + rnetcarto extensions to R v4.0.3 --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 01414465fa..518da3d330 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2782,6 +2782,12 @@ exts_list = [ ('AnalyzeFMRI', '1.1-23', { 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.4', { + 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], + }), ] moduleclass = 'lang' From 8b427daeeb3389e9322d9238da15ebfb5e252d24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Mar 2021 22:17:16 +0100 Subject: [PATCH 0423/2365] remove duplicate memoise and RcppParallel extensions in R v4.0.3 easyconfig --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 518da3d330..559545c064 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2650,9 +2650,6 @@ exts_list = [ ('gWidgets2', '1.0-8', { 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), - ('memoise', '1.1.0', { - 'checksums': ['b276f9452a26aeb79e12dd7227fcc8712832781a42f92d70e86040da0573980c'], - }), ('gWidgets2tcltk', '1.0-6', { 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], # need to run installation via xvfb-run to avoid problems on headless systems: @@ -2761,9 +2758,6 @@ exts_list = [ ('sensemakr', '0.1.3', { 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], }), - ('RcppParallel', '5.0.2', { - 'checksums': ['8ca200908c6365aafb2063be1789f0894969adc03c0f523c6cc45434b8236f81'], - }), ('CompQuadForm', '1.4.3', { 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], }), From a084fbf088c435c35f661fd63f09d0ec8433ee9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Mar 2021 11:23:45 +0100 Subject: [PATCH 0424/2365] adding easyconfigs: ASE-3.21.1-fosscuda-2020b.eb, spglib-python-1.16.0-fosscuda-2020b.eb --- .../a/ASE/ASE-3.21.1-fosscuda-2020b.eb | 66 +++++++++++++++++++ .../spglib-python-1.16.0-fosscuda-2020b.eb | 27 ++++++++ 2 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..2bd3e58084 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.21.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.3.3'), + ('spglib-python', '1.16.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('itsdangerous', '1.1.0', { + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Flask', '1.1.2', { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('pytest-mock', '3.5.1', { + 'checksums': ['a1e2aba6af9560d313c642dae7e00a2a12b022b80301d9d7fc8ec6858e1dd9fc'], + }), + ('ase', version, { + 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..fb660979cf --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['94d056e48e7e6fe2e6fe4161471e774ac03221a6225fd83d551d3184220c1edf'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From 0d2491c88f983a1320d972c4374f86a3261925b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Mar 2021 11:25:07 +0100 Subject: [PATCH 0425/2365] adding easyconfigs: numba-0.52.0-fosscuda-2020b.eb --- .../n/numba/numba-0.52.0-fosscuda-2020b.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..91d83aab01 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.52.0' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('LLVM', '10.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('llvmlite', '0.35.0', { + 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", + 'checksums': [ + '80e51d5aa02ad72da9870e89d21f9b152b0220ca551b4596a6c0614bcde336fc', # llvmlite-0.35.0.tar.gz + # llvmlite-0.31.0_fix-ffi-Makefile.patch + '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', + ], + }), + (name, version, { + 'checksums': ['44661c5bd85e3d3619be0a40eedee34e397e9ccb3d4c458b70e10bf95d1ce933'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' From ef16fe93a9ccbff93614139e5fa0afba5fe88f37 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Mar 2021 11:29:00 +0100 Subject: [PATCH 0426/2365] adding easyconfigs: RDFlib-5.0.0-GCCcore-10.2.0.eb --- .../r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9034563c84 --- /dev/null +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'RDFlib' +version = '5.0.0' + +homepage = 'https://github.com/RDFLib/rdflib' +description = """RDFLib is a Python library for working with RDF, a simple yet powerful language + for representing information.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +use_pip = True + +exts_list = [ + ('isodate', '0.6.0', { + 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], + }), + ('rdflib', version, { + 'checksums': ['78149dd49d385efec3b3adfbd61c87afaf1281c30d3fcaf1b323b34f603fb155'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From a5e6510aba602fbc6c1fa836673eb312006726ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Mar 2021 11:43:53 +0100 Subject: [PATCH 0427/2365] adding easyconfigs: PyTorch-Geometric-1.6.3-foss-2020b.eb --- .../PyTorch-Geometric-1.6.3-foss-2020b.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb new file mode 100644 index 0000000000..ea3f074a2a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '1.6.3' + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', '1.7.1'), + ('scikit-learn', '0.23.2'), + ('scikit-image', '0.18.1'), + ('numba', '0.52.0'), + ('h5py', '3.1.0'), + ('tqdm', '4.56.2'), + ('RDFlib', '5.0.0'), + ('ASE', '3.21.1'), +] + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '0.7.3', { + 'checksums': ['5ac55b685cfcb3e8f70f3c5c2660bd1f6431a892a5319a612792b1ec09aec0f0'], + }), + ('torch_scatter', '2.0.5', { + 'checksums': ['148fbe634fb9e9465dbde2ab337138f63650ed8abbac42bb3f565e3fe92e9b2f'], + }), + ('torch_sparse', '0.6.8', { + 'checksums': ['312fb5ae6e4e575fca4bbc0bd092af85e7679d5b8e53459f24492fc2a073c7b6'], + }), + ('torch_cluster', '1.5.8', { + 'checksums': ['a0a32f63faac40a026ab1e9da31f6babdb4d937e53be40bd1c91d9b5a286eee6'], + }), + ('torch_spline_conv', '1.2.1', { + 'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'], + }), + ('python-louvain', '0.15', { + 'checksums': ['2a856edfbe29952a60a5538a84bb78cca18f6884a88b9325e85a11c8dd4917eb'], + 'modulename': 'community.community_louvain', + }), + ('torch_geometric', version, { + 'checksums': ['347f693bebcc8a621eda4867dafab91c04db5f596d7ed7ecb89b242f8ab5c6a1'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 1504282affde08c51aab0347b5e44376ff7a7aa7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Mar 2021 11:46:00 +0100 Subject: [PATCH 0428/2365] adding easyconfigs: PyTorch-Geometric-1.6.3-fosscuda-2020b.eb --- .../PyTorch-Geometric-1.6.3-fosscuda-2020b.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..d60a329fe1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '1.6.3' + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', '1.7.1'), + ('scikit-learn', '0.23.2'), + ('scikit-image', '0.18.1'), + ('numba', '0.52.0'), + ('h5py', '3.1.0'), + ('tqdm', '4.56.2'), + ('RDFlib', '5.0.0'), + ('ASE', '3.21.1'), +] + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '0.7.3', { + 'checksums': ['5ac55b685cfcb3e8f70f3c5c2660bd1f6431a892a5319a612792b1ec09aec0f0'], + }), + ('torch_scatter', '2.0.5', { + 'checksums': ['148fbe634fb9e9465dbde2ab337138f63650ed8abbac42bb3f565e3fe92e9b2f'], + }), + ('torch_sparse', '0.6.8', { + 'checksums': ['312fb5ae6e4e575fca4bbc0bd092af85e7679d5b8e53459f24492fc2a073c7b6'], + }), + ('torch_cluster', '1.5.8', { + 'checksums': ['a0a32f63faac40a026ab1e9da31f6babdb4d937e53be40bd1c91d9b5a286eee6'], + }), + ('torch_spline_conv', '1.2.1', { + 'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'], + }), + ('python-louvain', '0.15', { + 'checksums': ['2a856edfbe29952a60a5538a84bb78cca18f6884a88b9325e85a11c8dd4917eb'], + 'modulename': 'community.community_louvain', + }), + ('torch_geometric', version, { + 'checksums': ['347f693bebcc8a621eda4867dafab91c04db5f596d7ed7ecb89b242f8ab5c6a1'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 46553c33053a1cb3cb420ebe56755a8a2fd6735d Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 2 Mar 2021 11:53:57 +0000 Subject: [PATCH 0429/2365] libgcrypt and libgpg-error bumped up to latest --- .../libgcrypt-1.9.2-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ .../libgpg-error-1.41-GCCcore-10.2.0.eb | 27 +++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.41-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bee537ec24 --- /dev/null +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# based on libgcrypt-1.8.5-GCCcore-8.3.0.eb +# uploaded by J. Sassmannshausen + + +easyblock = 'ConfigureMake' + +name = 'libgcrypt' +version = '1.9.2' + +homepage = 'https://gnupg.org/related_software/libgcrypt/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['b2c10d091513b271e47177274607b1ffba3d95b188bbfa8797f948aec9053c5a'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('libgpg-error', '1.41')] + +sanity_check_paths = { + 'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.41-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.41-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..652f4aa22a --- /dev/null +++ b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.41-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# based on libgpg-error-1.38-GCCcore-8.3.0.eb +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'libgpg-error' +version = '1.41' + +homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['64b078b45ac3c3003d7e352a5e05318880a5778c42331ce1ef33d1a0d9922742'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/gpg-error-config', 'include/gpg-error.h', 'lib/libgpg-error.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From b971d02795af02e5ce4dd97e350d4774959e5daf Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 2 Mar 2021 13:08:20 +0000 Subject: [PATCH 0430/2365] New EC for libcotp and libbaseencode created --- .../libbaseencode-1.0.11-GCCcore-10.2.0.eb | 34 ++++++++++++++++++ .../l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c277c47c1f --- /dev/null +++ b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'libbaseencode' +version = '1.0.11' + +homepage = 'https://github.com/paolostivanin/libbaseencode' +description = """Library written in C for encoding and decoding +data using base32 or base64 according to RFC-4648""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/paolostivanin/libbaseencode/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['645329236992ee85f05569475da2af0f0d81aaccd4aebc8d0b8603e54a320935'] # v1.0.11.tar.gz + +builddependencies = [ + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), +] + +parallel = 1 + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libbaseencode.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bb91a4503b --- /dev/null +++ b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'libcotp' +version = '1.2.3' + +homepage = 'https://github.com/paolostivanin/libcotp' +description = """C library that generates TOTP and HOTP according to RFC-6238""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/paolostivanin/libcotp/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f122aea37337cdfcdaa1ce979ecfb5177ad7dcb273caf2d6056820f1dbf92e93'] # v1.2.3.tar.gz + +builddependencies = [ + ('CMake', '3.18.4'), + ('libgcrypt', '1.9.2'), + ('libbaseencode', '1.0.11'), + ('pkg-config', '0.29.2'), +] + +parallel = 1 + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libcotp.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'lib' From bbbfd997e75735df6ff6d72bd199b4aa562eed55 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 2 Mar 2021 14:29:22 +0100 Subject: [PATCH 0431/2365] LncLOOM: separate out pyBigWig, networkx --- .../g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb | 2 ++ .../l/LncLOOM/LncLOOM-2.0-foss-2020b.eb | 9 ++---- .../pyBigWig-0.3.18-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 3 files changed, 34 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb index 8885e2b6be..9e05e99db0 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb @@ -21,6 +21,8 @@ dependencies = [ ('Python', '3.8.6'), ] +sanity_check_commands = ["gurobi_cl --help"] + license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb b/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb index 8d8ba2eedc..d6ef6c36bf 100644 --- a/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb @@ -17,6 +17,8 @@ dependencies = [ ('BLAST+', '2.11.0'), ('Gurobi', '9.1.1'), ('Biopython', '1.78'), + ('pyBigWig', '0.3.18'), + ('networkx', '2.5'), ] use_pip = True @@ -26,18 +28,11 @@ exts_list = [ ('amply', '0.1.4', { 'checksums': ['cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38'], }), - ('networkx', '2.5', { - 'checksums': ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'], - }), ('PuLP', '2.4', { 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/coin-or/pulp/archive/'], 'checksums': ['d52d52b6078ea2c503b33814738866902d661cfe60d7a76251d50423e4af3ad0'], }), - ('pyBigWig', '0.3.18', { - 'modulename': 'pyBigWig', - 'checksums': ['4c2a8c571b4100ad7c4c318c142eb48558646be52aaab28215a70426f5be31bc'], - }), (name, version, { 'modulename': 'LncLOOMv2', 'patches': ['LncLOOM-2.0-config-from-environment.patch'], diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3bca83e40e --- /dev/null +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pyBigWig' +version = '0.3.18' + +github_account = 'deeptools' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """A python extension, written in C, for quick access to bigBed + files and access to and creation of bigWig files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['552564d8ce8720a8ae70ed5e5534617fb0cab306b666468d1c61b6d389b8a10c'] + +dependencies = [ + ('Python', '3.8.6'), + ('binutils', '2.35'), + ('cURL', '7.72.0'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' From 988b04c78fa2d425e5ac19e1fbe5cbbe8160bebb Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 2 Mar 2021 14:44:21 +0000 Subject: [PATCH 0432/2365] Binutils added --- .../l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb index c277c47c1f..694e34a5a2 100644 --- a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb @@ -20,6 +20,7 @@ checksums = ['645329236992ee85f05569475da2af0f0d81aaccd4aebc8d0b8603e54a320935'] builddependencies = [ ('CMake', '3.18.4'), ('pkg-config', '0.29.2'), + ('binutils', '2.35'), ] parallel = 1 diff --git a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb index bb91a4503b..5fd70b9bac 100644 --- a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('libgcrypt', '1.9.2'), ('libbaseencode', '1.0.11'), ('pkg-config', '0.29.2'), + ('binutils', '2.35'), ] parallel = 1 From 83ebe5156f8635d8477ecc3059869ccbed510786 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 2 Mar 2021 22:01:56 +0100 Subject: [PATCH 0433/2365] use dependency on Flask for ASE v3.21.1 --- .../a/ASE/ASE-3.21.1-foss-2020b.eb | 26 +++---------------- .../a/ASE/ASE-3.21.1-fosscuda-2020b.eb | 26 +++---------------- .../a/ASE/ASE-3.21.1-intel-2020b.eb | 26 +++---------------- 3 files changed, 9 insertions(+), 69 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb index 55cc585912..355fed1b39 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb @@ -15,9 +15,10 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Tkinter', '%(pyver)s'), + ('Flask', '1.1.2'), ('matplotlib', '3.3.3'), - ('spglib-python', '1.16.0'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional ] use_pip = True @@ -26,27 +27,6 @@ sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ - ('MarkupSafe', '1.1.1', { - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('Jinja2', '2.11.2', { - 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], - }), - ('Werkzeug', '1.0.1', { - 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('itsdangerous', '1.1.0', { - 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], - }), - ('Flask', '1.1.2', { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), - ('pytest-mock', '3.5.1', { - 'checksums': ['a1e2aba6af9560d313c642dae7e00a2a12b022b80301d9d7fc8ec6858e1dd9fc'], - }), ('ase', version, { 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], }), diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb index 2bd3e58084..2f564e84aa 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb @@ -15,9 +15,10 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Tkinter', '%(pyver)s'), + ('Flask', '1.1.2'), ('matplotlib', '3.3.3'), - ('spglib-python', '1.16.0'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional ] use_pip = True @@ -26,27 +27,6 @@ sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ - ('MarkupSafe', '1.1.1', { - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('Jinja2', '2.11.2', { - 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], - }), - ('Werkzeug', '1.0.1', { - 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('itsdangerous', '1.1.0', { - 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], - }), - ('Flask', '1.1.2', { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), - ('pytest-mock', '3.5.1', { - 'checksums': ['a1e2aba6af9560d313c642dae7e00a2a12b022b80301d9d7fc8ec6858e1dd9fc'], - }), ('ase', version, { 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], }), diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb index 528d78658c..c29ffe0592 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb @@ -15,9 +15,10 @@ toolchain = {'name': 'intel', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Tkinter', '%(pyver)s'), + ('Flask', '1.1.2'), ('matplotlib', '3.3.3'), - ('spglib-python', '1.16.0'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional ] use_pip = True @@ -30,27 +31,6 @@ check_ldshared = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ - ('MarkupSafe', '1.1.1', { - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('Jinja2', '2.11.2', { - 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], - }), - ('Werkzeug', '1.0.1', { - 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('itsdangerous', '1.1.0', { - 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], - }), - ('Flask', '1.1.2', { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), - ('pytest-mock', '3.5.1', { - 'checksums': ['a1e2aba6af9560d313c642dae7e00a2a12b022b80301d9d7fc8ec6858e1dd9fc'], - }), ('ase', version, { 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], }), From 9578ef8c74a71c595c84be509cd0ba2b6bc09d49 Mon Sep 17 00:00:00 2001 From: Alin M Elena Date: Tue, 2 Mar 2021 19:18:44 +0000 Subject: [PATCH 0434/2365] add dl poly 4 easyconfigs --- .../d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb | 19 +++++++++++++++++++ .../DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb new file mode 100644 index 0000000000..0a650f75d7 --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb @@ -0,0 +1,19 @@ +easyblock = 'CMakeMake' +name = "DL_POLY_4" +version = "5.0.0" +homepage = "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx" +description = "classical md" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://gitlab.com/ccp5/dl-poly/-/archive/%(version)s/'] +sources = ['dl_poly_%(version)s.tar.bz2'] +checksums = ['603019172ab37115149bee9c043c7d76db9e5fd60c2bdabde0e4cb2f14f09728'] +builddependencies = [('CMake', '3.18.4')] + +sanity_check_paths = { + 'files': ['bin/DLPOLY.Z'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb new file mode 100644 index 0000000000..b44019c119 --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb @@ -0,0 +1,19 @@ +easyblock = 'CMakeMake' +name = "DL_POLY_4" +version = "5.0.0" +homepage = "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx" +description = "classical md" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://gitlab.com/ccp5/dl-poly/-/archive/%(version)s/'] +sources = ['dl_poly_%(version)s.tar.bz2'] +checksums = ['603019172ab37115149bee9c043c7d76db9e5fd60c2bdabde0e4cb2f14f09728'] +builddependencies = [('CMake', '3.18.4')] + +sanity_check_paths = { + 'files': ['bin/DLPOLY.Z'], + 'dirs': [] +} + +moduleclass = 'chem' From de056d525330f266bc52159d913f91a5d215048c Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Tue, 2 Mar 2021 21:30:55 +0000 Subject: [PATCH 0435/2365] Update easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb index 0a650f75d7..a6ef70157e 100644 --- a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb @@ -2,7 +2,7 @@ easyblock = 'CMakeMake' name = "DL_POLY_4" version = "5.0.0" homepage = "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx" -description = "classical md" +description = "DL_POLY is a general purpose classical molecular dynamics (MD) simulation software" toolchain = {'name': 'foss', 'version': '2020b'} From 67a74620fdbc08d21a71df0bde47b7a1e7bd8123 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Tue, 2 Mar 2021 21:31:04 +0000 Subject: [PATCH 0436/2365] Update easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb index b44019c119..77e8e8fecd 100644 --- a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb +++ b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb @@ -2,7 +2,7 @@ easyblock = 'CMakeMake' name = "DL_POLY_4" version = "5.0.0" homepage = "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx" -description = "classical md" +description = "DL_POLY is a general purpose classical molecular dynamics (MD) simulation software" toolchain = {'name': 'intel', 'version': '2020b'} From d681ea2ac3bf9133e5770f82e09fd60d3b8a5ac5 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 3 Mar 2021 08:57:53 +0000 Subject: [PATCH 0437/2365] adding easyconfigs: tensorflow-probability-0.12.1-foss-2020b-Python-3.8.6.eb, tensorflow-probability-0.12.1-fosscuda-2020b-Python-3.8.6.eb, dm-tree-0.1.5-GCCcore-10.2.0.eb --- .../d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a047c7fe01 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'dm-tree' +version = '0.1.5' + +homepage = 'https://github.com/deepmind/tree' +description = """dm-tree provides tree, a library for working with nested data structures. In a way, +tree generalizes the builtin map function which only supports flat sequences, and +allows to apply a function to each "leaf" preserving the overall structure.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a951d2239111dfcc468071bc8ff792c7b1e3192cab5a3c94d33a8b2bda3127fa'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bazel', '3.7.2'), +] +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True + +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'tree'} + +moduleclass = 'lib' From eca628625b9e137e529ca81d0e2e0a11f415ffa9 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 3 Mar 2021 09:12:16 +0000 Subject: [PATCH 0438/2365] Removed unused version suffix. --- ...ensorflow-probability-0.12.1-foss-2020b.eb | 48 +++++++++++++++++++ ...rflow-probability-0.12.1-fosscuda-2020b.eb | 48 +++++++++++++++++++ 2 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb new file mode 100644 index 0000000000..703eaf3b6b --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'PythonBundle' + +name = 'tensorflow-probability' +version = '0.12.1' + +homepage = 'https://www.tensorflow.org/probability' +description = """TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('TensorFlow', '2.4.1'), + ('dm-tree', '0.1.5'), +] + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +use_pip = True + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + (name, version, { + 'modulename': 'tensorflow_probability', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/probability/archive/'], + 'unpack_sources': False, + 'checksums': ['1fe89e85fd053bf36e8645a5a1a53b729bc254cf1516bc224fcbd1e4ff50083a'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..77a2363663 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'PythonBundle' + +name = 'tensorflow-probability' +version = '0.12.1' + +homepage = 'https://www.tensorflow.org/probability' +description = """TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('TensorFlow', '2.4.1'), + ('dm-tree', '0.1.5'), +] + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +use_pip = True + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + (name, version, { + 'modulename': 'tensorflow_probability', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/probability/archive/'], + 'unpack_sources': False, + 'checksums': ['1fe89e85fd053bf36e8645a5a1a53b729bc254cf1516bc224fcbd1e4ff50083a'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +sanity_pip_check = True + +moduleclass = 'lib' From fa37dd186b16f90bf988a06c23b34be9a380a1ea Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 3 Mar 2021 08:48:36 -0800 Subject: [PATCH 0439/2365] fix file name typo --- .../SRA-Toolkit-2.10.9-gompi-2020b.eb | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb new file mode 100644 index 0000000000..02c2d54a58 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb @@ -0,0 +1,104 @@ +easyblock = 'Bundle' + +name = 'SRA-Toolkit' +version = '2.10.9' + +homepage = 'https://github.com/ncbi/sra-tools' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" +github_account = 'ncbi' + +toolchain = {'name': 'gompi', 'version': '2020b'} + +builddependencies = [ + ('Perl', '5.32.0'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('NGS', '2.10.9'), + ('file', '5.39'), # provides libmagic + ('HDF5', '1.10.7'), + ('libxml2', '2.9.10'), +] + +# Add addtional libraries needed to statically link HDF5 from EB +local_base_preconfig = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl && " + +# Change default build directory and add paths to dependencies in EB +local_base_config = '--build-prefix=%(builddir)s --with-ngs-sdk-prefix=$EBROOTNGS ' +local_base_config += '--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2' +local_vdb_config = local_base_config + ' --with-ngs-java-prefix=$EBROOTNGS/jar/ngs-java.jar' +# SRA-Tools need the source and build directory of NCBI-VDB +local_sra_config = local_base_config + ' --with-ncbi-vdb-sources=%(builddir)s/ncbi-vdb-%(version)s' +local_sra_config += ' --with-ncbi-vdb-build=%(builddir)s/ncbi-vdb ' + +# Replace hardcoded optimization flags with flags from EB +local_base_prebuild = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && " +local_base_prebuild += 'EBFLAGS="$CFLAGS" ' +local_base_preinstall = 'EBFLAGS="$CFLAGS" ' + +# Standalone compilation of utf8proc to ensure that its shared objects are available +local_sra_prebuild = "make -C tools/driver-tool/utf8proc && " +# Add addtional libraries needed to statically link HDF5 from EB +local_sra_prebuild += "sed -i 's/-sm/-sm -lmpi -lsz/' tools/pacbio-load/Makefile && " +# Add additional libraries needed to statically link libxml2 from EB +local_sra_prebuild += "find build/ -name \"ld*.sh\" -exec sed -i 's/-lxml2/-lxml2 -lz -llzma/g' {} + && " +local_sra_prebuild += local_base_prebuild + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'start_dir': '%(namelower)s-%(version)s', + 'preconfigopts': local_base_preconfig, + 'preinstallopts': local_base_preinstall, +} + +components = [ + # NCBI-VDB has to be installed as component instead of dependency because SRA-Tools needs its sources + ('NCBI-VDB', version, { + 'patches': ['NCBI-VDB-%(version)s_fix-LD_LIBRARY_PATH.patch'], + 'checksums': [ + '3707f81412dbf6ce2b29d3e65e364116c86acc534543e5a084cf8a666b81960d', # NCBI-VDB-2.10.9.tar.gz + # NCBI-VDB-2.10.9_fix-LD_LIBRARY_PATH.patch + '054a927baea72d508033974ad6ac072e58aae715d437adb2179b3bc8b62c89d9', + ], + 'configopts': local_vdb_config, + 'prebuildopts': local_base_prebuild, + }), + ('SRA-Tools', version, { + 'patches': ['SRA-Toolkit-%(version)s_fix-LD_LIBRARY_PATH.patch'], + 'checksums': [ + '9f9f31cd861bb52a49114c553ea38a0166e4e161345f12c364167865f4dbdaae', # SRA-Tools-2.10.9.tar.gz + # SRA-Toolkit-2.10.9_fix-LD_LIBRARY_PATH.patch + 'dd2b6a14d42104a513cc7aeb28a37ac9f685aa2b1713cc02ef27c49280e775f3', + ], + 'configopts': local_sra_config, + 'prebuildopts': local_sra_prebuild, + }), +] + +local_bin = ['abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', + 'fastq-dump', 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'kget', + 'latf-load', 'magic', 'pacbio-load', 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', + 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', 'sratools', 'srf-load', 'test-sra', 'vdb-config', + 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock', 'vdb-passwd', 'vdb-unlock', + 'vdb-validate'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin] + + ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + + [('lib/libncbi-%s.%s' % (l, e), 'lib64/libncbi-%s.%s' % (l, e)) + for l in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [] +} + +sanity_check_commands = [ + "abi-dump --help", + "kar --help", + "sra-sort --help", +] + +moduleclass = 'bio' From f1a5530759339fbe129090c613877791159e41ce Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 3 Mar 2021 10:42:13 -0800 Subject: [PATCH 0440/2365] fix checksum --- .../easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb index 02c2d54a58..ba95e2ddc3 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb @@ -63,7 +63,7 @@ components = [ 'checksums': [ '3707f81412dbf6ce2b29d3e65e364116c86acc534543e5a084cf8a666b81960d', # NCBI-VDB-2.10.9.tar.gz # NCBI-VDB-2.10.9_fix-LD_LIBRARY_PATH.patch - '054a927baea72d508033974ad6ac072e58aae715d437adb2179b3bc8b62c89d9', + 'd59fe4a4fa302485f72a6313a6348c3eda3570f9c9309737ddfb77abf28701b5', ], 'configopts': local_vdb_config, 'prebuildopts': local_base_prebuild, From e76ce0269c8e14d1a9cfcdad95dd390ec3670124 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 4 Mar 2021 11:58:49 +0200 Subject: [PATCH 0441/2365] adding easyconfigs: GROMACS-2021-fosscuda-2020b.eb --- .../g/GROMACS/GROMACS-2021-fosscuda-2020b.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb new file mode 100644 index 0000000000..5a529a9533 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb @@ -0,0 +1,87 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI builds. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', +] +checksums = [ + 'efa78ab8409b0f5bf0fbca174fb8fbcf012815326b5c71a9d7c385cde9a8f87b', # gromacs-2021.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch + '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 6152ae96a482d9678e5a69deb4ff5fac20ab8cd3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 4 Mar 2021 15:24:09 +0100 Subject: [PATCH 0442/2365] adding easyconfigs: CP2K-7.1-foss-2020b-psmp.eb --- .../c/CP2K/CP2K-7.1-foss-2020b-psmp.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb new file mode 100644 index 0000000000..b30d1ea594 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb @@ -0,0 +1,37 @@ +name = 'CP2K' +version = '7.1' +versionsuffix = '-psmp' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ccd711a09a426145440e666310dd01cc5772ab103493c4ae6a3470898cd0addb'] + +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '4.3.4'), + ('libxsmm', '1.16.1'), + ('FFTW', '3.3.8'), + ('PLUMED', '2.6.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.1'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' From b3de1c8560207b4389988761a14e68f39950b649 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 4 Mar 2021 16:17:21 -0800 Subject: [PATCH 0443/2365] change toolchain, remove suffix --- .../d/DBD-mysql/DBD-mysql-4.050-GCC-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-10.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-10.2.0.eb new file mode 100644 index 0000000000..b9c2fcbe4a --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.050' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78'] + +dependencies = [ + ('Perl', '5.32.0'), + ('MariaDB', '10.5.8'), + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql'], +} + +moduleclass = 'data' From 3b52d34313c8750ba0d22cf918fc6d1a375a13c6 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 4 Mar 2021 17:07:33 -0800 Subject: [PATCH 0444/2365] drop suffix --- .../Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb new file mode 100644 index 0000000000..147bdf54a2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'Bio-DB-HTS' +version = '3.01' + +homepage = 'https://metacpan.org/release/Bio-DB-HTS' +description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/'] +sources = ['Bio-DB-HTS-%(version)s.tar.gz'] +checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('Perl', '5.32.0'), + ('BioPerl', '1.7.8'), + ('HTSlib', '1.11'), +] + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' From fd8c8ae596774ff1d9a50495dee8aa3d72a052dd Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 5 Mar 2021 09:05:48 +0200 Subject: [PATCH 0445/2365] adding easyconfigs: POV-Ray-3.7.0.8-GCC-10.2.0.eb, POV-Ray-3.7.0.8-iccifort-2020.4.304.eb, SDL2-2.0.14-GCCcore-10.2.0.eb --- .../p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb | 64 +++++++++++++++++++ .../POV-Ray-3.7.0.8-iccifort-2020.4.304.eb | 64 +++++++++++++++++++ .../s/SDL2/SDL2-2.0.14-GCCcore-10.2.0.eb | 38 +++++++++++ 3 files changed, 166 insertions(+) create mode 100644 easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.14-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb new file mode 100644 index 0000000000..324aa70c0d --- /dev/null +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb @@ -0,0 +1,64 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'POV-Ray' +version = '3.7.0.8' + +homepage = 'http://www.povray.org/' +description = """The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program + which generates images from a text-based scene description, and is available for a variety + of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning + three-dimensional graphics. The source code is available for those wanting to do their own ports.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/POV-Ray/povray/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['POV-Ray-3.7.0.7_dont-touch-home.patch'] +checksums = [ + '53d11ebd2972fc452af168a00eb83aefb61387662c10784e81b63e44aa575de4', # v3.7.0.8.tar.gz + '45103afca808e279dcdee80194c65e2a760c76d011d351392a46e817b0b655f7', # POV-Ray-3.7.0.7_dont-touch-home.patch +] + +dependencies = [ + ('Boost', '1.74.0'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('X11', '20201008'), + ('LibTIFF', '4.1.0'), + ('SDL2', '2.0.14'), +] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " +preconfigopts += " ./prebuild.sh && cd .. && " +configopts = "COMPILED_BY='EasyBuild' " +configopts += "--with-boost=$EBROOTBOOST --with-zlib=$EBROOTZLIB --with-libpng=$EBROOTLIBPNG " +configopts += "--with-libtiff=$EBROOTLIBTIFF --with-libjpeg=$EBROOTLIBJPEGMINTURBO --with-libsdl=$EBROOTSDL2 " +# configopts += " --with-libmkl=DIR " ## upstream needs to fix this, still in BETA + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/povray'], + 'dirs': ['etc/povray/%(version_major_minor)s', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..4af74f0acd --- /dev/null +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb @@ -0,0 +1,64 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'POV-Ray' +version = '3.7.0.8' + +homepage = 'http://www.povray.org/' +description = """The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program + which generates images from a text-based scene description, and is available for a variety + of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning + three-dimensional graphics. The source code is available for those wanting to do their own ports.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/POV-Ray/povray/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['POV-Ray-3.7.0.7_dont-touch-home.patch'] +checksums = [ + '53d11ebd2972fc452af168a00eb83aefb61387662c10784e81b63e44aa575de4', # v3.7.0.8.tar.gz + '45103afca808e279dcdee80194c65e2a760c76d011d351392a46e817b0b655f7', # POV-Ray-3.7.0.7_dont-touch-home.patch +] + +dependencies = [ + ('Boost', '1.74.0'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('X11', '20201008'), + ('LibTIFF', '4.1.0'), + ('SDL2', '2.0.14'), +] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " +preconfigopts += " ./prebuild.sh && cd .. && " +configopts = "COMPILED_BY='EasyBuild' " +configopts += "--with-boost=$EBROOTBOOST --with-zlib=$EBROOTZLIB --with-libpng=$EBROOTLIBPNG " +configopts += "--with-libtiff=$EBROOTLIBTIFF --with-libjpeg=$EBROOTLIBJPEGMINTURBO --with-libsdl=$EBROOTSDL2 " +# configopts += " --with-libmkl=DIR " ## upstream needs to fix this, still in BETA + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/povray'], + 'dirs': ['etc/povray/%(version_major_minor)s', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bd457ee7f5 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.14-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.14' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d8215b571a581be1332d2106f8036fcb03d12a70bae01e20f424976d275432bc'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('X11', '20201008'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 8729a57ce397606f808b11afcede91356a8f1bb4 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 5 Mar 2021 09:29:01 +0200 Subject: [PATCH 0446/2365] Change http: to https: --- easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb | 2 +- .../p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb index 324aa70c0d..9e1a9b5183 100644 --- a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'POV-Ray' version = '3.7.0.8' -homepage = 'http://www.povray.org/' +homepage = 'https://www.povray.org/' description = """The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb index 4af74f0acd..ca4823d48b 100644 --- a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'POV-Ray' version = '3.7.0.8' -homepage = 'http://www.povray.org/' +homepage = 'https://www.povray.org/' description = """The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning From 81ac1b42374415d2687420b46e622c96bc37aebd Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 5 Mar 2021 09:42:58 +0100 Subject: [PATCH 0447/2365] use 'openmp': True --- easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb index b30d1ea594..ce2ab7909a 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb @@ -9,7 +9,7 @@ description = """CP2K is a freely available (GPL) program, written in Fortran 95 classical pair and many-body potentials. """ toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'openmp': True} source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] sources = [SOURCELOWER_TAR_BZ2] From c612bdb3a239dd799dc862808f5a7b5c8d742f16 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 5 Mar 2021 12:37:40 +0100 Subject: [PATCH 0448/2365] adding easyconfigs: spglib-1.16.1-GCCcore-10.2.0.eb, pFUnit-4.2.0-gompi-2020b.eb --- .../p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb | 65 +++++++++++++++++++ .../s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb | 29 +++++++++ 2 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb new file mode 100644 index 0000000000..4b91fe9623 --- /dev/null +++ b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'pFUnit' +version = '4.2.0' +local_fargparse_major_minor_version = '1.1' +local_gftl_major_minor_version = '1.3' +local_gftl_shared_major_minor_version = '1.2' + +homepage = 'https://github.com/Goddard-Fortran-Ecosystem/pFUnit' +description = """pFUnit is a unit testing framework enabling JUnit-like testing of serial + and MPI-parallel software written in Fortran.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +# Release does not include git submodules so do explicit clone instead +sources = [{ + 'git_config': { + 'url': 'https://github.com/Goddard-Fortran-Ecosystem', + 'repo_name': 'pFUnit', + 'commit': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +# can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' +checksums = [None] + +builddependencies = [('CMake', '3.18.4')] +dependencies = [('Python', '3.8.6')] + +sanity_check_paths = { + 'files': [ + 'PFUNIT-%(version_major_minor)s/bin/funitproc', + 'PFUNIT-%(version_major_minor)s/lib/libpfunit.a' + ], + 'dirs': [ + 'FARGPARSE-%s' % local_fargparse_major_minor_version, + 'GFTL-%s' % local_gftl_major_minor_version, + 'GFTL_SHARED-%s' % local_gftl_shared_major_minor_version, + ], +} + +modextrapaths = { + 'PATH': ['PFUNIT-%(version_major_minor)s/bin'], + 'CPATH': [ + 'FARGPARSE-%s/include' % local_fargparse_major_minor_version, + 'GFTL-%s/include' % local_gftl_major_minor_version, + 'GFTL_SHARED-%s/include' % local_gftl_shared_major_minor_version, + 'PFUNIT-%(version_major_minor)s/include', + ], + 'LD_LIBRARY_PATH': [ + 'FARGPARSE-%s/lib' % local_fargparse_major_minor_version, + 'GFTL-%s/lib' % local_gftl_major_minor_version, + 'GFTL_SHARED-%s/lib' % local_gftl_shared_major_minor_version, + 'PFUNIT-%(version_major_minor)s/lib', + ], + 'CMAKE_PREFIX_PATH': [ + 'FARGPARSE-%s/cmake' % local_fargparse_major_minor_version, + 'GFTL-%s/cmake' % local_gftl_major_minor_version, + 'GFTL_SHARED-%s/cmake' % local_gftl_shared_major_minor_version, + 'PFUNIT-%(version_major_minor)s/cmake', + ], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..466567a921 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spglib' +version = '1.16.1' + +homepage = 'https://spglib.github.io/spglib/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/spglib/spglib/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e90682239e4ef63b492fa4e44f7dbcde2e2fe2e688579d96b01f2730dfdf5b2e'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': [ + 'include/spglib.h', + 'lib/libsymspg.a', + 'lib/libsymspg.%s' % SHLIB_EXT + ], + 'dirs': [''], +} + +moduleclass = 'chem' From 17a4b2200487f9a9aa3f7460f3640826b6534704 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 5 Mar 2021 13:17:13 +0000 Subject: [PATCH 0449/2365] netCDF:add patch fixing MPI_Info_f2c OpenMPI issue This affects versions 4.6.2 to 4.7.4, see https://github.com/Unidata/netcdf-c/pull/1957 --- easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020b.eb index f7f2694014..a4b54ce60d 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020b.eb @@ -11,10 +11,14 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['netCDF-%(version)s_fix-ocdebug.patch'] +patches = [ + 'netCDF-%(version)s_fix-ocdebug.patch', + 'netCDF-%(version)s-fix-mpi-info-f2c.patch', +] checksums = [ '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b', # v4.7.4.tar.gz '94c9883005f189a4551947e04191a68199cf4cdcada4b2d313115720fb4690e9', # netCDF-4.7.4_fix-ocdebug.patch + '7ff8a922ca3be35fca261a94f725abde32807f17c196c475053a570f03eb7396', # netCDF-4.7.4-fix-mpi-info-f2c.patch ] builddependencies = [ From 284e1533368ac8ef3e94f122996f46d31982ebbd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Mar 2021 15:02:01 +0100 Subject: [PATCH 0450/2365] add SourceForge fallback source URL for recent freetype easyconfigs --- .../easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb index 85cc3b228e..c9318c29a8 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb @@ -14,7 +14,10 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = [GNU_SAVANNAH_SOURCE] +source_urls = [ + GNU_SAVANNAH_SOURCE, + SOURCEFORGE_SOURCE, +] sources = [SOURCE_TAR_GZ] checksums = ['9dfb4e11efd6e460a87b1991a64bc69344ee7dc219d9b29e7faabc1c168ce8b0'] From edcd9fa6d402487cae99ced7bc08f9c5220d3587 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 5 Mar 2021 16:19:37 +0200 Subject: [PATCH 0451/2365] Fix style issues identified by @akesandgren in PR #12336 --- .../easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb | 9 ++++----- .../p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb | 9 ++++----- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb index 9e1a9b5183..d62876e7b1 100644 --- a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb @@ -32,6 +32,10 @@ checksums = [ '45103afca808e279dcdee80194c65e2a760c76d011d351392a46e817b0b655f7', # POV-Ray-3.7.0.7_dont-touch-home.patch ] +builddependencies = [ + ('Autotools', '20200321'), +] + dependencies = [ ('Boost', '1.74.0'), ('zlib', '1.2.11'), @@ -42,11 +46,6 @@ dependencies = [ ('SDL2', '2.0.14'), ] -builddependencies = [ - ('binutils', '2.35'), - ('Autotools', '20200321'), -] - preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " preconfigopts += " ./prebuild.sh && cd .. && " configopts = "COMPILED_BY='EasyBuild' " diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb index ca4823d48b..6891669c1a 100644 --- a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb @@ -32,6 +32,10 @@ checksums = [ '45103afca808e279dcdee80194c65e2a760c76d011d351392a46e817b0b655f7', # POV-Ray-3.7.0.7_dont-touch-home.patch ] +builddependencies = [ + ('Autotools', '20200321'), +] + dependencies = [ ('Boost', '1.74.0'), ('zlib', '1.2.11'), @@ -42,11 +46,6 @@ dependencies = [ ('SDL2', '2.0.14'), ] -builddependencies = [ - ('binutils', '2.35'), - ('Autotools', '20200321'), -] - preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " preconfigopts += " ./prebuild.sh && cd .. && " configopts = "COMPILED_BY='EasyBuild' " From 60c693cafe5e603ecd221ee3342f81e8c4a03fbd Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Fri, 5 Mar 2021 14:36:47 +0000 Subject: [PATCH 0452/2365] adding easyconfigs: R-4.0.3-fosscuda-2020b.eb --- .../easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 2804 +++++++++++++++++ 1 file changed, 2804 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..eb09ea2bb5 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -0,0 +1,2804 @@ +name = 'R' +version = "4.0.3" + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.9'), +] +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('PCRE2', '10.35'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.5'), # for plottting in R + ('LibTIFF', '4.1.0'), + ('Java', '11', '', True), + ('Tk', '8.6.10'), # for tcltk + ('cURL', '7.72.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.0'), # for igraph + ('NLopt', '2.6.2'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '67.1'), # for rJava & gdsfmt + ('HDF5', '1.10.7'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.10-35'), # for animation + ('GLPK', '4.65'), # for Rglpk + ('nodejs', '12.19.0'), # for V8 (required by rstan) + ('pocl', '1.6'), # for OpenCL support (particularly on POWER) + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +# replace hardcoded CUDA compute capabilitites in liquidSVM +local_cuda_cc = [c.replace('.', '') for c in cuda_compute_capabilities] +local_cuda_arch = "-arch sm_%s" % local_cuda_cc[0] +local_cuda_gencode = ' '.join(['-gencode=arch=compute_%s,code=sm_%s' % (c, c) for c in local_cuda_cc]) +local_liquidSVM_sed = "sed -i 's/-arch sm_30/%s %s/' src/Makevars.in" % (local_cuda_arch, local_cuda_gencode) +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 10 Nov 2020 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9', { + 'checksums': ['b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.5', { + 'checksums': ['b8462c643bcc6fe3b0e9caee9e0cd76c5f7f0e34ee2e7397f93c4c43885c5c04'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '4.0.4', { + 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], + }), + ('bnlearn', '4.6.1', { + 'checksums': ['e4544465af3330e53e4777079c448585a8a97be2d3862a5264169007c20daeaf'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.15', { + 'checksums': ['65f964aa768d0703ceb7a199adc5e79ca79a6d29d7bc053a262eb533697686c0'], + }), + ('formatR', '1.7', { + 'checksums': ['a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb'], + }), + ('gtools', '3.8.2', { + 'checksums': ['503ba60a41f3c61b8129c25de62c74dab29761d2e661d4addd106e2e02f1dcde'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('highr', '0.8', { + 'checksums': ['4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.9', { + 'checksums': ['2ccf97d2940a09539dc051c7a9a1aee90ef04b34e9bc6c0b64b4435fb3c2fa80'], + }), + ('xfun', '0.19', { + 'checksums': ['3b027bade119637478eb25733fc6702ad8de48aa199e044e4b3cbd40e78bde97'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-1', { + 'checksums': ['748141d56531a39dc4d37cf0a5165a40b653a04c507e916854053ed77119e0e6'], + }), + ('NLP', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '5.4.6', { + 'checksums': ['d4ffcf36bf709ad42dccb2387263f67ca32012b0707f0ef6eda32730b5c286fc'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('segmented', '1.3-0', { + 'checksums': ['a58fe9503570d89b2521237ba5c2be274ea40f0a3d854fc68c4422891cb536a9'], + }), + ('som', '0.3-5.1', { + 'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'], + }), + ('SuppDists', '1.1-9.5', { + 'checksums': ['680b67145c07d44e200275e08e48602fe19cd99fb106c05422b3f4a244c071c4'], + }), + ('stabledist', '0.7-1', { + 'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'], + }), + ('survivalROC', '1.0.3', { + 'checksums': ['1449e7038e048e6ad4d3f7767983c0873c9c7a7637ffa03a4cc7f0e25c31cd72'], + }), + ('pspline', '1.0-18', { + 'checksums': ['f71cf293bd5462e510ac5ad16c4a96eda18891a0bfa6447dd881c65845e19ac7'], + }), + ('timeDate', '3043.102', { + 'checksums': ['377cba03cddab8c6992e31d0683c1db3a73afa9834eee3e95b3b0723f02d7473'], + }), + ('longmemo', '1.1-2', { + 'checksums': ['7964e982287427dd58f98e1144e468ae0cbd572d25a4bea6ca9ae9c7522f3207'], + }), + ('ADGofTest', '0.3', { + 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], + }), + ('MASS', '7.3-53', { + 'checksums': ['41824e70ada302a620226c0f17b1b2c880c6d1a3a100b53bd6df8e8c97e64b38'], + }), + ('pixmap', '0.4-11', { + 'checksums': ['6fa010749a59cdf56aad9f81271473b7d55697036203f2cd5d81372bcded7412'], + }), + ('lattice', '0.20-41', { + 'checksums': ['54ca557f0cb33df60eb10b883c2ed2847e061ddd57ed9b5dd7695149609d57b5'], + }), + ('sp', '1.4-4', { + 'checksums': ['fa878a6541a8565fe831c02991427b94fa7195aab5ce957708631516dd0bfc7f'], + }), + ('pkgconfig', '2.0.3', { + 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], + }), + ('rlang', '0.4.8', { + 'checksums': ['2580d4aef178248b3d44767f5e735a6d2752a566045cbeb53154f1fb17b7107d'], + }), + ('ellipsis', '0.3.1', { + 'checksums': ['4f8a15158dfc27cdc0f7554c7a61e92b02e4d70bfc3d968f01a99da2189b75db'], + }), + ('digest', '0.6.27', { + 'checksums': ['f485f75122907da24c41d4a62c91a232f0c371befd2f77e973342a1bef00253f'], + }), + ('glue', '1.4.2', { + 'checksums': ['9f7354132a26e9a876428fa87629b9aaddcd558f9932328e6ac065b95b8ef7ad'], + }), + ('vctrs', '0.3.4', { + 'checksums': ['eb47411c9e980a555f5819a7bce46896775df2ca7c9eaa7bf0a9c16f067b7877'], + }), + ('hms', '0.5.3', { + 'checksums': ['4e2b67c8cf65fe86179f24f42d82b3ca9377d5907837bda98b4fc6c2318853ad'], + }), + ('prettyunits', '1.1.1', { + 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], + }), + ('R6', '2.5.0', { + 'checksums': 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['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-7', { + 'checksums': ['b3b186559b157497fb78a11ec46e2b49045ba04879e3faf30a75c1c73317464f'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.11-2', { + 'checksums': ['8385be32f6b6b6f1b32df15f42073b191d714d870bbb4f95875b64aff6112bbf'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('visNetwork', '2.0.9', { + 'checksums': ['5e0b3dc3a91e66e0a359433f03cc856d04b981b0f9ad228d8fa9c96b7fcaa420'], + }), + ('servr', '0.20', { + 'checksums': ['83863e68e78c49d84c5b56c67fa88a69837d575eeb889ce3e29160c3e62ea75f'], + }), + ('rgexf', '0.16.0', { + 'checksums': ['2a671df9ac70cfefd4092754317cb28e32a33df345b80e1975bf838e838245ee'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.6.1', { + 'checksums': ['be4e4c520a3692902ce405e8225aef9f3d5f0cd11fcde614f6541e981b63673d'], + }), + ('sem', '3.1-11', { + 'checksums': ['33b1ad7695db13af8cdd214f5d388db494528b433c61c7ad89970cefcc8b430e'], + }), + ('network', '1.16.1', { + 'checksums': ['eb6435794cacc81abe1664391e8dcf1c10112bbb76fff9016dd6dbb8e83efeb1'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('statnet.common', '4.4.1', { + 'checksums': ['4ecf2b84718d7fb60f196215b4cf6f52cd6b26cc9148a6da6981b26e885509fd'], + }), + ('sna', '2.6', { + 'checksums': ['3a016550d9f424a0613c3f5b0b680dbd3a1f20a343173d39a96034340ad9202a'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.4.1', { + 'checksums': ['78ef9eae464d52c5247998b9514a81b178419b857b1a6c00d885e3ae6c03a886'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('BDgraph', '2.63', { + 'checksums': ['cc474e1315a04f67fbf14461d35004c899d031c31f18be7d3db076dbf66a0617'], + }), + ('pbapply', '1.4-3', { + 'checksums': ['8fe6287535be766b5a688810e2cc1ca4e668ac6b42b6e832473fe5701133eb21'], + }), + ('graphlayouts', '0.7.1', { + 'checksums': ['380f8ccb0b08735694e83f661fd56a0d592a78448ae91b89c290ba8582d66717'], + }), + ('tweenr', '1.0.1', { + 'checksums': ['efd68162cd6d5a4f6d833dbf785a2bbce1cb7b9f90ba3fb060931a4bd705096b'], + }), + ('ggforce', '0.3.2', { + 'checksums': ['4cce8acb60ce06af44c1c76bbacd7de129eed9b51ed6a85e03a9bf55b0eff4d2'], + }), + ('tidygraph', '1.2.0', { + 'checksums': ['057d6c42fc0144109f3ace7f5058cca7b2fe493c761daa991448b23f86b6129f'], + }), + ('ggraph', '2.0.3', { + 'checksums': ['78fb263fb7999c4c060efb6ee66c5de0547f17e2ec4bec066be612f58134e0df'], + }), + ('qgraph', '1.6.5', { + 'checksums': ['2295ccca41f84cba34ad0e6c1b31af8bde79bda7373754c255e0ee9e63d29e5f'], + }), + ('HWxtest', '1.1.9', { + 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], + 'checksums': [ + 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + ], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.19', { + 'checksums': ['4cd2d080628482f4c6ecab593313d7e42516f5ff13fbf9f90e461fcad0580738'], + }), + ('geepack', '1.3-1', { + 'checksums': ['823153ca28e1a8bd8a45de778279480c1c35e063d62c8955b6cea1602f28d6df'], + }), + ('biom', '0.3.12', { + 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], + }), + ('pim', '2.0.2', { + 'checksums': ['1195dbdbd67348dfef4b6fc34fcec643da685ebe58d34bbe049ab121aca9944f'], + }), + ('minpack.lm', '1.2-1', { + 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], + }), + ('rootSolve', '1.8.2.1', { + 'checksums': ['488451182663197ae4513e46e24f72cadb2297d35a58a3007a0dbf1bf0833031'], + }), + ('diagram', '1.6.5', { + 'checksums': ['e9c03e7712e0282c5d9f2b760bafe2aac9e99a9723578d9e6369d60301f574e4'], + }), + ('FME', '1.3.6.1', { + 'checksums': ['ae0c69f75614e2ef9f2096c205c7f8eb90485c6311213762c1416ece4036be18'], + }), + ('bmp', '0.3', { + 'checksums': ['bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649'], + }), + ('tiff', '0.1-5', { + 'checksums': ['9514e6a9926fcddc29ce1dd12b1072ad8265900373f738de687ef4a1f9124e2b'], + }), + ('readbitmap', '0.1.5', { + 'checksums': ['737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291'], + }), + ('imager', '0.42.3', { + 'checksums': ['6fc308153df8251cef48f1e13978abd5d29ec85046fbe0b27c428801d05ebbf3'], + }), + ('signal', '0.7-6', { + 'checksums': ['6b60277b07cf0167f8272059b128cc82f27a9bab1fd33d74c2a9e1f2abca5def'], + }), + ('tuneR', '1.3.3', { + 'checksums': ['bdc3c2017b162d2ba0a249e80361a4f47202e763c21aecfc57380a482a3a692b'], + }), + ('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-7', { + 'checksums': ['52e0397a45325aa9586ec68b94ab9e505bdefaf2a588d634fcb57a6a11659c74'], + }), + ('fftw', '1.0-6', { + 'checksums': ['397ef5ec354b919884f74fba4202bfc13ad11a70b16285c41677aad1d3b170ce'], + }), + ('seewave', '2.1.6', { + 'checksums': ['84a0a0035737574a65f371fa4a20a1a3a66de195efe41975f21be8fb001e7088'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('oce', '1.2-0', { + 'checksums': ['99072f2b20ad471b5a2afeb4d0690cad57cc770d60769a5cb20d001511439aa2'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.3', { + 'checksums': ['276164d5eb92c78726c647be16232d2443acbf7061371ddde2672b4fdb7a069a'], + }), + ('memuse', '4.1-0', { + 'checksums': ['58d6d1ca5d6bd481f4ed299eff6a9d5660eb0f8db1abe54c49e144093cba72ad'], + }), + ('pinfsc50', '1.2.0', { + 'checksums': ['ed1fe214b9261feef8abfbf724c2bd9070d68e99a6ea95208aff2c57bbef8794'], + }), + ('vcfR', '1.12.0', { + 'checksums': ['dd87ff010365de363864a44ca49887c0fdad0dd18d0d9c66e44e39c2d4581d52'], + }), + ('glmmML', '1.1.1', { + 'checksums': ['255fe2640933d83ef7ea5813ba8006038c18195147d1f34f47a759210a674dd4'], + }), + ('cowplot', '1.1.0', { + 'checksums': ['30b941bd6b6d86d614489b18f42c01e8053c6e2d2b9caa167bd0a6d8c9bba511'], + }), + ('tsne', '0.1-3', { + 'checksums': ['66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69'], + }), + ('sn', '1.6-2', { + 'checksums': ['2fd4730c315efc48958b47990ddb0cbc6ce075f7a27255944a292fb4fc593d9d'], + }), + ('tclust', '1.4-2', { + 'checksums': ['95dcd07dbd16383f07f5cea8561e7f3bf314e4a7483879841103b149fc8c65d9'], + }), + ('ranger', '0.12.1', { + 'checksums': ['fc308e0ac06718272799928e1a19612de16b05bde481d8f38e11a101df5425ef'], + }), + ('hexbin', '1.28.1', { + 'checksums': ['42d092c709ebc84b18df8121beb6bd1d8a3f6f357afd5c3490757c4c4795c6e7'], + }), + ('pryr', '0.1.4', { + 'checksums': ['d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b'], + }), + ('moments', '0.14', { + 'checksums': ['2a3b81e60dafdd092d2bdd3513d7038855ca7d113dc71df1229f7518382a3e39'], + }), + ('laeken', '0.5.1', { + 'checksums': ['1aa94a1768969eb999f7a41212af2d8b2943b43a68a92f99c9f77929e19439a5'], + }), + ('VIM', '6.0.0', { + 'checksums': ['3bf2a34ca5233f6f1724ab6cf0021a4c3c134da338b82bb3405884b48962b035'], + }), + ('proxy', '0.4-24', { + 'checksums': ['8cff9bf036475941a7c44ba9bb5e2f6d4777d49ab3daaeb52d23f4b2af6d9c7c'], + }), + ('smoother', '1.1', { + 'checksums': 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['c1b8b24100c98a5ca1f174e216db484cdfb576787614ccf31cb830277118bf1c'], + }), + ('mpath', '0.3-26', { + 'checksums': ['bc1fb539fd7c793dd4421216c3ffef840e8ddd637da1c51bb629d3f693632f7a'], + }), + ('timereg', '1.9.8', { + 'checksums': ['00b200764743e7074d1697ddbe8534ca7599e26ef20c34020fa1f6a29fa6bb18'], + }), + ('peperr', '1.1-7.1', { + 'checksums': ['5d4eff0f0b61c0b3e479c2ac2978c8e32373b9630565bf58fee48ead6166698a'], + }), + ('heatmap3', '1.1.7', { + 'checksums': ['bab39bdcc462ed9e15dda54d58385b7c8d2bca800cd0e6ee2fce12475661b2bd'], + }), + ('GlobalOptions', '0.1.2', { + 'checksums': ['47890699668cfa9900a829c51f8a32e02a7a7764ad07cfac972aad66f839753e'], + }), + ('circlize', '0.4.11', { + 'checksums': ['4d101e1ae0b221e70db4c569a620f7fc1103b12258f51e8c080c8f3d0fed04e9'], + }), + ('GetoptLong', '1.0.4', { + 'checksums': ['e64dba01aba7d4efa2bdcab86ab76ebbe4f3509a69112b8f1c8f5dd45b523751'], + }), + ('dendextend', '1.14.0', { + 'checksums': 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+ ('tidyverse', '1.3.0', { + 'checksums': ['6d8acb81e994f9bef5e4dcf908bcea3786d108adcf982628235b6c8c80f6fe09'], + }), + ('R.rsp', '0.44.0', { + 'checksums': ['8969075bdcabd43bad40eef6b82223e119426279fded041163fd41e55cee3a59'], + }), + ('listenv', '0.8.0', { + 'checksums': ['fd2aaf3ff2d8d546ce33d1cb38e68401613975117c1f9eb98a7b41facf5c485f'], + }), + ('globals', '0.13.1', { + 'checksums': ['8c65281334faad0befa186ed5867ea73057e2ae3839c858672d051d6dda909b2'], + }), + ('parallelly', '1.21.0', { + 'checksums': ['6059788df2435dd17449473454b9e176e0565380adfa7c5feae49f0c674099c2'], + }), + ('future', '1.20.1', { + 'checksums': ['66d18ff335d9a676f6b19c1ef9b3987f47ba57dca21f6cda39eefdc4d0036092'], + }), + ('gdistance', '1.3-6', { + 'checksums': ['2ccabeb2f8cf44630c0bd2da79815fe357b812737ebece1bed8f90b27c126a24'], + }), + ('vioplot', '0.3.5', { + 'checksums': ['1b64833c1bd6851036cf1c400c7d0036a047e71def94a399c897263b4b303e2a'], + }), + ('emulator', '1.2-20', { + 'checksums': ['7cabf2cf74d879ad9dbaed8fdee54a5c94a8658a0645c021d160b2ef712ce287'], + }), + ('gmm', '1.6-5', { + 'checksums': ['b17090892261fa6707f895c591173a2a6f8f646b420b8229b6148a1c737e9f8a'], + }), + ('tmvtnorm', '1.4-10', { + 'checksums': ['1a9f35e9b4899672e9c0b263affdc322ecb52ec198b2bb015af9d022faad73f0'], + }), + ('IDPmisc', '1.1.20', { + 'checksums': ['bcb9cd7b8097e5089d1936286ef310ac2030ea7791350df706382ba470afc67f'], + }), + ('gap', '1.2.2', { + 'checksums': ['9c66a52b371b282b20295676bdd86a11d59a6fb2acddb19170376e1a5c65b834'], + }), + ('qrnn', '2.0.5', { + 'checksums': ['3bd83ee8bd83941f9defdab1b5573d0ceca02bf06759a67665e5b9358ff92f52'], + }), + ('TMB', '1.7.18', { + 'checksums': ['7e5cfab4759fca7ea17d87d30ffb676b036a1efce98721adb73945ab45d27735'], + }), + ('glmmTMB', '1.0.2.1', { + 'checksums': ['4b0923027bbe2a304282273fa626044063c195f4eee8d2fea88d85df598765a8'], + }), + ('gmp', '0.6-1', { + 'checksums': ['20d90cb783139825a6eacd0bb4283f24742fff88fa6fe0c849e1deec2a3e3487'], + }), + ('ROI', '1.0-0', { + 'checksums': ['b0d87fb4ed2137d982734f3c5cdc0305aabe6e80f95de29655d02a9e82a0a341'], + }), + ('Rglpk', '0.6-4', { + 'checksums': ['a28dbc3130b9618d6ed2ef718d2c55df8ed8c44a47161097c53fe15fa3bfbfa6'], + }), + ('ROI.plugin.glpk', '1.0-0', { + 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], + }), + ('spaMM', '3.5.0', { + 'checksums': ['042a61e137b0f70973288fee16edc975b3dc6b29f9aad87cb781b18f63976a60'], + }), + ('qgam', '1.3.2', { + 'checksums': ['273a40d0bfdc340c049bcb85aea83acd887868d8a69c0062b8399e0b24137a52'], + }), + ('DHARMa', '0.3.3.0', { + 'checksums': ['29712e1ea88b143ce800c77d2fcb8a667bb3b4cf22a089ef32105d6935abbc88'], + }), + ('mvnfast', '0.2.5.1', { + 'checksums': ['6393f4d2c3f67ec2d633975320309b83e9c240b59e78c0d46de70ec6378870a4'], + }), + ('bridgesampling', '1.0-0', { + 'checksums': ['9e182e15ba4e0a0fefd6edc58f1939fd971dd5c53c444ca9c1820bb2c1de90ab'], + }), + ('BayesianTools', '0.1.7', { + 'checksums': ['af49389bdeb794da3c39e1d63f59e6219438ecb8613c5ef523b00c6fed5a600c'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.5', { + 'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3.1', { + 'checksums': ['052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.5', { + 'checksums': ['d042d448671355d0664d37fd64dc90932eb780e6494c479d4431d1faae2071a1'], + }), + ('Rssa', '1.0.2', { + 'checksums': ['3991ad98e0170034b06ae8bb5b6337cbc418dc31ce465d02030cedf4ab69ff91'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.32', { + 'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'], + }), + ('DistributionUtils', '0.6-0', { + 'checksums': ['7443d6cd154760d55b6954142908eae30385672c4f3f838dd49876ec2f297823'], + }), + ('gapfill', '0.9.6', { + 'checksums': ['850d0be9d05e3f3620f0f5143496321f1004ed966299bffd6a67a9abd8d9040d'], + }), + ('gee', '4.13-20', { + 'checksums': ['53014cee059bd87dc22f9679dfbf18fe6813b9ab41dfe90361921159edfbf798'], + }), + ('Matching', '4.9-7', { + 'checksums': ['1956ecb5ebe1c88e2112cd277ae5c2ab4b8d8f60743e6e856a2c2e40aa05fc6d'], + }), + ('MatchIt', '3.0.2', { + 'checksums': ['782b159a2b5172e758e3993177930d604140ae668fd8a7c98c30792df80de9de'], + }), + ('RItools', '0.1-17', { + 'checksums': ['75654780e9ca39cb3c43acfaca74080ad74de50f92c5e36e95694aafdfdc0cea'], + }), + ('optmatch', '0.9-13', { + 'checksums': ['f8f327faa95c808773376570793bbabdbc185a6c7fcdce3b96a09c998134d0d8'], + }), + ('SPAtest', '3.1.2', { + 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], + }), + ('SKAT', '2.0.1', { + 'checksums': ['c8637cf5786b926f6bbef3f4ef1d3af5130cc0cfd9094d4835839724b2d0e8c7'], + }), + ('GillespieSSA', '0.6.1', { + 'checksums': ['272e9b6b26001d166fd7ce8d04f32831ba23c676075fbd1e922e27ba2c962052'], + }), + ('startupmsg', '0.9.6', { + 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], + }), + ('distr', '2.8.0', { + 'checksums': ['bb7df05d6b946bcdbbec2e3397c7c7e349b537cabfcbb13a34bcf6312a71ceb7'], + }), + ('distrEx', '2.8.0', { + 'checksums': ['b064cde7d63ce93ec9969c8c4463c1e327758b6f8ea7765217d77f9ba9d590bf'], + }), + ('KODAMA', '1.5', { + 'checksums': ['8ecf53732c1be2bd1e111b3c6de65b66caf28360306e683fe945dc76d4c267dd'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-2', { + 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + }), + ('dtw', '1.22-3', { + 'checksums': ['df7cf9adf613422ddb22a160597eb5f5475ab6c67c0d790092edb7f72ba98f00'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.2', { + 'checksums': ['b03a775df279a71f259470335decf033b0b9e34b7ee5726681b302ae4e11ff0e'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-1', { + 'checksums': ['546e700a39c4ad1dbecf06ba8724e4cf73cb500009027c28762511d52bb7cee6'], + }), + ('rappdirs', '0.3.1', { + 'checksums': ['2fd891ec16d28862f65bb57e4a78f77a597930abb59380e757afd8b6c6d3264a'], + }), + ('reticulate', '1.18', { + 'checksums': ['b33f855a58f446eefbe38df8a1a4865390f5d4ebd64b2c72266baaee64628513'], + }), + ('hdf5r', '1.3.3', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['a0f83cbf21563e81dbd1a1bd8379623ed0c9c4df4e094c75013abfd7a5271545'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('pulsar', '0.3.7', { + 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], + }), + ('bayesm', '3.1-4', { + 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('energy', '1.7-7', { + 'checksums': ['67b88fb33ee6e7bec2e4fe356a4efd36f70c3cf9b0ebe2f6d9da9ec96de9968f'], + }), + ('compositions', '2.0-0', { + 'checksums': ['19cb515e5e61348c1f3672c8d00e8c3491c84774716729e62559e0948c255d77'], + }), + ('clustree', '0.4.3', { + 'checksums': ['5ff3afc3fb3e1d20d033328935084de574250d29545c0a5b69180fe4846fbe53'], + }), + ('plotly', '4.9.2.1', { + 'checksums': ['f45eae325ab7e7924b0be098bad866ce003d657cf63e137104401c2dd4401db8'], + }), + ('tweedie', '2.3.2', { + 'checksums': ['9a6226e64e3d56eb7eb2a408f8b825c2ad6ee0ea203a9220e85e7789514adb81'], + }), + ('RcppGSL', '0.3.8', { + 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], + }), + ('mvabund', '4.1.3', { + 'checksums': ['4b98049026fcc5a262163f6801d5b98b8543267cf7b0edac8382d5311b81a8fc'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.2.2', { + 'checksums': ['5efa9ecc957407cf130f093bd5cce376e753ac6399ec78d7a313cdec3ea899a4'], + }), + ('grpreg', '3.3.0', { + 'checksums': ['d7c93c62659bd0f0d944cc1470f13443ffdebfeac5ef21ffb604ff6acbeb455b'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('ergm', '3.11.0', { + 'checksums': ['4e5506b44badc2343be3657acbf2bca51b47d7c187ff499d5a5e70a9811fe9f2'], + }), + ('networkDynamic', '0.10.1', { + 'checksums': ['22eed8d9dea8d70877c1619eb2bc3f1ac5142ce3db6fd6eb3e0879ca56b76ca0'], + }), + ('tergm', '3.7.0', { + 'checksums': ['afd2b160bda691127f8fc57c4caff61f688cc03e71e622f8e833b2a26dc635df'], + }), + ('ergm.count', '3.4.0', { + 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], + }), + ('tsna', '0.3.1', { + 'checksums': ['bba4b5e04ba647784581a2137f653f60b4c83cfd726c399556054c5a6d2cbd95'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.4-9', { + 'checksums': ['2c45c188c753f566eb9b0429ca4e5af779309dadbaa689752cc63f77788b53bb'], + }), + ('shinythemes', '1.1.2', { + 'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.13', { + 'checksums': ['a9429e5325368cd3ed30ccaaa8147a960ee7970e83bc80eb42bc56cfeddaf6f8'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + # Replace hardcoded CUDA compute capabilities with settings from EB + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': local_liquidSVM_sed + " && LIQUIDSVM_TARGET='empty'", + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.32.0.1', { + 'checksums': ['86161b81e4aecf0243b17cabcd1f887cf4b9104918d91c804810be603d50ab66'], + }), + ('mlegp', '3.1.8', { + 'checksums': ['eac1df085a608451828575028ca05b78dc6b5035da14cabc141bfee5ef986de9'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.5.1', { + 'checksums': ['7204200631039f5f00dc0dd36ea21bf979b33c99c1561d54914129cfadbf7d9d'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.2.0', { + 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.5', { + 'checksums': ['9c41ca817104ab076bfd62cccac7d024658ebf4a11dcd91654f0588868aa8d74'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0-1', { + 'checksums': ['9fc1f7432a40d8911393701ca33e2ad64356c3bd12128f01dd216399b16e3d93'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.16', { + 'checksums': ['d216a46d65e2b7f5dae2eb06ff44bee16262f1d29605e3267456191b39143575'], + }), + ('BMA', '3.18.12', { + 'checksums': 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['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.2', { + 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], + }), + ('ENMeval', '0.3.1', { + 'checksums': ['e7f20c1b4d7ede82a3aca86e3ce3fc4ae46337f812dfc171b499c2558b0183d0'], + }), + ('plotmo', '3.6.0', { + 'checksums': ['c05afcc442f9542868beea5c3c40fb93b049f9b61c42725b2a1e2bc750c241e3'], + }), + ('earth', '5.3.0', { + 'checksums': ['05ace806271a74b3ddf8718a93237fe2a8550a8659ebd87f8079c0bda5e02437'], + }), + ('mda', '0.5-2', { + 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], + }), + ('biomod2', '3.4.6', { + 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], + }), + ('poLCA', '1.4.1', { + 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], + }), + ('PermAlgo', '1.1', { + 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.12', { + 'checksums': ['9acdf912f0e7a68a5b6a7946d5ebb0c2007b3d6cd2e39075eddae2b586354e89'], + }), + ('data.tree', '1.0.0', { + 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('gsl', '2.1-6', { + 'checksums': ['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5', { + 'checksums': ['d526b99d17c1dfd5e399f4af1bc09c8a267add80d3b0a454790728420f0e8fd7'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-18', { + 'patches': ['dbarts-0.9-18_fix-simd-on-non-x86.patch'], + 'checksums': [ + 'fd99f99d1a24c16596767246618cf240ebd8d86fa82b0e5ce65b737b9afb4ac4', # dbarts_0.9-18.tar.gz + # dbarts-0.9-18_fix-simd-on-non-x86.patch + '80a7e84c691d418da4e90a38db1caebed31d01771e4e7f64d24676ee8d84c104', + ], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.4.0', { + 'checksums': ['49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.2', { + 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], + }), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), + ('assertive.base', '0.0-7', { + 'checksums': ['f02d4eca849f512500abb266a2a751d1fa2cf064f7142e5161a77c20b7f643f7'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '2.1', { + 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], + }), + ('lmom', '2.8', { + 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], + }), + ('gld', '2.6.2', { + 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], + }), + ('DescTools', '0.99.38', { + 'checksums': ['bd8edce64a8f9e295611959295b85cf8d7bbf915093158016169bd334e0e1104'], + }), + ('orthopolynom', '1.0-5', { + 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], + }), + ('gaussquad', '1.0-2', { + 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.0', { + 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], + }), + ('tableone', '0.12.0', { + 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], + }), + ('jstable', '1.0.1', { + 'checksums': ['2e4cfce264a2353e4655d0faafc93969222d67a21c0c9cc61a2454abd99c5cdc'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.2', { + 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], + }), + ('sensemakr', '0.1.3', { + 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.3-12', { + 'checksums': ['9a44a21343e1dcced0c65c3117edc5ab2412513c258f1422fd39852e4d9cd706'], + }), + ('metafor', '2.4-0', { + 'checksums': ['b64a678b762e91f1e0a6360b15e79fe19159b243c9f40ad9cc0be833bb4ba9ac'], + }), + ('fmri', '1.9.6', { + 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + }), + ('AnalyzeFMRI', '1.1-23', { + 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.4', { + 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], + }), + # Specific packages for GPUs + ('OpenCL', '0.2-1', { + 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], + }), + ('RViennaCL', '1.7.1.8', { + 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], + }), +] + +moduleclass = 'lang' From 7f5ee46fda388e56cf75f9dc780eb941e68d15f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Mar 2021 18:17:00 +0100 Subject: [PATCH 0453/2365] {bio}[iimpi/2020b] LPJmL v4.0.003 (+ json-c v0.15) --- .../j/json-c/json-c-0.15-GCCcore-10.2.0.eb | 30 ++++++++++++ .../l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb | 49 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3368d5ac78 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.15' +local_suff = '-20200726' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['4ba9a090a42cf1e12b84c64e4464bb6fb893666841d5843cc5bef90774028882'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb b/easybuild/easyconfigs/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb new file mode 100644 index 0000000000..2e298acfdc --- /dev/null +++ b/easybuild/easyconfigs/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'LPJmL' +version = '4.0.003' + +homepage = 'https://github.com/PIK-LPJmL/LPJmL' +description = "Dynamic global vegetation model with managed land and river routing" + +toolchain = {'name': 'iimpi', 'version': '2020b'} + +source_urls = ['https://github.com/PIK-%(name)s/%(name)s/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['024499cab8510c49e061c8dc4f1aa007e8c898a2ac08565331cab40f076afb9b'] + +dependencies = [ + ('GMP', '6.2.0'), + ('HDF5', '1.10.7'), + ('netCDF', '4.7.4'), + ('UDUNITS', '2.2.26'), + ('expat', '2.2.9'), + ('cURL', '7.72.0'), + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), + ('json-c', '0.15'), +] + +skipsteps = ['configure'] + +prebuildopts = "./configure.sh && " +buildopts = 'all LPJFLAGS="-DUSE_MPI -DUSE_NETCDF4 -DUSE_UDUNITS -DUSE_JSON" OPTFLAGS="$CFLAGS" ' + +installopts = "LPJROOT=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/cru2clm', 'bin/lpjcat', 'bin/lpjcheck', 'bin/lpjrun', 'bin/lpjprint', 'bin/txt2clm'], + 'dirs': [], +} + +sanity_check_commands = [ + "cru2clm -h", + "lpjrun -h", + "txt2clm -h", +] + +modextravars = { + 'LPJROOT': '%(installdir)s', +} + +moduleclass = 'bio' From b6f8223202c814c20d5763eebd7003be258b97e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Mar 2021 18:47:40 +0100 Subject: [PATCH 0454/2365] revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0 --- .../n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb | 2 +- .../s/Seaborn/Seaborn-0.10.1-intel-2020b.eb | 29 +++++++++++++++++++ 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb index 4f8ea405c7..56f58aee1c 100644 --- a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('nanomath', '1.2.0'), ('nanoget', '1.15.0'), - ('Seaborn', '0.11.1'), + ('Seaborn', '0.10.1'), ('plotly.py', '4.14.3'), ('pauvre', '0.1924'), ('statsmodels', '0.12.1'), diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb new file mode 100644 index 0000000000..8829db33c7 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.10.1' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2d1a0c9d6bd1bc3cadb0364b8f06540f51322a670cf8438d0fde1c1c7317adc0'] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From fe8691539ffbc0da4f88dc5cdff8e819b8f0dddc Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 5 Mar 2021 11:03:51 -0800 Subject: [PATCH 0455/2365] {bio}[GCCcor/10.2.0] BioPerl 1.7.8 --- .../b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e16f7e4642 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Perl', '5.32.0'), + ('XML-LibXML', '2.0206'), + ('DB_File', '1.855'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + ('XML::DOM::XPath', '0.14', { + 'source_tmpl': 'XML-DOM-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': ['0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), + ('BioPerl', version, { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' From 86c44293d50c03935059c8303ed3d448d88e0982 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 6 Mar 2021 11:48:06 +0100 Subject: [PATCH 0456/2365] stick to ASE 3.20.1 as dependency for PyTorch-Geometric 1.6.3 --- .../p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb index ea3f074a2a..307b6dd2f8 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb @@ -17,7 +17,7 @@ dependencies = [ ('h5py', '3.1.0'), ('tqdm', '4.56.2'), ('RDFlib', '5.0.0'), - ('ASE', '3.21.1'), + ('ASE', '3.20.1'), ] exts_default_options = {'source_urls': [PYPI_SOURCE]} From c4c9a7807b1c55c47590c8398b9d4821c299070e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 6 Mar 2021 14:16:29 +0100 Subject: [PATCH 0457/2365] stick to ASE 3.20.1 as dependency for PyTorch-Geometric 1.6.3 --- .../a/ASE/ASE-3.20.1-fosscuda-2020b.eb | 46 +++++++++++++++++++ .../PyTorch-Geometric-1.6.3-fosscuda-2020b.eb | 2 +- 2 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..6f5ab3edf2 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.20.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Flask', '1.1.2'), + ('matplotlib', '3.3.3'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('ase', version, { + 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb index d60a329fe1..bd807a939a 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb @@ -17,7 +17,7 @@ dependencies = [ ('h5py', '3.1.0'), ('tqdm', '4.56.2'), ('RDFlib', '5.0.0'), - ('ASE', '3.21.1'), + ('ASE', '3.20.1'), ] exts_default_options = {'source_urls': [PYPI_SOURCE]} From 0f914a19fc4d5deb20bc5117720cef5b3a6f5361 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 Mar 2021 17:10:56 +0100 Subject: [PATCH 0458/2365] move Qtconsole 5.0.2 to GCCcore toolchain --- .../Qtconsole-5.0.2-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..530c2fc18d --- /dev/null +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Qtconsole' +version = '5.0.2' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a terminal, +but provides a number of enhancements only possible in a GUI, +such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['404994edfe33c201d6bd0c4bd501b00c16125071573c938533224992bea0b30f'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), + ('QtPy', '1.9.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 6017144148b535da61e57bea8237953ab9a74af2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 Mar 2021 17:28:40 +0100 Subject: [PATCH 0459/2365] specify installation prefix via -prefix option of configure script in LPJmL easyconfig --- easybuild/easyconfigs/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb b/easybuild/easyconfigs/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb index 2e298acfdc..3291ad1ac3 100644 --- a/easybuild/easyconfigs/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb +++ b/easybuild/easyconfigs/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb @@ -24,13 +24,11 @@ dependencies = [ ('json-c', '0.15'), ] -skipsteps = ['configure'] +configure_cmd = './configure.sh' +prefix_opt = '-prefix ' -prebuildopts = "./configure.sh && " buildopts = 'all LPJFLAGS="-DUSE_MPI -DUSE_NETCDF4 -DUSE_UDUNITS -DUSE_JSON" OPTFLAGS="$CFLAGS" ' -installopts = "LPJROOT=%(installdir)s" - sanity_check_paths = { 'files': ['bin/cru2clm', 'bin/lpjcat', 'bin/lpjcheck', 'bin/lpjrun', 'bin/lpjprint', 'bin/txt2clm'], 'dirs': [], From 84e3d92a42ebb4c451285c13405ecb0bb15d3150 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 8 Mar 2021 08:51:25 +0100 Subject: [PATCH 0460/2365] Use tarball as sources since these contain submodule code --- .../p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb index 4b91fe9623..997e71d68c 100644 --- a/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb @@ -12,18 +12,9 @@ description = """pFUnit is a unit testing framework enabling JUnit-like testing toolchain = {'name': 'gompi', 'version': '2020b'} -# Release does not include git submodules so do explicit clone instead -sources = [{ - 'git_config': { - 'url': 'https://github.com/Goddard-Fortran-Ecosystem', - 'repo_name': 'pFUnit', - 'commit': 'v%(version)s', - 'recursive': True, - }, - 'filename': SOURCE_TAR_GZ, -}] -# can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' -checksums = [None] +source_urls = ['https://github.com/Goddard-Fortran-Ecosystem/pFUnit/releases/download/v%(version)s'] +sources = [SOURCE_TAR] +checksums = ['33df62f80cf03827455508b67d53f820ddffa2ec0f1ba999790ff1f87592ce16'] builddependencies = [('CMake', '3.18.4')] dependencies = [('Python', '3.8.6')] From 6e5667d8abc4616727db617976d884f4f1bb92fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 Mar 2021 11:08:24 +0100 Subject: [PATCH 0461/2365] add sanity check command for pFUnit 4.2.0 + keep setting $PFUNIT environment variable --- easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb | 4 ++++ .../easyconfigs/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb index 997e71d68c..1924ee814f 100644 --- a/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb @@ -31,6 +31,8 @@ sanity_check_paths = { ], } +sanity_check_commands = ["funitproc --help"] + modextrapaths = { 'PATH': ['PFUNIT-%(version_major_minor)s/bin'], 'CPATH': [ @@ -53,4 +55,6 @@ modextrapaths = { ], } +modextravars = {'PFUNIT': '%(installdir)s'} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb index 466567a921..6e6442b602 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb @@ -23,7 +23,7 @@ sanity_check_paths = { 'lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT ], - 'dirs': [''], + 'dirs': [], } moduleclass = 'chem' From 1b6a1c84452d8ccd82db15895a7956796b31a8e4 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 9 Mar 2021 10:18:33 +0100 Subject: [PATCH 0462/2365] adding easyconfigs: delly-0.8.7-gompi-2020b.eb, maze-20170124-foss-2020b.eb, sansa-0.0.7-gompi-2020b.eb, suave-20160529-foss-2020b.eb, MUMmer-4.0.0beta2-GCCcore-10.2.0.eb, LAST-1179-gompi-2020b.eb and patches: maze-setup-py-python3.patch, suave-setup-py-python3.patch --- .../MUMmer-4.0.0beta2-GCCcore-10.2.0.eb | 36 +++++++++++++ .../m/maze/maze-20170124-foss-2020b.eb | 49 ++++++++++++++++++ .../s/sansa/sansa-0.0.7-gompi-2020b.eb | 40 +++++++++++++++ .../s/suave/suave-20160529-foss-2020b.eb | 50 +++++++++++++++++++ 4 files changed, 175 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/sansa/sansa-0.0.7-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ac9a89a287 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'MUMmer' +version = '4.0.0beta2' + +homepage = 'http://mummer.sourceforge.net/' + +description = """ + MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['cece76e418bf9c294f348972e5b23a0230beeba7fd7d042d5584ce075ccd1b93'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', + 'bin/repeat-match', 'bin/show-aligns', 'bin/show-coords', + 'bin/show-tiling', 'bin/show-snps', 'bin/show-diff', 'bin/exact-tandems', + 'bin/mummerplot', 'bin/promer', 'bin/dnadiff', + ], + 'dirs': ['include', 'lib', 'libexec'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb b/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb new file mode 100644 index 0000000000..bba584205d --- /dev/null +++ b/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'maze' +version = '20170124' + +homepage = 'https://github.com/dellytools/maze' +description = """In a similar manner to dot plots, maze highlights local +sequence similarity between two DNA sequences. In particular, maximal exact +substring matches are computed with MUMmer3 and visualised.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('MUMmer', '4.0.0beta2'), + ('LAST', '1179'), + ('Flask', '1.1.2'), + ('Pysam', '0.16.0.1'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} +exts_list = [ + ('Click', '7.0', { + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + (name, version, { + 'patches': [('maze-setup-py-python3.patch', 1)], + 'source_tmpl': '106803d350719188181ce39cbb5c832822b724da.tar.gz', + 'source_urls': ['https://github.com/dellytools/maze/archive'], + 'checksums': [ + # 106803d350719188181ce39cbb5c832822b724da.tar.gz + 'aac74021b5f3652723d593f1983a417e8db73147079d06dad9a18acdfdb00f93', + '6d8d127582463c366c41e1fff737f8d24469397657e0a7a04c1516640d3b97f4', # maze-setup-py-python3.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/maze_server', 'bin/extract_reference_slices'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/templates'], +} + +sanity_check_commands = ['maze_server --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sansa/sansa-0.0.7-gompi-2020b.eb b/easybuild/easyconfigs/s/sansa/sansa-0.0.7-gompi-2020b.eb new file mode 100644 index 0000000000..6358b766a7 --- /dev/null +++ b/easybuild/easyconfigs/s/sansa/sansa-0.0.7-gompi-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'sansa' +version = '0.0.7' + +homepage = 'https://github.com/dellytools/sansa/' +description = """Structural variant (SV) annotation, a companion to the 'dolly' +tool.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True} + +github_account = 'dellytools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['fa76c071be2956c35f9e9c5b4c37a0cb064bdd9514c3a04762b2424c03d2da7b'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('HTSlib', '1.11.2'), + ('Boost', '1.74.0'), +] + +build_cmd = 'make all -B src/sansa' + +files_to_copy = [ + (['src/sansa'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/sansa'], + 'dirs': ['bin'] +} + +sanity_check_commands = ['sansa'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb b/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb new file mode 100644 index 0000000000..8a156ae761 --- /dev/null +++ b/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'suave' +version = '20160529' + +homepage = 'https://github.com/dellytools/suave' +description = """suave is an interactive web application to visualize read depth +ratios between two samples and the structural variants of one of the samples +(typically the "case" sample in a case/control setup such as tumor/normal +comparison).""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Flask', '1.1.2'), + ('h5py', '3.1.0'), + ('Pysam', '0.16.0.1'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} +exts_list = [ + ('Click', '7.0', { + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + (name, version, { + 'modulename': 'suave_server', + 'patches': [('suave-setup-py-python3.patch', 1)], + 'source_tmpl': '45e4963d1a2c84cc0acdfaa603f29df10ff2ce49.tar.gz', + 'source_urls': ['https://github.com/dellytools/suave/archive'], + 'checksums': [ + # 45e4963d1a2c84cc0acdfaa603f29df10ff2ce49.tar.gz + 'f585f27adcf1f3a8aeaead2e5f190f6f0d23522cf6bbe1c3388f4c3270d0fb9c', + '47b404c0150a117936b3e18aa479012b5f055eea7d85e663c9b44e0f8bfe8247', # suave-setup-py-python3.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/suave_server', 'bin/suave_bam_to_h5'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/templates'], +} + +sanity_check_commands = ['suave_server --help'] + +moduleclass = 'bio' From c45f3888a5eedc15644427f68f9a80f4b8ce56ba Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 9 Mar 2021 10:57:05 +0100 Subject: [PATCH 0463/2365] delly: fix HTSlib dependency --- easybuild/easyconfigs/s/sansa/sansa-0.0.7-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sansa/sansa-0.0.7-gompi-2020b.eb b/easybuild/easyconfigs/s/sansa/sansa-0.0.7-gompi-2020b.eb index 6358b766a7..bb50f6ae9c 100644 --- a/easybuild/easyconfigs/s/sansa/sansa-0.0.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/sansa/sansa-0.0.7-gompi-2020b.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('HTSlib', '1.11.2'), + ('HTSlib', '1.11'), ('Boost', '1.74.0'), ] From 7b5c923688945ed453a6ebfd9b786c81085fd2db Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Mar 2021 10:52:38 +0000 Subject: [PATCH 0464/2365] Adds R 4.0.4 and its dependencies. --- .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 2829 +++++++++++++++++ 1 file changed, 2829 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb new file mode 100644 index 0000000000..7efd892015 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -0,0 +1,2829 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Robert Mijakovic +# reciPY derived from preexisting reciPys for 4.0.3 and 4.0.0 with updated versions. +## +name = 'R' +version = '4.0.4' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.9'), +] +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('PCRE2', '10.35'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.5'), # for plottting in R + ('LibTIFF', '4.2.0'), + ('Java', '15.0.2', '', True), + ('Tk', '8.6.11'), # for tcltk + ('cURL', '7.72.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.1'), # for igraph + ('NLopt', '2.6.2'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '67.1'), # for rJava & gdsfmt + ('HDF5', '1.10.7'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.10-35'), # for animation + ('GLPK', '4.65'), # for Rglpk + ('nodejs', '12.19.0'), # for V8 (required by rstan) + ('GDAL', '3.2.1'), # for sf + ('SQLite', '3.33.0') # for sf + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 08 Mar 2021 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9.1', { + 'checksums': ['99e02a955935040bf0834d44d1dc10a3794c8260fd072d3aff3e15ab249e0ac9'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.6', { + 'checksums': ['c9f24756bc000f7a989bd4f9aa93d57f7739dcde77946703f8bb32332a35f012'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '4.0.4', { + 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], + }), + ('bnlearn', '4.6.1', { + 'checksums': ['e4544465af3330e53e4777079c448585a8a97be2d3862a5264169007c20daeaf'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.16', { + 'checksums': ['e7dea648ee018e2c8c8834084051c76f7e8b2b42067772c62035a941c32457a9'], + }), + ('formatR', '1.7', { + 'checksums': ['a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb'], + }), + ('gtools', '3.8.2', { + 'checksums': ['503ba60a41f3c61b8129c25de62c74dab29761d2e661d4addd106e2e02f1dcde'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('highr', '0.8', { + 'checksums': ['4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.10', { + 'checksums': ['783233a15a817a7530d140e9825565a661aa4bdea7c635d11b9c74faa33be3f7'], + }), + ('xfun', '0.21', { + 'checksums': ['648e171881e2cd14be482c15b3407bfdadbcdf7dc82a969b680223eb02d212a3'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-3', { + 'checksums': ['b1f92be633243185ab86e880a1e1ac5a4dd3c535d01ebd187a4872d0a8c6f194'], + }), + ('NLP', 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('distillery', '1.2', { + 'checksums': ['1eb129b019b5fe9a4599c3e902ecc222c7aa3ff0602b45ee25495c086e82d082'], + }), + ('extRemes', '2.1', { + 'checksums': ['2d760b8d9db81fa70ac20735c10ef612908cea39cc779cc71b171afaebc8c9ac'], + }), + ('tkrplot', '0.0-25', { + 'checksums': ['21ae0e869e024838b9bf42a0c06d55672a2683453dc9218327409086a611ed5c'], + }), + ('misc3d', '0.9-0', { + 'checksums': ['a1e9291d625bd1312bae5b0e26d48b9362f66a8a0fabbf48891ba1d2432e4e82'], + }), + ('multicool', '0.1-11', { + 'checksums': ['1c907e64af2ac39facdf431a5691e69649f64af1f50e198ae39da5bf30026476'], + }), + ('plot3D', '1.3', { + 'checksums': ['b9e4ec2789e34ad249318900e186868650e1a33466b385cb492a45466db3dfc9'], + }), + ('plot3Drgl', '1.0.1', { + 'checksums': ['466d428d25c066c9c96d892f24da930513d42b1bdf76d3b53628c3ba13c3e48a'], + }), + ('OceanView', '1.0.5', { + 'checksums': ['c16e1bed97f4ede46dc017fdd6bd7575d925b57bd2601317bd3ad2357609f885'], + }), + ('ks', '1.12.0', { + 'checksums': ['e6affe52bbfe73e31387462c57dfe56058c5d64f54e5c7b7c794187c6936cee9'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-18.1', { + 'checksums': ['2fa5f78a7603cbae94a5e38e791938596a053d48c609a7c120a19cbb7d93c66f'], + }), + ('penalized', '0.9-51', { + 'checksums': ['eaa80dca99981fb9eb576261f30046cfe492d014cc2bf286c447b03a92e299fd'], + }), + ('clusterRepro', '0.9', { + 'checksums': ['940d84529ff429b315cf4ad25700f93e1156ccacee7b6c38e4bdfbe2d4c6f868'], + }), + ('data.tree', '1.0.0', { + 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('visNetwork', '2.0.9', { + 'checksums': ['5e0b3dc3a91e66e0a359433f03cc856d04b981b0f9ad228d8fa9c96b7fcaa420'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.6.1', { + 'checksums': ['be4e4c520a3692902ce405e8225aef9f3d5f0cd11fcde614f6541e981b63673d'], + }), + ('randomForestSRC', '2.10.1', { + 'checksums': ['222c3b094a933e966a30cf99c52d2d6ad72959723f054134660e627adf51fadd'], + }), + ('sm', '2.2-5.6', { + 'checksums': ['b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-7', { + 'checksums': ['b3b186559b157497fb78a11ec46e2b49045ba04879e3faf30a75c1c73317464f'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.11-2', { + 'checksums': ['8385be32f6b6b6f1b32df15f42073b191d714d870bbb4f95875b64aff6112bbf'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('servr', '0.21', { + 'checksums': ['3fc0da063dd04b796a49ce62bf8e69d5854679520da90cc92ee3fc0a0b2ad389'], + }), + ('rgexf', '0.16.0', { + 'checksums': ['2a671df9ac70cfefd4092754317cb28e32a33df345b80e1975bf838e838245ee'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('sem', '3.1-11', { + 'checksums': ['33b1ad7695db13af8cdd214f5d388db494528b433c61c7ad89970cefcc8b430e'], + }), + ('network', '1.16.1', { + 'checksums': ['eb6435794cacc81abe1664391e8dcf1c10112bbb76fff9016dd6dbb8e83efeb1'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('statnet.common', '4.4.1', { + 'checksums': ['4ecf2b84718d7fb60f196215b4cf6f52cd6b26cc9148a6da6981b26e885509fd'], + }), + ('sna', '2.6', { + 'checksums': ['3a016550d9f424a0613c3f5b0b680dbd3a1f20a343173d39a96034340ad9202a'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.4.1', { + 'checksums': ['78ef9eae464d52c5247998b9514a81b178419b857b1a6c00d885e3ae6c03a886'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('BDgraph', '2.63', { + 'checksums': ['cc474e1315a04f67fbf14461d35004c899d031c31f18be7d3db076dbf66a0617'], + }), + ('pbapply', '1.4-3', { + 'checksums': ['8fe6287535be766b5a688810e2cc1ca4e668ac6b42b6e832473fe5701133eb21'], + }), + ('graphlayouts', '0.7.1', { + 'checksums': ['380f8ccb0b08735694e83f661fd56a0d592a78448ae91b89c290ba8582d66717'], + }), + ('tweenr', '1.0.1', { + 'checksums': ['efd68162cd6d5a4f6d833dbf785a2bbce1cb7b9f90ba3fb060931a4bd705096b'], + }), + ('ggforce', '0.3.3', { + 'checksums': ['2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f'], + }), + ('tidygraph', '1.2.0', { + 'checksums': ['057d6c42fc0144109f3ace7f5058cca7b2fe493c761daa991448b23f86b6129f'], + }), + ('ggraph', '2.0.5', { + 'checksums': ['e36ad49dba92ee8652e18b1fb197be0ceb9f0a2f8faee2194453a62578449654'], + }), + ('qgraph', '1.6.9', { + 'checksums': ['b125a9c1b505632da8b404811c8d6d667736f229d95994ca7913beacabc36b94'], + }), + ('HWxtest', '1.1.9', { + 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], + 'checksums': [ + 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + ], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.19', { + 'checksums': ['4cd2d080628482f4c6ecab593313d7e42516f5ff13fbf9f90e461fcad0580738'], + }), + ('geepack', '1.3-2', { + 'checksums': ['99b53e40f7e5fda7422b143e6fee16513e2f880cb04a97cd403e98c4760670a6'], + }), + ('biom', '0.3.12', { + 'checksums': 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('imager', '0.42.7', { + 'checksums': ['edba2d70c1f2512ae7b5428bd4917334cd974ea0b536b61232d3d66ce9ca00b7'], + }), + ('signal', '0.7-6', { + 'checksums': ['6b60277b07cf0167f8272059b128cc82f27a9bab1fd33d74c2a9e1f2abca5def'], + }), + ('tuneR', '1.3.3', { + 'checksums': ['bdc3c2017b162d2ba0a249e80361a4f47202e763c21aecfc57380a482a3a692b'], + }), + ('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-7', { + 'checksums': ['52e0397a45325aa9586ec68b94ab9e505bdefaf2a588d634fcb57a6a11659c74'], + }), + ('fftw', '1.0-6', { + 'checksums': ['397ef5ec354b919884f74fba4202bfc13ad11a70b16285c41677aad1d3b170ce'], + }), + ('seewave', '2.1.6', { + 'checksums': ['84a0a0035737574a65f371fa4a20a1a3a66de195efe41975f21be8fb001e7088'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('sf', '0.9-7', { + 'checksums': 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+ ('tsne', '0.1-3', { + 'checksums': ['66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69'], + }), + ('sn', '1.6-2', { + 'checksums': ['2fd4730c315efc48958b47990ddb0cbc6ce075f7a27255944a292fb4fc593d9d'], + }), + ('tclust', '1.4-2', { + 'checksums': ['95dcd07dbd16383f07f5cea8561e7f3bf314e4a7483879841103b149fc8c65d9'], + }), + ('ranger', '0.12.1', { + 'checksums': ['fc308e0ac06718272799928e1a19612de16b05bde481d8f38e11a101df5425ef'], + }), + ('hexbin', '1.28.2', { + 'checksums': ['6241f8d3a6c6be2c1c693c3ddb99554bc103e3c6cf602d0c2787c0ce6fd1702d'], + }), + ('pryr', '0.1.4', { + 'checksums': ['d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b'], + }), + ('moments', '0.14', { + 'checksums': ['2a3b81e60dafdd092d2bdd3513d7038855ca7d113dc71df1229f7518382a3e39'], + }), + ('laeken', '0.5.1', { + 'checksums': ['1aa94a1768969eb999f7a41212af2d8b2943b43a68a92f99c9f77929e19439a5'], + }), + ('VIM', '6.1.0', { + 'checksums': 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['1f7f07558e347e7d1f1adff68631764670bc672777a7d990901c4fa94cc0e629'], + }), + ('WriteXLS', '6.2.0', { + 'checksums': ['f95a974aac3ec7082512675937aa2cce4d92b8324180a87f336fe781576eb40f'], + }), + ('bst', '0.3-23', { + 'checksums': ['70957f1db8800bf0d628a9e6f72b7273329786dd119427790b326844591aa0f3'], + }), + ('pamr', '1.56.1', { + 'checksums': ['d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779'], + }), + ('WeightSVM', '1.7-5', { + 'checksums': ['dd895fe3a400897cea18d9de3e406e040efca9f84495739757b52570c98f820a'], + }), + ('mpath', '0.4-2.18', { + 'checksums': ['102f5c94076ff7b26fb2e664a801e3d9b8ead8b309e4ffe3538bcb0aa922e737'], + }), + ('timereg', '1.9.8', { + 'checksums': ['00b200764743e7074d1697ddbe8534ca7599e26ef20c34020fa1f6a29fa6bb18'], + }), + ('peperr', '1.2', { + 'checksums': ['d5ab2455382f5fcd1f87c13a7397a7f58e92d71a49d76ddc4341b9db43781d14'], + }), + ('heatmap3', '1.1.9', { + 'checksums': ['594c33947b2be2cc8a592075f41a0df2398c892add7d63a15c613a5eeb8fdb69'], + }), + ('GlobalOptions', '0.1.2', { + 'checksums': ['47890699668cfa9900a829c51f8a32e02a7a7764ad07cfac972aad66f839753e'], + }), + ('circlize', '0.4.12', { + 'checksums': ['b3b60caa5292cf980cf474c85f59582f6862925631a4da86a78eac05903252f4'], + }), + ('GetoptLong', '1.0.5', { + 'checksums': ['8c237986ed3dfb72d956ad865ef7768644eebf144675ad66140acfd1aca9d701'], + }), + ('dendextend', '1.14.0', { + 'checksums': ['3789461bc474e146b077ad26566b1fa05be32fc7e57ab1fb5e78bdabcc797858'], + }), + ('RInside', '0.2.16', { + 'checksums': ['7ae4ade128ea05f37068d59e610822ff0b277f9d39d8900f7eb31759ad5a2a0e'], + }), + ('limSolve', '1.5.6', { + 'checksums': ['b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0'], + }), + ('dbplyr', '2.1.0', { + 'checksums': ['d40877e19445e4ab01be797ed80240bffcf4dd7295007451c0738dec7a74a0ea'], + }), + ('modelr', '0.1.8', { + 'checksums': ['825ba77d95d60cfb94920bec910872ca2ffe7790a44148b2992be2759cb361c4'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('reprex', '1.0.0', { + 'checksums': ['dd961de0619997336a9033cb3ca807068f4001c527f41b4be21211da1ce8df1e'], + }), + ('selectr', '0.4-2', { + 'checksums': ['5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127'], + }), + ('rvest', '0.3.6', { + 'checksums': ['6a2ee3a25d2d738031edbc1b5e2410f2a4538dfbb9705af145f9039504b902fa'], + }), + ('tidyverse', '1.3.0', { + 'checksums': ['6d8acb81e994f9bef5e4dcf908bcea3786d108adcf982628235b6c8c80f6fe09'], + }), + ('R.rsp', '0.44.0', { + 'checksums': ['8969075bdcabd43bad40eef6b82223e119426279fded041163fd41e55cee3a59'], + }), + ('listenv', '0.8.0', { + 'checksums': ['fd2aaf3ff2d8d546ce33d1cb38e68401613975117c1f9eb98a7b41facf5c485f'], + }), + ('globals', '0.14.0', { + 'checksums': ['203dbccb829ca9cc6aedb6f5e79cb126ea31f8dd379dff9111ec66e3628c32f3'], + }), + ('parallelly', '1.23.0', { + 'checksums': ['376ce2381587380a4da60f9563710d63084a605f93aa364e9349f2523e83bc08'], + }), + ('future', '1.21.0', { + 'checksums': ['909e6602068eba543a6d2e464b911123cc29efdb600a7000eff0e5624ff0d12d'], + }), + ('gdistance', '1.3-6', { + 'checksums': ['2ccabeb2f8cf44630c0bd2da79815fe357b812737ebece1bed8f90b27c126a24'], + }), + ('vioplot', '0.3.5', { + 'checksums': ['1b64833c1bd6851036cf1c400c7d0036a047e71def94a399c897263b4b303e2a'], + }), + ('emulator', '1.2-20', { + 'checksums': ['7cabf2cf74d879ad9dbaed8fdee54a5c94a8658a0645c021d160b2ef712ce287'], + }), + ('gmm', '1.6-6', { + 'checksums': ['b1b321ad1b4a4a14a2825a2c3eb939ce2f2bcef995247a1d638eca250e59739b'], + }), + ('tmvtnorm', '1.4-10', { + 'checksums': ['1a9f35e9b4899672e9c0b263affdc322ecb52ec198b2bb015af9d022faad73f0'], + }), + ('IDPmisc', '1.1.20', { + 'checksums': ['bcb9cd7b8097e5089d1936286ef310ac2030ea7791350df706382ba470afc67f'], + }), + ('gap', '1.2.2', { + 'checksums': ['9c66a52b371b282b20295676bdd86a11d59a6fb2acddb19170376e1a5c65b834'], + }), + ('qrnn', '2.0.5', { + 'checksums': ['3bd83ee8bd83941f9defdab1b5573d0ceca02bf06759a67665e5b9358ff92f52'], + }), + ('TMB', '1.7.19', { + 'checksums': ['9a30063aafc2762c8cbc3564f5afa0a5127ff55a6f348a68e45ada571a82d26e'], + }), + ('glmmTMB', '1.0.2.1', { + 'checksums': ['4b0923027bbe2a304282273fa626044063c195f4eee8d2fea88d85df598765a8'], + }), + ('gmp', '0.6-2', { + 'checksums': ['6bfcb45b3f1e7da27d8773f911027355cab371d150c3dabf7dbaf8fba85b7f0e'], + }), + ('ROI', '1.0-0', { + 'checksums': ['b0d87fb4ed2137d982734f3c5cdc0305aabe6e80f95de29655d02a9e82a0a341'], + }), + ('Rglpk', '0.6-4', { + 'checksums': ['a28dbc3130b9618d6ed2ef718d2c55df8ed8c44a47161097c53fe15fa3bfbfa6'], + }), + ('ROI.plugin.glpk', '1.0-0', { + 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], + }), + ('spaMM', '3.7.2', { + 'checksums': ['2580a38b2b6165477255bb025913b3d3342c000cc2c6aba10c0748178b04f2d1'], + }), + ('qgam', '1.3.2', { + 'checksums': ['273a40d0bfdc340c049bcb85aea83acd887868d8a69c0062b8399e0b24137a52'], + }), + ('DHARMa', '0.3.3.0', { + 'checksums': ['29712e1ea88b143ce800c77d2fcb8a667bb3b4cf22a089ef32105d6935abbc88'], + }), + ('mvnfast', '0.2.5.1', { + 'checksums': ['6393f4d2c3f67ec2d633975320309b83e9c240b59e78c0d46de70ec6378870a4'], + }), + ('bridgesampling', '1.0-0', { + 'checksums': ['9e182e15ba4e0a0fefd6edc58f1939fd971dd5c53c444ca9c1820bb2c1de90ab'], + }), + ('BayesianTools', '0.1.7', { + 'checksums': ['af49389bdeb794da3c39e1d63f59e6219438ecb8613c5ef523b00c6fed5a600c'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.5', { + 'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3.1', { + 'checksums': ['052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.5', { + 'checksums': ['d042d448671355d0664d37fd64dc90932eb780e6494c479d4431d1faae2071a1'], + }), + ('Rssa', '1.0.3', { + 'checksums': ['d3dc8a22c428148b955d84b703ca0bf3993318a86b067edfe4c4de271b3054ea'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.32', { + 'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'], + }), + ('DistributionUtils', '0.6-0', { + 'checksums': ['7443d6cd154760d55b6954142908eae30385672c4f3f838dd49876ec2f297823'], + }), + ('gapfill', '0.9.6-1', { + 'checksums': ['22f04755873e34a9077bb1b1de8d16f5bc56cb8c395c4f797f9ad0b209b1b996'], + }), + ('gee', '4.13-20', { + 'checksums': ['53014cee059bd87dc22f9679dfbf18fe6813b9ab41dfe90361921159edfbf798'], + }), + ('Matching', '4.9-7', { + 'checksums': ['1956ecb5ebe1c88e2112cd277ae5c2ab4b8d8f60743e6e856a2c2e40aa05fc6d'], + }), + ('MatchIt', '4.1.0', { + 'checksums': ['b34767cbb8cfb70c6b781849d5430b11480fac43af0a2d53460a1c57c7997ba1'], + }), + ('RItools', '0.1-17', { + 'checksums': ['75654780e9ca39cb3c43acfaca74080ad74de50f92c5e36e95694aafdfdc0cea'], + }), + ('optmatch', '0.9-13', { + 'checksums': ['f8f327faa95c808773376570793bbabdbc185a6c7fcdce3b96a09c998134d0d8'], + }), + ('SPAtest', '3.1.2', { + 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], + }), + ('SKAT', '2.0.1', { + 'checksums': ['c8637cf5786b926f6bbef3f4ef1d3af5130cc0cfd9094d4835839724b2d0e8c7'], + }), + ('GillespieSSA', '0.6.1', { + 'checksums': ['272e9b6b26001d166fd7ce8d04f32831ba23c676075fbd1e922e27ba2c962052'], + }), + ('startupmsg', '0.9.6', { + 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], + }), + ('distr', '2.8.0', { + 'checksums': ['bb7df05d6b946bcdbbec2e3397c7c7e349b537cabfcbb13a34bcf6312a71ceb7'], + }), + ('distrEx', '2.8.0', { + 'checksums': ['b064cde7d63ce93ec9969c8c4463c1e327758b6f8ea7765217d77f9ba9d590bf'], + }), + ('KODAMA', '1.5', { + 'checksums': ['8ecf53732c1be2bd1e111b3c6de65b66caf28360306e683fe945dc76d4c267dd'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-2', { + 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + }), + ('dtw', '1.22-3', { + 'checksums': ['df7cf9adf613422ddb22a160597eb5f5475ab6c67c0d790092edb7f72ba98f00'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.3', { + 'checksums': ['f5eafab17f2d4a8a2a83821ad3e96ae7c26b62bbce9de414484c657383c7b42e'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-3', { + 'checksums': ['776d5456e14398e44b78b3d7db526559bb7a3537e546a29c88aa192141c756de'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('reticulate', '1.18', { + 'checksums': ['b33f855a58f446eefbe38df8a1a4865390f5d4ebd64b2c72266baaee64628513'], + }), + ('hdf5r', '1.3.3', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['a0f83cbf21563e81dbd1a1bd8379623ed0c9c4df4e094c75013abfd7a5271545'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('pulsar', '0.3.7', { + 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], + }), + ('bayesm', '3.1-4', { + 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('gsl', '2.1-6', { + 'checksums': ['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], + }), + ('energy', '1.7-8', { + 'checksums': ['de08e8de037bb30068bbf0c1880b153a586d342304681f4ba103ab808c7f4789'], + }), + ('compositions', '2.0-1', { + 'checksums': ['84a291308faf858e5a9d9570135c2da5e57b0887f407903485fa85d09da61a0f'], + }), + ('clustree', '0.4.3', { + 'checksums': ['5ff3afc3fb3e1d20d033328935084de574250d29545c0a5b69180fe4846fbe53'], + }), + ('plotly', '4.9.3', { + 'checksums': ['d44d1a16d96de28bc2d36f1c897384215eeec44d109546c6e9c2707db0880120'], + }), + ('tweedie', '2.3.3', { + 'checksums': ['a032cad512dac37a8619e6f66cb513eb82a88a5a2ffbe91e92c2d44d1756d0d9'], + }), + ('RcppGSL', '0.3.8', { + 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], + }), + ('mvabund', '4.1.9', { + 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.2.3', { + 'checksums': ['154bf7e65452186841036a2a7f2af89664965a63040ff0bee33f8b3fab8c0e4b'], + }), + ('grpreg', '3.3.0', { + 'checksums': ['d7c93c62659bd0f0d944cc1470f13443ffdebfeac5ef21ffb604ff6acbeb455b'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('ergm', '3.11.0', { + 'checksums': ['4e5506b44badc2343be3657acbf2bca51b47d7c187ff499d5a5e70a9811fe9f2'], + }), + ('networkDynamic', '0.10.1', { + 'checksums': ['22eed8d9dea8d70877c1619eb2bc3f1ac5142ce3db6fd6eb3e0879ca56b76ca0'], + }), + ('tergm', '3.7.0', { + 'checksums': ['afd2b160bda691127f8fc57c4caff61f688cc03e71e622f8e833b2a26dc635df'], + }), + ('ergm.count', '3.4.0', { + 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], + }), + ('tsna', '0.3.1', { + 'checksums': ['bba4b5e04ba647784581a2137f653f60b4c83cfd726c399556054c5a6d2cbd95'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.5-0', { + 'checksums': ['795ffd3d62bf14d3ecb3f5307bd329cd75798cf4b270ff0e768bc71a35de0ace'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.15', { + 'checksums': ['73d20ff1abd752a9d8267eea9d97be58818554ffe072923810db576c449ecbc2'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.32.0.1', { + 'checksums': ['86161b81e4aecf0243b17cabcd1f887cf4b9104918d91c804810be603d50ab66'], + }), + ('mlegp', '3.1.8', { + 'checksums': ['eac1df085a608451828575028ca05b78dc6b5035da14cabc141bfee5ef986de9'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.6', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.2.0', { + 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.5', { + 'checksums': ['9c41ca817104ab076bfd62cccac7d024658ebf4a11dcd91654f0588868aa8d74'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0-1', { + 'checksums': ['9fc1f7432a40d8911393701ca33e2ad64356c3bd12128f01dd216399b16e3d93'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.17', { + 'checksums': ['792857b2ebd408d6523424d2f6bb7297e241d4b28ab32372f6a9240c8cd554f3'], + }), + ('BMA', '3.18.14', { + 'checksums': ['3bc0fd44001c5817dc6a8eda9fb266967407f8a05ac0a5c05b10c87df462cb23'], + }), + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-58', { + 'checksums': ['2ab6662eaa1103a7b633477e8ebd266b262ed54fac6f9326b160067a2ded9ce7'], + }), + ('bdsmatrix', '1.3-4', { + 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.19.3', { + 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.4', { + 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.9', { + 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '3.0', { + 'checksums': ['ada4e1f8cbb08ba8ff16275ec5f9a453857e0cab63b70d42753989ab4c716b7b'], + }), + ('bbmle', '1.0.23.1', { + 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('terra', '1.0-10', { + 'checksums': ['b4afca161da08890ab520b19b4e8afc7bd1a9cb252c4d4ec2b9c6c5a0bbaaaab'], + }), + ('rasterVis', '0.50', { + 'checksums': ['1186283ba5915234edfac066763579ccd58d04fbdeca0c1aa8b15f354a93ee54'], + }), + ('tictoc', '1.0', { + 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], + }), + ('ISOcodes', '2021.02.24', { + 'checksums': ['152769bcb4ae99d06a767384541c2000c94990a2c6983780837f85e885b539a6'], + }), + ('stopwords', '2.2', { + 'checksums': ['b66bccc786200c6ec600be8340e2801bbc7ee787fa5c5a15bc201306861706b9'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0.1', { + 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + }), + ('topicmodels', '0.2-12', { + 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + }), + ('tidytext', '0.3.0', { + 'checksums': ['7d36be1e504f751c33dc2239751a600bd4ff05af24a0b9cdd549aff909778bc5'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-11', { + 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.4.1', { + 'checksums': ['bc21fb6b4a93a7e95ee1be57e4e787d731895fb8b4743c26b30b43adee475b50'], + }), + ('RcppParallel', '5.0.3', { + 'checksums': ['71121138f25fcc97885b14545b7e7eb92e5f3953aec15e7df3822ae26d8e0c46'], + }), + ('StanHeaders', '2.21.0-7', { + 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], + }), + ('V8', '3.4.0', { + 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + }), + ('rstan', '2.21.2', { + 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.1', { + 'checksums': ['506e684071332dac62005c709833d419f4944a85478e2f4395f218ac314f5e66'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.7.0', { + 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.4.0', { + 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.1.1', { + 'checksums': ['cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481'], + }), + ('leiden', '0.3.7', { + 'checksums': ['770994d2d763c195b53e3e09a987188cbf844fbb3bca2d175e46798663b13892'], + }), + ('future.apply', '1.7.0', { + 'checksums': ['2ffa6adb55f239918ce9679b7eac8dcc4bf2e6bed35c9cbedf4bf90d906345db'], + }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), + ('packrat', '0.5.0', { + 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], + }), + ('shinyjs', '2.0.0', { + 'checksums': ['c2cdd9fab41f6b46bb41b288cd9b3fb3a7fe9627b664e3a58a0cb5dd4c19f8ff'], + }), + ('colourpicker', '1.1.0', { + 'checksums': ['2dfbb6262d187d3b17357ff9c22670ced3621feda5b2a2a500558478e4d551e2'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), + ('findpython', '1.0.7', { + 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], + }), + ('argparse', '2.0.3', { + 'checksums': ['d26139c610ea0adf8d6632699cd34c4595ae3e7963bfc7a00cb3b7504f2059b0'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), + ('qqman', '0.1.4', { + 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], + }), + ('rstantools', '2.1.1', { + 'checksums': ['c95b15de8ec577eeb24bb5206e7b685d882f88b5e6902efda924b7217f463d2d'], + }), + ('bayesplot', '1.8.0', { + 'checksums': ['a605f9929e681593a3ef3ca9c836e713314994aaea00f359f71cfc42d151c948'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.16', { + 'checksums': ['3f728c6a5153dca28f69b9355ae9d18c5f7e70d12495c0c047eef673c1053116'], + }), + ('shinystan', '2.5.0', { + 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'], + }), + ('optimx', '2020-4.2', { + 'checksums': ['6381c25c322287fc98ab1b2965d3f68c9a92c587c76aca1d33fd6428b2167101'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('projpred', '2.0.2', { + 'checksums': ['af0a9fb53f706090fe81b6381b27b0b6bd3f7ae1e1e44b0ada6f40972b09a55b'], + }), + ('brms', '2.14.4', { + 'checksums': ['3295f775de69a181f09140e224df836c4c82010a2a04fc0d2d80d8fa208cfc57'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.0', { + 'checksums': ['b423df43e9c4bb8ffafe2de88b93fdcf3a90f964f136580ea1b849a83dba7400'], + }), + ('mcmcse', '1.4-1', { + 'checksums': ['6b181f56d60ddf55c9c08a2468ef9ffe3ec8a1b16cfa9a7742c3872597f85d17'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.6.1', { + 'checksums': ['798f261dc62caa0c858065651308e119f83880f4bf89b12cd43eedf7e16a29fc'], + }), + ('drugCombo', '1.1.1', { + 'checksums': ['9fdc3a7cf63552c32f1c7573258fc4ceacdaf5c475fe79aa4ca8c9226b9f8a38'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.0.1', { + 'checksums': ['a3bb9bdc7a4a79ea38482df3f8cbb6e9082332a0d894eeb4b3dc816344cec0e4'], + }), + ('maxlike', '0.1-8', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-16', { + 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.2', { + 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], + }), + ('ENMeval', '0.3.1', { + 'checksums': ['e7f20c1b4d7ede82a3aca86e3ce3fc4ae46337f812dfc171b499c2558b0183d0'], + }), + ('plotmo', '3.6.0', { + 'checksums': ['c05afcc442f9542868beea5c3c40fb93b049f9b61c42725b2a1e2bc750c241e3'], + }), + ('earth', '5.3.0', { + 'checksums': ['05ace806271a74b3ddf8718a93237fe2a8550a8659ebd87f8079c0bda5e02437'], + }), + ('mda', '0.5-2', { + 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], + }), + ('biomod2', '3.4.6', { + 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], + }), + ('poLCA', '1.4.1', { + 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], + }), + ('PermAlgo', '1.1', { + 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.12', { + 'checksums': ['9acdf912f0e7a68a5b6a7946d5ebb0c2007b3d6cd2e39075eddae2b586354e89'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-1', { + 'checksums': ['e8abadc5614f132edc3fb9cb1c82ce4dacc1315b727fbd49db7399aee24115ba'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-19', { + 'checksums': ['6c7eed2d238ab4d8ebcd624e05a68849fa57bf2929b893bcd1a0990b5fcc304d'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.4.0', { + 'checksums': ['49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + ('memoise', '2.0.0', { + 'checksums': ['ff9ae3a1a95ad6271d98e6eca016768b790e44bd613356b8e86b685aefd9ecaf'], + }), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.2', { + 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], + }), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '2.1', { + 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], + }), + ('lmom', '2.8', { + 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], + }), + ('gld', '2.6.2', { + 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], + }), + ('DescTools', '0.99.40', { + 'checksums': ['53954f0477eac77328efac562716c8b078e76b5ad5edf0227ba2624aa2b8c7dd'], + }), + ('orthopolynom', '1.0-5', { + 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], + }), + ('gaussquad', '1.0-2', { + 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.0', { + 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], + }), + ('tableone', '0.12.0', { + 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], + }), + ('jstable', '1.0.1', { + 'checksums': ['2e4cfce264a2353e4655d0faafc93969222d67a21c0c9cc61a2454abd99c5cdc'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.2', { + 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], + }), + ('sensemakr', '0.1.3', { + 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], + }), + ('RcppParallel', '5.0.3', { + 'checksums': ['71121138f25fcc97885b14545b7e7eb92e5f3953aec15e7df3822ae26d8e0c46'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.3-15', { + 'checksums': ['f73ead024bc3b65bdb0c5e5cd5458845158914eb579c07be2fd697a3573ebe6f'], + }), + ('metafor', '2.4-0', { + 'checksums': ['b64a678b762e91f1e0a6360b15e79fe19159b243c9f40ad9cc0be833bb4ba9ac'], + }), + ('fmri', '1.9.6', { + 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + }), + ('AnalyzeFMRI', '1.1-23', { + 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], + }), +] + +moduleclass = 'lang' From bf6de00e4d3d43f0e49b743fb44a5a610164d742 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Mar 2021 11:32:56 +0000 Subject: [PATCH 0465/2365] Fixes reported comment formatting issues. --- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 7efd892015..c0abb895c3 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -1,9 +1,9 @@ -## +# # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Robert Mijakovic # reciPY derived from preexisting reciPys for 4.0.3 and 4.0.0 with updated versions. -## +# name = 'R' version = '4.0.4' @@ -51,8 +51,8 @@ dependencies = [ ('ImageMagick', '7.0.10-35'), # for animation ('GLPK', '4.65'), # for Rglpk ('nodejs', '12.19.0'), # for V8 (required by rstan) - ('GDAL', '3.2.1'), # for sf - ('SQLite', '3.33.0') # for sf + ('GDAL', '3.2.1'), # for sf + ('SQLite', '3.33.0') # for sf # OS dependency should be preferred if the os version is more recent then # this version, it's nice to have an up to date openssl for security # reasons From 0c25bacb9dcc55e3e01b63da58c445ef86f537bf Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 9 Mar 2021 13:03:51 +0100 Subject: [PATCH 0466/2365] #168 r-inla --- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb index d292d071b1..1f70515297 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] From 0f41786d90742b8e4525b8ded02e4437f681c08e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 9 Mar 2021 13:05:14 +0100 Subject: [PATCH 0467/2365] #171 manta --- easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index 1708d2d677..68da86b69d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -9,11 +9,13 @@ toolchainopts = {'pic': True} source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +# patch of a missing include file that has been fixed in 1.75.0 https://github.com/boostorg/serialization/issues/219 patches = ['Boost-%(version)s-library_version_type_serialization.patch'] checksums = [ 'afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5', # boost_1_74_0.tar.gz # Boost-1.74.0-library_version_type_serialization.patch - 'ee61e889ce9473ad82b69c9a8cbe1bf9650d633b74fdf7e4f4a4825aa990feca', + '882b4bdf1029ff0a31d092a0a92d920f5b5f0cea40feb153256bfb5a9098936d', ] dependencies = [ From 42e9fe95423783d9f433b1843e4dd84b72b55597 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Mar 2021 12:10:37 +0000 Subject: [PATCH 0468/2365] Removes duplicated dependency and extensions. --- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index c0abb895c3..cd9b8bc9c1 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -52,7 +52,6 @@ dependencies = [ ('GLPK', '4.65'), # for Rglpk ('nodejs', '12.19.0'), # for V8 (required by rstan) ('GDAL', '3.2.1'), # for sf - ('SQLite', '3.33.0') # for sf # OS dependency should be preferred if the os version is more recent then # this version, it's nice to have an up to date openssl for security # reasons @@ -1677,9 +1676,6 @@ exts_list = [ ('rgexf', '0.16.0', { 'checksums': ['2a671df9ac70cfefd4092754317cb28e32a33df345b80e1975bf838e838245ee'], }), - ('influenceR', '0.1.0', { - 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], - }), ('sem', '3.1-11', { 'checksums': ['33b1ad7695db13af8cdd214f5d388db494528b433c61c7ad89970cefcc8b430e'], }), @@ -2116,9 +2112,6 @@ exts_list = [ ('fitdistrplus', '1.1-3', { 'checksums': ['776d5456e14398e44b78b3d7db526559bb7a3537e546a29c88aa192141c756de'], }), - ('rappdirs', '0.3.3', { - 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], - }), ('reticulate', '1.18', { 'checksums': ['b33f855a58f446eefbe38df8a1a4865390f5d4ebd64b2c72266baaee64628513'], }), @@ -2692,9 +2685,6 @@ exts_list = [ ('gWidgets2', '1.0-8', { 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), - ('memoise', '2.0.0', { - 'checksums': ['ff9ae3a1a95ad6271d98e6eca016768b790e44bd613356b8e86b685aefd9ecaf'], - }), ('gWidgets2tcltk', '1.0-6', { 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], # need to run installation via xvfb-run to avoid problems on headless systems: @@ -2803,9 +2793,6 @@ exts_list = [ ('sensemakr', '0.1.3', { 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], }), - ('RcppParallel', '5.0.3', { - 'checksums': ['71121138f25fcc97885b14545b7e7eb92e5f3953aec15e7df3822ae26d8e0c46'], - }), ('CompQuadForm', '1.4.3', { 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], }), From eebcf0a15984f8dadd5af84202c5d4cd9f534df2 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 9 Mar 2021 13:22:36 +0100 Subject: [PATCH 0469/2365] cleaned up --- easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index 68da86b69d..ddff402f15 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -1,3 +1,6 @@ +## +# Authors:: Denis Kristak +## name = 'Boost' version = '1.74.0' @@ -9,8 +12,6 @@ toolchainopts = {'pic': True} source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] - -# patch of a missing include file that has been fixed in 1.75.0 https://github.com/boostorg/serialization/issues/219 patches = ['Boost-%(version)s-library_version_type_serialization.patch'] checksums = [ 'afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5', # boost_1_74_0.tar.gz @@ -18,6 +19,7 @@ checksums = [ '882b4bdf1029ff0a31d092a0a92d920f5b5f0cea40feb153256bfb5a9098936d', ] +# patch of a missing include file that has been fixed in 1.75.0 https://github.com/boostorg/serialization/issues/219 dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), From 0846e2c07dfb01675438ec2dce37fe6531b17855 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Mar 2021 12:34:11 +0000 Subject: [PATCH 0470/2365] Downgrades LibTIFF and GMP to older releases for R package. --- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index cd9b8bc9c1..58e18d6d35 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -35,12 +35,12 @@ dependencies = [ ('PCRE2', '10.35'), ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R - ('LibTIFF', '4.2.0'), + ('LibTIFF', '4.1.0'), ('Java', '15.0.2', '', True), ('Tk', '8.6.11'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML - ('GMP', '6.2.1'), # for igraph + ('GMP', '6.2.0'), # for igraph ('NLopt', '2.6.2'), # for nloptr ('FFTW', '3.3.8'), # for fftw ('libsndfile', '1.0.28'), # for seewave @@ -51,7 +51,7 @@ dependencies = [ ('ImageMagick', '7.0.10-35'), # for animation ('GLPK', '4.65'), # for Rglpk ('nodejs', '12.19.0'), # for V8 (required by rstan) - ('GDAL', '3.2.1'), # for sf + ('GDAL', '3.2.1') # for sf # OS dependency should be preferred if the os version is more recent then # this version, it's nice to have an up to date openssl for security # reasons From ff4d0db5c796b0fd97a08d8fb40dd916823d0539 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Mar 2021 13:01:52 +0000 Subject: [PATCH 0471/2365] Downgrades and removes newer R dependencies. --- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 58e18d6d35..2e24510146 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '15.0.2', '', True), - ('Tk', '8.6.11'), # for tcltk + ('Java', '11', '', True), + ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML ('GMP', '6.2.0'), # for igraph From 2ae0bab9da3a364f5500882f1e9991a64247028c Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 9 Mar 2021 16:21:40 +0100 Subject: [PATCH 0472/2365] cleaned up --- .../manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..aef74b24d0 --- /dev/null +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,69 @@ +## +# Authors:: Denis Kristak +## +easyblock = 'CMakeMake' + +name = 'manta' +version = '1.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Illumina/manta' +description = """ +Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. +It is optimized for analysis of germline variation in small sets of individuals and +somatic variation in tumor/normal sample pairs. Manta discovers, assembles and +scores large-scale SVs, medium-sized indels and large insertions within a +single efficient workflow. +""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'Illumina' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['76ce7c4a95a3b92cb16381f9a3b091afa234948ae6f028982abbd49e21206421'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('Boost', '1.74.0'), + ('zlib', '1.2.11'), +] + +buildopts = "FLAGS='-I$EBROOTPYTHON/include -L$EBROOTPYTHON/lib -lpython ' " + +# following are necessary should anyone try to make manta compatible with python3 +# making included pyflow compatible with python3 +# preinstallopts = "sed -i 's/0755/0o755/g' ./redist/pyflow-*/src/pyflow.py && " +# preinstallopts += "sed -i 's/DataDirException, e/DataDirException(e)/g' ./redist/pyflow-*/src/pyflow.py && " +# preinstallopts += "sed -i 's/raise Exception(\"pyflow module has only been tested for python versions \ +# \[2.4,3.0)/pass #/g' ./redist/pyflow-*/src/pyflow.py && " +# preinstallopts += "sed -i 's/raise Exception(\"Manta does not currently support python3/pass #/g' \ +# ../manta-%(version)s/src/python/lib/makeRunScript.py && " + +local_binaries = ['CheckSVLoci', 'DumpSVLoci', 'EstimateSVLoci', 'GenerateSVCandidates', 'GetAlignmentStats', + 'GetChromDepth', 'MergeAlignmentStats', 'MergeSVLoci', 'SummarizeAlignmentStats', 'SummarizeSVLoci', + 'TestAssembler'] + +sanity_check_paths = { + 'files': [ + ['bin/%s' % x for x in ['configManta.py', 'runMantaWorkflowDemo.py']] + + ['libexec/%s' % x for x in ['denovo_scoring.py', 'extractSmallIndelCandidates.py']], + ], + 'dirs': ['libexec'], +} + +sanity_check_commands = [ + 'python %(installdir)s/bin/runMantaWorkflowDemo.py' +] + +modextrapaths = { + 'PATH': 'libexec', + 'PYTHONPATH': 'lib/python', +} + +moduleclass = 'bio' From def7b3e00847f2f7669002e9f6cb7ffd3084a572 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 9 Mar 2021 16:32:14 +0100 Subject: [PATCH 0473/2365] adding easyconfigs: Elk-7.0.12-foss-2020b.eb, libxc-5.1.2-GCC-10.2.0.eb --- .../e/Elk/Elk-7.0.12-foss-2020b.eb | 60 +++++++++++++++++++ .../l/libxc/libxc-5.1.2-GCC-10.2.0.eb | 41 +++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb b/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb new file mode 100644 index 0000000000..4cb91d01d7 --- /dev/null +++ b/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb @@ -0,0 +1,60 @@ +easyblock = 'MakeCp' + +name = 'Elk' +version = '7.0.12' + +homepage = 'http://elk.sourceforge.net/' +description = """An all-electron full-potential linearised +augmented-plane wave (FP-LAPW) code with many advanced features. Written +originally at Karl-Franzens-Universität Graz as a milestone of the +EXCITING EU Research and Training Network, the code is designed to be as +simple as possible so that new developments in the field of density +functional theory (DFT) can be added quickly and reliably. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True, 'opt': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TGZ] +checksums = ['9995387c681d0e5a9bd52cb274530b23c0370468b6be86f6c90a6ec445cb8a01'] + +dependencies = [ + ('libxc', '5.1.2'), + ('Wannier90', '3.1.0'), +] + + +# make.inc file is generated interactively by "setup" command, creating it here +prebuildopts = 'echo "F90_OPTS = -std=legacy $FFLAGS" > make.inc && ' +prebuildopts += 'echo "F77_OPTS = -std=legacy $FFLAGS" >> make.inc && ' +prebuildopts += 'echo "LIB_LPK = $LIBLAPACK" >> make.inc && ' +prebuildopts += 'echo "LIB_FFT = $LIBFFT" >> make.inc && ' +prebuildopts += 'echo "LIB_W90 = -lwannier" >> make.inc && ' +prebuildopts += 'echo "LIB_libxc = -lxcf90 -lxc" >> make.inc && ' +prebuildopts += 'echo "SRC_libxc = libxcf90.f90 libxcifc.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_FFT = zfftifc_fftw.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_OBLAS = oblas_stub.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_BLIS = blis_stub.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_MKL = mkl_stub.f90" >> make.inc && ' + +buildopts = 'all' + +runtest = 'test' + +parallel = 1 + +files_to_copy = [( + [ + 'src/elk', 'src/spacegroup/spacegroup', 'src/eos/eos', + 'utilities/elk-bands/elk-bands', 'utilities/elk-optics/elk-optics.py', + 'utilities/wien2k-elk/se.pl' + ], 'bin' +)] + +sanity_check_paths = { + 'files': ['bin/elk', 'bin/spacegroup', 'bin/eos'], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..e38add051d --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '5.1.2' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['180d52b5552921d1fac8a10869dd30708c0fb41dc202a3bbee0e36f43872718a'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Perl', '5.32.0'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +parallel = 1 + +moduleclass = 'chem' From 6951a81bf04f77a4388df69f4e7347158a898f45 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 9 Mar 2021 16:45:25 +0100 Subject: [PATCH 0474/2365] cleaned up --- easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index ddff402f15..9d48212c07 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -12,10 +12,10 @@ toolchainopts = {'pic': True} source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -patches = ['Boost-%(version)s-library_version_type_serialization.patch'] +patches = ['Boost-%(version)s-GCC-library_version_type_serialization.patch'] checksums = [ 'afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5', # boost_1_74_0.tar.gz - # Boost-1.74.0-library_version_type_serialization.patch + # Boost-1.74.0-GCC-library_version_type_serialization.patch '882b4bdf1029ff0a31d092a0a92d920f5b5f0cea40feb153256bfb5a9098936d', ] From 0b833721d08ba419ceba7bad5fdfdb61d54c7e0b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 9 Mar 2021 17:39:56 +0100 Subject: [PATCH 0475/2365] cleaned up --- easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index 9d48212c07..7e7244dd47 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -12,11 +12,11 @@ toolchainopts = {'pic': True} source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -patches = ['Boost-%(version)s-GCC-library_version_type_serialization.patch'] +patches = ['Boost-%(version)s-library_version_type_serialization.patch'] checksums = [ 'afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5', # boost_1_74_0.tar.gz - # Boost-1.74.0-GCC-library_version_type_serialization.patch - '882b4bdf1029ff0a31d092a0a92d920f5b5f0cea40feb153256bfb5a9098936d', + # Boost-1.74.0-library_version_type_serialization.patch + 'ee61e889ce9473ad82b69c9a8cbe1bf9650d633b74fdf7e4f4a4825aa990feca', ] # patch of a missing include file that has been fixed in 1.75.0 https://github.com/boostorg/serialization/issues/219 From 6c0eb4c517c7f301a4d2a1646acfe3ae6debaddc Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Mar 2021 16:41:04 +0000 Subject: [PATCH 0476/2365] adding easyconfigs: Emacs-27.1-GCCcore-10.2.0.eb --- .../e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2115ee1003 --- /dev/null +++ b/easybuild/easyconfigs/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +# +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Robert Mijakovic +# reciPY derived from preexisting reciPy for GCCcore-9.2.0. +# +easyblock = 'ConfigureMake' + +name = 'Emacs' +version = '27.1' + +homepage = 'https://www.gnu.org/software/emacs/' +description = """GNU Emacs is an extensible, customizable text editor--and more. + At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming + language with extensions to support text editing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] +checksums = ['ffbfa61dc951b92cf31ebe3efc86c5a9d4411a1222b8a4ae6716cfd0e2a584db'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('ncurses', '6.2'), + ('LibTIFF', '4.1.0'), + ('X11', '20201008'), + ('GTK+', '3.24.23'), +] + +# If you want to use Emacs plugins you must install the gnutls command line tools +# osdependencies = [('gnutls-utils')] + +configopts = '--with-gif=no --with-tiff=yes --with-x-toolkit=yes --with-xpm=yes --with-gnutls=no ' + +sanity_check_paths = { + 'files': ["bin/emacs", "bin/emacs-%(version)s", "bin/emacsclient", "bin/etags"], + 'dirs': [] +} + +moduleclass = 'tools' From 9c44ec459ae0c5efe67e495950e77a93b24a2cb4 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Mar 2021 17:56:49 +0000 Subject: [PATCH 0477/2365] adding easyconfigs: AOCC-2.3.0-GCCcore-10.2.0.eb --- .../a/AOCC/AOCC-2.3.0-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-2.3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2ff631e5f7 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Robert Mijakovic +# reciPY derived from preexisting reciPy for GCCcore-9.3.0. +# +name = 'AOCC' +version = '2.3.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = [ + '9f8a1544a5268a7fb8cd21ac4bdb3f8d1571949d1de5ca48e2d3309928fc3d15', # aocc-compiler-2.3.0.tar +] + +dependencies = [ + ('binutils', '2.35'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +moduleclass = 'compiler' From 87e03cb53f2ca2104be5c8c44f83aa44bb9a7a42 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 10 Mar 2021 09:18:24 +0100 Subject: [PATCH 0478/2365] Update easybuild/easyconfigs/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb index 2115ee1003..2c9a2063b3 100644 --- a/easybuild/easyconfigs/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb @@ -22,6 +22,7 @@ checksums = ['ffbfa61dc951b92cf31ebe3efc86c5a9d4411a1222b8a4ae6716cfd0e2a584db'] builddependencies = [ ('binutils', '2.35'), + ('pkg-config', '0.29.2'), ] dependencies = [ From 65584438487fa66a8dad8cf7977383cc865836b6 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 10 Mar 2021 12:40:52 +0000 Subject: [PATCH 0479/2365] Updates the versions and adds the missing linkcomm extension. --- .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 34 +++++++++++-------- 1 file changed, 20 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 2e24510146..7ed6463d54 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -386,8 +386,8 @@ exts_list = [ ('Matrix', '1.3-2', { 'checksums': ['950ba5d91018e711fd2743b3486a50dc47ae9c271389fce587792f0a9aab9531'], }), - ('RcppArmadillo', '0.10.2.1.0', { - 'checksums': ['65db3ea24a70c926be3d88b14677c2a48940f2df62a970ef4560b32af0b5290e'], + ('RcppArmadillo', '0.10.2.2.0', { + 'checksums': ['3865d31d40fd6f217b4171c3cc92011a1e56e2a354f40c251e968dbb8dac7aa4'], }), ('plyr', '1.8.6', { 'checksums': ['ea55d26f155443e9774769531daa5d4c20a0697bb53abd832e891b126c935287'], @@ -560,8 +560,8 @@ exts_list = [ ('robustbase', '0.93-7', { 'checksums': ['8911d2d0fdca5e2627033e046279f9d106e25ce98d588f9ccc4d8e4b42680956'], }), - ('zoo', '1.8-8', { - 'checksums': ['4e8cc4065047ba12e103b9664f3b607c770673096e9c2b694fad2b2ec3203ce7'], + ('zoo', '1.8-9', { + 'checksums': ['b7be259067a8b9d4a8f5d387e0946a5ba1eb43474baa67ccf4f8bf4b15f772a3'], }), ('lmtest', '0.9-38', { 'checksums': ['32a22cea45398ffc5732d9f5c0391431d0cdd3a9e29cc7b77bea32c1eb4a216b'], @@ -716,8 +716,8 @@ exts_list = [ ('gamlss.data', '5.1-4', { 'checksums': ['0d3777d8c3cd76cef273aa6bde40a91688719be401195ed9bfd1e85bd7d5eeb5'], }), - ('gamlss.dist', '5.1-7', { - 'checksums': ['9871c38c893a8df7874c533351858dfe4e7587c71021dbbf88c0c76ff3c0ef5b'], + ('gamlss.dist', '5.3-2', { + 'checksums': ['0caa92cd20c3d2d11b1af4656fd0de09adf145992345cba07fdcd33b7716ced3'], }), ('gamlss', '5.3-1', { 'checksums': ['99474316dfdb620a539c9a56a38413ad8b118c03da815ca23595f7f8c933eed9'], @@ -1079,8 +1079,8 @@ exts_list = [ ('phylobase', '0.8.10', { 'checksums': ['5a44380ff49bab333a56f6f96157324ade8afb4af0730e013194c4badb0bf94b'], }), - ('magick', '2.6.0', { - 'checksums': ['66585336e3ff18793ae9e2726af67a6672622f270468670ab5fe5e013bc48ecc'], + ('magick', '2.7.0', { + 'checksums': ['97e93b7a9033f8a7136bd8b63fd65a154bc67c0406024461d6b59d7b8d8c3354'], }), ('animation', '2.6', { 'checksums': ['90293638920ac436e7e4de76ebfd92e1643ccdb0259b62128f16dd0b13245b0a'], @@ -1295,8 +1295,8 @@ exts_list = [ ('leaps', '3.1', { 'checksums': ['3d7c3a102ce68433ecf167ece96a7ebb4207729e4defd0ac8fc00e7003f5c3b6'], }), - ('pbkrtest', '0.5-0.1', { - 'checksums': ['f56525488c6efe4a5cbf849bf9a82747041478605b166c29bad54e464e46f469'], + ('pbkrtest', '0.5.1', { + 'checksums': ['b2a3452003d93890f122423b3f2487dcb6925440f5b8a05578509e98b6aec7c5'], }), ('carData', '3.0-4', { 'checksums': ['cda6f5e3efc1d955a4a0625e9c33f90d49f5455840e88b3bd757129b86044724'], @@ -1926,8 +1926,8 @@ exts_list = [ ('selectr', '0.4-2', { 'checksums': ['5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127'], }), - ('rvest', '0.3.6', { - 'checksums': ['6a2ee3a25d2d738031edbc1b5e2410f2a4538dfbb9705af145f9039504b902fa'], + ('rvest', '1.0.0', { + 'checksums': ['a358bf258a91b3362b3736fb5f957c12e98cddf21b6066fb2abdd26ecd665713'], }), ('tidyverse', '1.3.0', { 'checksums': ['6d8acb81e994f9bef5e4dcf908bcea3786d108adcf982628235b6c8c80f6fe09'], @@ -2365,8 +2365,8 @@ exts_list = [ ('SOAR', '0.99-11', { 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], }), - ('terra', '1.0-10', { - 'checksums': ['b4afca161da08890ab520b19b4e8afc7bd1a9cb252c4d4ec2b9c6c5a0bbaaaab'], + ('terra', '1.1-4', { + 'checksums': ['6f6929d6bc7757281c7e314b43875d79b5bcfd1174d62d3462509b82752950ef'], }), ('rasterVis', '0.50', { 'checksums': ['1186283ba5915234edfac066763579ccd58d04fbdeca0c1aa8b15f354a93ee54'], @@ -2811,6 +2811,12 @@ exts_list = [ ('AnalyzeFMRI', '1.1-23', { 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.4', { + 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], + }), ] moduleclass = 'lang' From 5ea44f210678071f1ea4fc1bfe4e41628065da8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Mar 2021 15:14:13 +0100 Subject: [PATCH 0480/2365] adding easyconfigs: ArviZ-0.11.1-intel-2020b.eb --- .../a/ArviZ/ArviZ-0.11.1-intel-2020b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb new file mode 100644 index 0000000000..830df127df --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'ArviZ' +version = '0.11.1' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb0730ab62223a44ec99072b12f9e9f24521a36e6b7ba2624df9f9908eba1d82'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # numpy, scipy, pandas + ('netcdf4-python', '1.5.5.1'), + ('xarray', '0.16.2'), + ('matplotlib', '3.3.3'), + ('typing-extensions', '3.7.4.3'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' From fdfe9c37c00ef0c6e1b7e61f573a363566b546b8 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 10 Mar 2021 18:37:02 +0000 Subject: [PATCH 0481/2365] adding easyconfigs: libdwarf-20201201-GCCcore-10.2.0.eb --- .../libdwarf-20201201-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ce8f2c2684 --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '20201201' + +homepage = 'http://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.prevanders.net'] +sources = [SOURCE_TAR_GZ] +checksums = ['62db1028dfd8fd877d01ae75873ac1fe311437012ef48a0ac4157189e1e9b2c9'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('libelf', '0.8.13'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' From 25f9004222b3083e347b7cec4eee6fb4a57468f0 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 10 Mar 2021 18:46:02 +0000 Subject: [PATCH 0482/2365] adding easyconfigs: PAPI-6.0.0-GCCcore-10.2.0.eb --- .../p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f94945b421 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Robert Mijakovic +# reciPY derived from the reciPY for GCCcore 9.3.0 by Fotis Georgatos. +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '6.0.0' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3442709dae3405c2845b304c06a8b15395ecf4f3899a89ceb4d715103cb4055f'] + +builddependencies = [ + ('binutils', '2.35'), +] + +start_dir = 'src' + +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' From 4b6d5f31dea48a085d8cf6c1f63b6de0ed8ae52a Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 10 Mar 2021 19:01:34 +0000 Subject: [PATCH 0483/2365] Added forgotten header and a dependency --- .../libdwarf-20201201-GCCcore-10.2.0.eb | 6 ++++ .../l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb index ce8f2c2684..b15da2ad9a 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb @@ -1,3 +1,9 @@ +# +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Robert Mijakovic +# reciPY derived from preexisting reciPy for 20190529 with updated version. +# easyblock = 'ConfigureMake' name = 'libdwarf' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ebf7cadc6d --- /dev/null +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +# +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Robert Mijakovic +# reciPY derived from preexisting reciPy for GCCcore-9.3.0. +# +easyblock = 'ConfigureMake' + +name = 'libelf' +version = '0.8.13' + +homepage = 'http://www.mr511.de/software/english.html' +description = """libelf is a free ELF object file access library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'http://www.mr511.de/software/', + 'https://fossies.org/linux/misc/old/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d'] + +builddependencies = [ + ('binutils', '2.35'), +] + +modextrapaths = {'CPATH': 'include/libelf'} + +sanity_check_paths = { + 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'devel' From 9cdec9d4371276dd4259689cc541a5722e4e2047 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 10 Mar 2021 19:36:57 +0000 Subject: [PATCH 0484/2365] Fixes the homepage and source_url and simplifies the header --- .../l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb | 3 --- .../l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb | 10 ++-------- 2 files changed, 2 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb index b15da2ad9a..f0a6b1b1c8 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb @@ -1,8 +1,5 @@ # -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# # Author: Robert Mijakovic -# reciPY derived from preexisting reciPy for 20190529 with updated version. # easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb index ebf7cadc6d..f2b0813415 100644 --- a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb @@ -1,23 +1,17 @@ # -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# # Author: Robert Mijakovic -# reciPY derived from preexisting reciPy for GCCcore-9.3.0. # easyblock = 'ConfigureMake' name = 'libelf' version = '0.8.13' -homepage = 'http://www.mr511.de/software/english.html' +homepage = 'https://www.prevanders.net/dwarf.html' description = """libelf is a free ELF object file access library""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [ - 'http://www.mr511.de/software/', - 'https://fossies.org/linux/misc/old/', -] +source_urls = ['https://fossies.org/linux/misc/old/'] sources = [SOURCE_TAR_GZ] checksums = ['591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d'] From 9db61b8322bbb8a74881b578239d592aac06b33e Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 10 Mar 2021 19:49:02 +0000 Subject: [PATCH 0485/2365] Adds https instead of http --- .../l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb | 4 ++-- .../easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb index f0a6b1b1c8..82b24be6a2 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb @@ -6,14 +6,14 @@ easyblock = 'ConfigureMake' name = 'libdwarf' version = '20201201' -homepage = 'http://www.prevanders.net/dwarf.html' +homepage = 'https://www.prevanders.net/dwarf.html' description = """The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and anyone interested in reading or writing DWARF information))""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.prevanders.net'] +source_urls = ['https://www.prevanders.net'] sources = [SOURCE_TAR_GZ] checksums = ['62db1028dfd8fd877d01ae75873ac1fe311437012ef48a0ac4157189e1e9b2c9'] diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb index f2b0813415..634267b115 100644 --- a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb @@ -6,7 +6,7 @@ easyblock = 'ConfigureMake' name = 'libelf' version = '0.8.13' -homepage = 'https://www.prevanders.net/dwarf.html' +homepage = 'https://sourceware.org/elfutils' description = """libelf is a free ELF object file access library""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From 0da065b3ed716db0139bd95c5d6f99709ff24948 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Mar 2021 13:49:22 +0100 Subject: [PATCH 0486/2365] rename 'delly' to 'Delly', stick to GCC toolchain for LAST 1179 --- .../d/Delly/Delly-0.8.7-gompi-2020b.eb | 44 +++++++++++++++++++ .../l/LAST/LAST-1179-GCC-10.2.0.eb | 29 ++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/d/Delly/Delly-0.8.7-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/l/LAST/LAST-1179-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/d/Delly/Delly-0.8.7-gompi-2020b.eb b/easybuild/easyconfigs/d/Delly/Delly-0.8.7-gompi-2020b.eb new file mode 100644 index 0000000000..f3283826a1 --- /dev/null +++ b/easybuild/easyconfigs/d/Delly/Delly-0.8.7-gompi-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'Delly' +version = '0.8.7' + +homepage = 'https://github.com/dellytools/delly/' +description = """Delly is an integrated structural variant (SV) prediction +method that can discover, genotype and visualize deletions, tandem duplications, +inversions and translocations at single-nucleotide resolution in short-read +massively parallel sequencing data. It uses paired-ends, split-reads and +read-depth to sensitively and accurately delineate genomic rearrangements +throughout the genome.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True} + +github_account = 'dellytools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['095e94c9994ae6c110f4acffb55dc1b68fdc9541a24fcbf6954fd12ff7ab6efb'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('HTSlib', '1.11'), + ('Boost', '1.74.0'), +] + +build_cmd = 'make PARELLEL=1 -B src/delly' + +files_to_copy = [ + (['src/delly'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/delly'], + 'dirs': ['bin'] +} + +sanity_check_commands = ['delly'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LAST/LAST-1179-GCC-10.2.0.eb b/easybuild/easyconfigs/l/LAST/LAST-1179-GCC-10.2.0.eb new file mode 100644 index 0000000000..ed590fe3da --- /dev/null +++ b/easybuild/easyconfigs/l/LAST/LAST-1179-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'LAST' +version = '1179' + +homepage = 'http://last.cbrc.jp/' +description = "LAST finds similar regions between sequences." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['http://last.cbrc.jp/'] +sources = ['last-%(version)s.zip'] +checksums = ['f78f68884ed936408e26e38afe1b8f9023747384e555a4ec92405ed23a1cd075'] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS -pthread -DHAS_CXX_THREADS"' +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['fastq-interleave', 'lastal', 'lastal8', 'lastdb', 'lastdb8', 'last-dotplot', + 'last-map-probs', 'last-merge-batches', 'last-pair-probs', 'last-postmask', + 'last-split', 'last-split8', 'last-train', 'maf-convert', 'maf-cut', + 'maf-join', 'maf-sort', 'maf-swap', 'parallel-fasta', 'parallel-fastq']], + 'dirs': [], +} + +moduleclass = 'bio' From a9f4afd1bd19a3fd670d32be86e7392b41d6ee71 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Mar 2021 18:11:18 +0000 Subject: [PATCH 0487/2365] HTSeq and SWIG updated to latest versions with latest toolchaine --- .../h/HTSeq/HTSeq-0.11.3-foss-2020b.eb | 45 +++++++++++++++++++ .../s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb | 4 ++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb new file mode 100644 index 0000000000..642570a3f0 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# +easyblock = 'PythonPackage' + +name = 'HTSeq' +version = '0.11.3' + +homepage = 'https://github.com/simon-anders/htseq' +description = """HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +checksums = ['abd13b48021340fea783a9dff110534c19a306b54182501e1aa7b324d458b080'] + +builddependencies = [('SWIG', '4.0.2')] + +dependencies = [ + ('Python', '3.8.6'), + ('Pysam', '0.16.0.1'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'], +} + +sanity_check_commands = ['%(namelower)s-count --help'] + +sanity_pip_check = True + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb index 90a44c127b..46a2801e91 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb @@ -1,3 +1,7 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + name = 'SWIG' version = '4.0.2' From 1b0072ac0d90c9ef5efeda4333cb45d5c67c1038 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Mar 2021 18:58:47 +0000 Subject: [PATCH 0488/2365] Removed author from files --- easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb | 5 +---- easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb | 4 ---- 2 files changed, 1 insertion(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb index 642570a3f0..be07f7b05f 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb @@ -1,8 +1,5 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen -# + easyblock = 'PythonPackage' name = 'HTSeq' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb index 46a2801e91..90a44c127b 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb @@ -1,7 +1,3 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen - name = 'SWIG' version = '4.0.2' From 3af63362c1ef1f3c7b839f83541db3b499434cd0 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Mar 2021 22:42:46 +0000 Subject: [PATCH 0489/2365] Corrected wrong builddep. and swapped lib over to include in sanity checks --- .../libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb | 2 +- .../l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb index 694e34a5a2..2823fc5897 100644 --- a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb @@ -29,7 +29,7 @@ separate_build_dir = True sanity_check_paths = { 'files': ['lib/libbaseencode.%s' % SHLIB_EXT], - 'dirs': ['lib'], + 'dirs': ['include'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb index 5fd70b9bac..c2da1b819d 100644 --- a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb @@ -18,19 +18,22 @@ checksums = ['f122aea37337cdfcdaa1ce979ecfb5177ad7dcb273caf2d6056820f1dbf92e93'] builddependencies = [ ('CMake', '3.18.4'), - ('libgcrypt', '1.9.2'), - ('libbaseencode', '1.0.11'), ('pkg-config', '0.29.2'), ('binutils', '2.35'), ] +dependencies = [ + ('libgcrypt', '1.9.2'), + ('libbaseencode', '1.0.11'), +] + parallel = 1 separate_build_dir = True sanity_check_paths = { 'files': ['lib/libcotp.%s' % SHLIB_EXT], - 'dirs': ['lib'], + 'dirs': ['include'], } moduleclass = 'lib' From 01b346408db799d394a782ca008ff071139e400f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Mar 2021 10:57:54 +0100 Subject: [PATCH 0490/2365] {toolchain} goblf/2020b (incl. LAPACK 3.9.0) --- easybuild/easyconfigs/g/goblf/goblf-2020b.eb | 32 +++++++++++++++++++ .../easyconfigs/h/HPL/HPL-2.3-goblf-2020b.eb | 21 ++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/goblf/goblf-2020b.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-goblf-2020b.eb diff --git a/easybuild/easyconfigs/g/goblf/goblf-2020b.eb b/easybuild/easyconfigs/g/goblf/goblf-2020b.eb new file mode 100644 index 0000000000..277dd9be18 --- /dev/null +++ b/easybuild/easyconfigs/g/goblf/goblf-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'Toolchain' + +name = 'goblf' +version = '2020b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, BLIS (BLAS support), LAPACK, FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_comp_name = 'GCC' +local_comp_version = '10.2.0' +local_comp = (local_comp_name, local_comp_version) + +local_gcccore = ('GCCcore', local_comp_version) + +# toolchain used to build dependencies +local_comp_mpi_tc_name = 'gompi' +local_comp_mpi_tc = (local_comp_mpi_tc_name, version) + +# compiler toolchain dependencies +dependencies = [ + local_comp, + ('OpenMPI', '4.0.5', '', local_comp), # part of gompi toolchain + ('BLIS', '0.8.0', '', local_gcccore), + ('LAPACK', '3.9.0', '', local_gcccore), + ('ScaLAPACK', '2.1.0', '-bf', local_comp_mpi_tc), + ('FFTW', '3.3.8', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-goblf-2020b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-goblf-2020b.eb new file mode 100644 index 0000000000..d62ec42b41 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-goblf-2020b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'goblf', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' From 3d19ce98f236291156cfabe44d1c2370677cf298 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Mar 2021 12:41:14 +0100 Subject: [PATCH 0491/2365] adding easyconfigs: pymatgen-2022.0.4-foss-2020b.eb --- .../pymatgen/pymatgen-2022.0.4-foss-2020b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb new file mode 100644 index 0000000000..56a123630c --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'pymatgen' +version = '2022.0.4' + +homepage = 'https://pypi.python.org/pypi/pymatgen' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + # required for numpy tests + ('hypothesis', '5.41.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('matplotlib', '3.3.3'), + ('spglib-python', '1.16.0'), + ('networkx', '2.5'), + ('sympy', '1.7.1'), + ('plotly.py', '4.14.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('numpy', '1.20.1', { + 'sources': ['numpy-%(version)s.zip'], + 'checksums': ['3bc63486a870294683980d76ec1e3efc786295ae00128f9ea38e2c6e74d5a60a'], + }), + ('monty', '2021.3.3', { + 'checksums': ['3e857506696433d4c4ee92d995d923e157a7015586806c3ec3b42ea0aa3b8782'], + }), + ('palettable', '3.3.0', { + 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], + }), + ('ruamel.yaml.clib', '0.2.2', { + 'checksums': ['2d24bd98af676f4990c4d715bcdc2a60b19c56a3fb3a763164d2d8ca0e806ba7'], + 'modulename': False, # skip import check, covered by import check for ruamel.yaml extension + }), + ('ruamel.yaml', '0.16.13', { + 'checksums': ['bb48c514222702878759a05af96f4b7ecdba9b33cd4efcf25c86b882cef3a942'], + }), + ('uncertainties', '3.1.5', { + 'checksums': ['9122c1e7e074196883b4a7a946e8482807b2f89675cb5e3798b87e0608ede903'], + }), + (name, version, { + 'checksums': ['7241498c10179e6039a62ad368a6833cb5b3aca959bf985dcdd27ff6187d0574'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pmg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pmg --help"] + +sanity_pip_check = True + +moduleclass = 'chem' From d004614e7253d7d6c6abe75b0a0515d14cde4e2c Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 12 Mar 2021 13:37:55 +0000 Subject: [PATCH 0492/2365] adding easyconfigs: NVHPC-21.2.eb --- easybuild/easyconfigs/n/NVHPC/NVHPC-21.2.eb | 74 +++++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-21.2.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.2.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.2.eb new file mode 100644 index 0000000000..81a0d1f4af --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.2.eb @@ -0,0 +1,74 @@ +## +# Author: Robert Mijakovic +## +name = 'NVHPC' +version = '21.2' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +# By downloading, you accept the HPC SDK Software License Agreement (https://docs.nvidia.com/hpc-sdk/eula/index.html) +accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +local_tarball_tmpl = 'nvhpc_2021_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'x86_64': + 'a3e3393040185ae844002fbc6c8eb4ffdfb97ce8b2ce29d796fe7e9a521fdc59', + local_tarball_tmpl % 'ppc64le': + '6b69b6e4ebec6a91b9f1627384c50adad79ebdd25dfb20a5f64cf01c3a07f11a', + local_tarball_tmpl % 'aarch64': + 'fe19c0232f7c9534f8699b7432483c9cc649f1e92e7f0961d1aa7c54d83297ff' + } +] + +local_gccver = '10.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.35', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) +] + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/21.2/cuda/) +# for NVHPC 21.2, those are: 11.2, 11.0, 10.2; +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="10.2" (for example) +default_cuda_version = '11.2' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDAcore as a dependency, for example +# dependencies = [('CUDAcore', '11.0.2')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From 14d5dcc51f78d0a203fb1dfb07e89a1d8a76f41e Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 29 Jan 2021 14:39:36 +0000 Subject: [PATCH 0493/2365] [esl] update lipspio to 0.2.4 and gcc 10.2.0 --- .../l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..93bb74df60 --- /dev/null +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpspio' +version = '0.2.4' + +homepage = 'https://gitlab.e-cam2020.eu/esl/pspio/' +description = """libpspio is a library to read and write pseudopotentials in multiple formats.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://gitlab.e-cam2020.eu/esl/pspio/uploads/7efa924be97bd46354237ca3fb89495e/'] +checksums = ['740861617e1feb50a9e00609769b12d8'] + +configopts = ' --enable-gsl --enable-fortran ' + +dependencies = [('GSL', '2.6')] + +sanity_check_paths = { + 'files': ['include/pspiof_m.mod', 'include/pspio.h'] + [('lib/libpspiof.a', 'lib64/libpspiof.a')], + 'dirs': [], +} + +moduleclass = 'phys' From 6d5b30239f5947ca3641c51cb5eeeec9434ae9f3 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Fri, 12 Mar 2021 15:10:01 +0100 Subject: [PATCH 0494/2365] adding easyconfigs: p7zip-17.03-GCCcore-10.2.0.eb --- .../p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f50b76f9c3 --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '17.03' + +homepage = 'https://github.com/jinfeihan57/p7zip/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of +7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'jinfeihan57' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' + +files_to_copy = [ + (['bin/7z', 'bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), + (['bin/7z.%s' % SHLIB_EXT, 'bin/Codecs'], 'libexec'), +] + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z.%s' % SHLIB_EXT], + 'dirs': ['libexec/Codecs'], +} + +sanity_check_commands = [ + '7z --help', + '7z x || test $? -gt 0', +] + +moduleclass = 'tools' From 8e17104987d7e5f9f205cee3b9835eb23632a275 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Fri, 12 Mar 2021 16:04:37 +0100 Subject: [PATCH 0495/2365] p7zip: style --- easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb index f50b76f9c3..7da7616f42 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -12,6 +12,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} github_account = 'jinfeihan57' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['bb4b9b21584c0e076e0b4b2705af0dbe7ac19d378aa7f09a79da33a5b3293187'] + +builddependencies = [ + ('binutils', '2.35'), +] prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' From 8326f1af71c0a2adfe3ea8720603c2eb65f9b23b Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Fri, 12 Mar 2021 15:21:38 +0000 Subject: [PATCH 0496/2365] adding easyconfigs: netCDF-4.7.4-gompic-2020b.eb, GDAL-3.2.1-fosscuda-2020b.eb, R-4.0.4-fosscuda-2020b.eb --- .../g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb | 61 + .../n/netCDF/netCDF-4.7.4-gompic-2020b.eb | 42 + .../easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 2834 +++++++++++++++++ 3 files changed, 2937 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb create mode 100644 easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..efb8bd1d9a --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.2.1' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + '6c588b58fcb63ff3f288eb9f02d76791c0955ba9210d98c3abd879c770ae28ea', # gdal-3.2.1.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('netCDF', '4.7.4'), + ('expat', '2.2.9'), + ('GEOS', '3.9.1'), + ('SQLite', '3.33.0'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('JasPer', '2.0.24'), + ('LibTIFF', '4.1.0'), + ('zlib', '1.2.11'), + ('cURL', '7.72.0'), + ('PCRE2', '10.35'), + ('PROJ', '7.2.1'), + ('libgeotiff', '1.6.0'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('HDF', '4.2.15'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb new file mode 100644 index 0000000000..9558e24aa1 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb @@ -0,0 +1,42 @@ +name = 'netCDF' +version = '4.7.4' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompic', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-%(version)s_fix-ocdebug.patch', + 'netCDF-%(version)s-fix-mpi-info-f2c.patch', +] +checksums = [ + '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b', # v4.7.4.tar.gz + '94c9883005f189a4551947e04191a68199cf4cdcada4b2d313115720fb4690e9', # netCDF-4.7.4_fix-ocdebug.patch + '7ff8a922ca3be35fca261a94f725abde32807f17c196c475053a570f03eb7396', # netCDF-4.7.4-fix-mpi-info-f2c.patch +] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('cURL', '7.72.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..20534135a0 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -0,0 +1,2834 @@ +name = 'R' +version = '4.0.4' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.9'), +] +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('PCRE2', '10.35'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.5'), # for plottting in R + ('LibTIFF', '4.1.0'), + ('Java', '11', '', True), + ('Tk', '8.6.10'), # for tcltk + ('cURL', '7.72.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.0'), # for igraph + ('NLopt', '2.6.2'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '67.1'), # for rJava & gdsfmt + ('HDF5', '1.10.7'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.10-35'), # for animation + ('GLPK', '4.65'), # for Rglpk + ('nodejs', '12.19.0'), # for V8 (required by rstan) + ('GDAL', '3.2.1'), # for sf + ('pocl', '1.6'), # for OpenCL support (particularly on POWER) + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +# replace hardcoded CUDA compute capabilitites in liquidSVM +local_cuda_cc = [c.replace('.', '') for c in cuda_compute_capabilities] +local_cuda_arch = "-arch sm_%s" % local_cuda_cc[0] +local_cuda_gencode = ' '.join(['-gencode=arch=compute_%s,code=sm_%s' % (c, c) for c in local_cuda_cc]) +local_liquidSVM_sed = "sed -i 's/-arch sm_30/%s %s/' src/Makevars.in" % (local_cuda_arch, local_cuda_gencode) + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 08 Mar 2021 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9.1', { + 'checksums': ['99e02a955935040bf0834d44d1dc10a3794c8260fd072d3aff3e15ab249e0ac9'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.6', { + 'checksums': ['c9f24756bc000f7a989bd4f9aa93d57f7739dcde77946703f8bb32332a35f012'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '4.0.4', { + 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], + }), + ('bnlearn', '4.6.1', { + 'checksums': ['e4544465af3330e53e4777079c448585a8a97be2d3862a5264169007c20daeaf'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.16', { + 'checksums': ['e7dea648ee018e2c8c8834084051c76f7e8b2b42067772c62035a941c32457a9'], + }), + ('formatR', '1.7', { + 'checksums': ['a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb'], + }), + ('gtools', '3.8.2', { + 'checksums': ['503ba60a41f3c61b8129c25de62c74dab29761d2e661d4addd106e2e02f1dcde'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('highr', '0.8', { + 'checksums': ['4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.10', { + 'checksums': ['783233a15a817a7530d140e9825565a661aa4bdea7c635d11b9c74faa33be3f7'], + }), + ('xfun', '0.21', { + 'checksums': ['648e171881e2cd14be482c15b3407bfdadbcdf7dc82a969b680223eb02d212a3'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-3', { + 'checksums': ['b1f92be633243185ab86e880a1e1ac5a4dd3c535d01ebd187a4872d0a8c6f194'], + }), + ('NLP', 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['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.6.1', { + 'checksums': ['be4e4c520a3692902ce405e8225aef9f3d5f0cd11fcde614f6541e981b63673d'], + }), + ('randomForestSRC', '2.10.1', { + 'checksums': ['222c3b094a933e966a30cf99c52d2d6ad72959723f054134660e627adf51fadd'], + }), + ('sm', '2.2-5.6', { + 'checksums': ['b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-7', { + 'checksums': ['b3b186559b157497fb78a11ec46e2b49045ba04879e3faf30a75c1c73317464f'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.11-2', { + 'checksums': ['8385be32f6b6b6f1b32df15f42073b191d714d870bbb4f95875b64aff6112bbf'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('servr', '0.21', { + 'checksums': ['3fc0da063dd04b796a49ce62bf8e69d5854679520da90cc92ee3fc0a0b2ad389'], + }), + ('rgexf', '0.16.0', { + 'checksums': ['2a671df9ac70cfefd4092754317cb28e32a33df345b80e1975bf838e838245ee'], + }), + ('sem', '3.1-11', { + 'checksums': ['33b1ad7695db13af8cdd214f5d388db494528b433c61c7ad89970cefcc8b430e'], + }), + ('network', '1.16.1', { + 'checksums': ['eb6435794cacc81abe1664391e8dcf1c10112bbb76fff9016dd6dbb8e83efeb1'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('statnet.common', '4.4.1', { + 'checksums': ['4ecf2b84718d7fb60f196215b4cf6f52cd6b26cc9148a6da6981b26e885509fd'], + }), + ('sna', '2.6', { + 'checksums': ['3a016550d9f424a0613c3f5b0b680dbd3a1f20a343173d39a96034340ad9202a'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.4.1', { + 'checksums': ['78ef9eae464d52c5247998b9514a81b178419b857b1a6c00d885e3ae6c03a886'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('BDgraph', '2.63', { + 'checksums': ['cc474e1315a04f67fbf14461d35004c899d031c31f18be7d3db076dbf66a0617'], + }), + ('pbapply', '1.4-3', { + 'checksums': ['8fe6287535be766b5a688810e2cc1ca4e668ac6b42b6e832473fe5701133eb21'], + }), + ('graphlayouts', '0.7.1', { + 'checksums': ['380f8ccb0b08735694e83f661fd56a0d592a78448ae91b89c290ba8582d66717'], + }), + ('tweenr', '1.0.1', { + 'checksums': ['efd68162cd6d5a4f6d833dbf785a2bbce1cb7b9f90ba3fb060931a4bd705096b'], + }), + ('ggforce', '0.3.3', { + 'checksums': ['2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f'], + }), + ('tidygraph', '1.2.0', { + 'checksums': ['057d6c42fc0144109f3ace7f5058cca7b2fe493c761daa991448b23f86b6129f'], + }), + ('ggraph', '2.0.5', { + 'checksums': ['e36ad49dba92ee8652e18b1fb197be0ceb9f0a2f8faee2194453a62578449654'], + }), + ('qgraph', '1.6.9', { + 'checksums': ['b125a9c1b505632da8b404811c8d6d667736f229d95994ca7913beacabc36b94'], + }), + ('HWxtest', '1.1.9', { + 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], + 'checksums': [ + 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + ], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.19', { + 'checksums': ['4cd2d080628482f4c6ecab593313d7e42516f5ff13fbf9f90e461fcad0580738'], + }), + ('geepack', '1.3-2', { + 'checksums': ['99b53e40f7e5fda7422b143e6fee16513e2f880cb04a97cd403e98c4760670a6'], + }), + ('biom', '0.3.12', { + 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], + }), + ('pim', '2.0.2', { + 'checksums': ['1195dbdbd67348dfef4b6fc34fcec643da685ebe58d34bbe049ab121aca9944f'], + }), + ('minpack.lm', '1.2-1', { + 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], + }), + ('rootSolve', '1.8.2.1', { + 'checksums': ['488451182663197ae4513e46e24f72cadb2297d35a58a3007a0dbf1bf0833031'], + }), + ('diagram', '1.6.5', { + 'checksums': ['e9c03e7712e0282c5d9f2b760bafe2aac9e99a9723578d9e6369d60301f574e4'], + }), + ('FME', '1.3.6.1', { + 'checksums': ['ae0c69f75614e2ef9f2096c205c7f8eb90485c6311213762c1416ece4036be18'], + }), + ('bmp', '0.3', { + 'checksums': ['bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649'], + }), + ('tiff', '0.1-7', { + 'checksums': ['b0e39e5129c89930820e1ba101fc4890131930d2e38dd239832d64074e373680'], + }), + ('readbitmap', '0.1.5', { + 'checksums': ['737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291'], + }), + ('imager', '0.42.7', { + 'checksums': ['edba2d70c1f2512ae7b5428bd4917334cd974ea0b536b61232d3d66ce9ca00b7'], + }), + ('signal', '0.7-6', { + 'checksums': ['6b60277b07cf0167f8272059b128cc82f27a9bab1fd33d74c2a9e1f2abca5def'], + }), + ('tuneR', '1.3.3', { + 'checksums': ['bdc3c2017b162d2ba0a249e80361a4f47202e763c21aecfc57380a482a3a692b'], + }), + ('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-7', { + 'checksums': ['52e0397a45325aa9586ec68b94ab9e505bdefaf2a588d634fcb57a6a11659c74'], + }), + ('fftw', '1.0-6', { + 'checksums': ['397ef5ec354b919884f74fba4202bfc13ad11a70b16285c41677aad1d3b170ce'], + }), + ('seewave', '2.1.6', { + 'checksums': ['84a0a0035737574a65f371fa4a20a1a3a66de195efe41975f21be8fb001e7088'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('sf', '0.9-7', { + 'checksums': ['4acac2f78badf9d252da5bf377975f984927c14a56a72d9f83d285c0adadae9c'], + }), + ('oce', '1.3-0', { + 'checksums': ['9afcbc4ee1c4411b9a6f2fe400747f5e5f6315a42f4e6302f9e725ea1389499c'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.3', { + 'checksums': ['276164d5eb92c78726c647be16232d2443acbf7061371ddde2672b4fdb7a069a'], + }), + ('memuse', '4.1-0', { + 'checksums': ['58d6d1ca5d6bd481f4ed299eff6a9d5660eb0f8db1abe54c49e144093cba72ad'], + }), + ('pinfsc50', '1.2.0', { + 'checksums': ['ed1fe214b9261feef8abfbf724c2bd9070d68e99a6ea95208aff2c57bbef8794'], + }), + ('vcfR', '1.12.0', { + 'checksums': ['dd87ff010365de363864a44ca49887c0fdad0dd18d0d9c66e44e39c2d4581d52'], + }), + ('glmmML', '1.1.1', { + 'checksums': ['255fe2640933d83ef7ea5813ba8006038c18195147d1f34f47a759210a674dd4'], + }), + ('cowplot', '1.1.1', { + 'checksums': ['c7dce625b456dffc59ba100c816e16226048d12fdd29a7335dc1f6f6e12eed48'], + }), + ('tsne', '0.1-3', { + 'checksums': ['66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69'], + }), + ('sn', '1.6-2', { + 'checksums': ['2fd4730c315efc48958b47990ddb0cbc6ce075f7a27255944a292fb4fc593d9d'], + }), + ('tclust', '1.4-2', { + 'checksums': ['95dcd07dbd16383f07f5cea8561e7f3bf314e4a7483879841103b149fc8c65d9'], + }), + ('ranger', '0.12.1', { + 'checksums': ['fc308e0ac06718272799928e1a19612de16b05bde481d8f38e11a101df5425ef'], + }), + ('hexbin', '1.28.2', { + 'checksums': ['6241f8d3a6c6be2c1c693c3ddb99554bc103e3c6cf602d0c2787c0ce6fd1702d'], + }), + ('pryr', '0.1.4', { + 'checksums': ['d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b'], + }), + ('moments', '0.14', { + 'checksums': ['2a3b81e60dafdd092d2bdd3513d7038855ca7d113dc71df1229f7518382a3e39'], + }), + ('laeken', '0.5.1', { + 'checksums': ['1aa94a1768969eb999f7a41212af2d8b2943b43a68a92f99c9f77929e19439a5'], + }), + ('VIM', '6.1.0', { + 'checksums': ['1f9eb2ad9b18b7a0435e6074d031b7b5bc7143ff4251514ba20a38a53de00aa9'], + }), + ('proxy', '0.4-25', { + 'checksums': 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['f95a974aac3ec7082512675937aa2cce4d92b8324180a87f336fe781576eb40f'], + }), + ('bst', '0.3-23', { + 'checksums': ['70957f1db8800bf0d628a9e6f72b7273329786dd119427790b326844591aa0f3'], + }), + ('pamr', '1.56.1', { + 'checksums': ['d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779'], + }), + ('WeightSVM', '1.7-5', { + 'checksums': ['dd895fe3a400897cea18d9de3e406e040efca9f84495739757b52570c98f820a'], + }), + ('mpath', '0.4-2.18', { + 'checksums': ['102f5c94076ff7b26fb2e664a801e3d9b8ead8b309e4ffe3538bcb0aa922e737'], + }), + ('timereg', '1.9.8', { + 'checksums': ['00b200764743e7074d1697ddbe8534ca7599e26ef20c34020fa1f6a29fa6bb18'], + }), + ('peperr', '1.2', { + 'checksums': ['d5ab2455382f5fcd1f87c13a7397a7f58e92d71a49d76ddc4341b9db43781d14'], + }), + ('heatmap3', '1.1.9', { + 'checksums': ['594c33947b2be2cc8a592075f41a0df2398c892add7d63a15c613a5eeb8fdb69'], + }), + ('GlobalOptions', '0.1.2', { + 'checksums': ['47890699668cfa9900a829c51f8a32e02a7a7764ad07cfac972aad66f839753e'], + }), + ('circlize', '0.4.12', { + 'checksums': ['b3b60caa5292cf980cf474c85f59582f6862925631a4da86a78eac05903252f4'], + }), + ('GetoptLong', '1.0.5', { + 'checksums': ['8c237986ed3dfb72d956ad865ef7768644eebf144675ad66140acfd1aca9d701'], + }), + ('dendextend', '1.14.0', { + 'checksums': ['3789461bc474e146b077ad26566b1fa05be32fc7e57ab1fb5e78bdabcc797858'], + }), + ('RInside', '0.2.16', { + 'checksums': ['7ae4ade128ea05f37068d59e610822ff0b277f9d39d8900f7eb31759ad5a2a0e'], + }), + ('limSolve', '1.5.6', { + 'checksums': ['b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0'], + }), + ('dbplyr', '2.1.0', { + 'checksums': ['d40877e19445e4ab01be797ed80240bffcf4dd7295007451c0738dec7a74a0ea'], + }), + ('modelr', '0.1.8', { + 'checksums': ['825ba77d95d60cfb94920bec910872ca2ffe7790a44148b2992be2759cb361c4'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('reprex', '1.0.0', { + 'checksums': ['dd961de0619997336a9033cb3ca807068f4001c527f41b4be21211da1ce8df1e'], + }), + ('selectr', '0.4-2', { + 'checksums': ['5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127'], + }), + ('rvest', '1.0.0', { + 'checksums': ['a358bf258a91b3362b3736fb5f957c12e98cddf21b6066fb2abdd26ecd665713'], + }), + ('tidyverse', '1.3.0', { + 'checksums': ['6d8acb81e994f9bef5e4dcf908bcea3786d108adcf982628235b6c8c80f6fe09'], + }), + ('R.rsp', '0.44.0', { + 'checksums': ['8969075bdcabd43bad40eef6b82223e119426279fded041163fd41e55cee3a59'], + }), + ('listenv', '0.8.0', { + 'checksums': ['fd2aaf3ff2d8d546ce33d1cb38e68401613975117c1f9eb98a7b41facf5c485f'], + }), + ('globals', '0.14.0', { + 'checksums': ['203dbccb829ca9cc6aedb6f5e79cb126ea31f8dd379dff9111ec66e3628c32f3'], + }), + ('parallelly', '1.23.0', { + 'checksums': ['376ce2381587380a4da60f9563710d63084a605f93aa364e9349f2523e83bc08'], + }), + ('future', '1.21.0', { + 'checksums': ['909e6602068eba543a6d2e464b911123cc29efdb600a7000eff0e5624ff0d12d'], + }), + ('gdistance', '1.3-6', { + 'checksums': ['2ccabeb2f8cf44630c0bd2da79815fe357b812737ebece1bed8f90b27c126a24'], + }), + ('vioplot', '0.3.5', { + 'checksums': ['1b64833c1bd6851036cf1c400c7d0036a047e71def94a399c897263b4b303e2a'], + }), + ('emulator', '1.2-20', { + 'checksums': ['7cabf2cf74d879ad9dbaed8fdee54a5c94a8658a0645c021d160b2ef712ce287'], + }), + ('gmm', '1.6-6', { + 'checksums': ['b1b321ad1b4a4a14a2825a2c3eb939ce2f2bcef995247a1d638eca250e59739b'], + }), + ('tmvtnorm', '1.4-10', { + 'checksums': ['1a9f35e9b4899672e9c0b263affdc322ecb52ec198b2bb015af9d022faad73f0'], + }), + ('IDPmisc', '1.1.20', { + 'checksums': ['bcb9cd7b8097e5089d1936286ef310ac2030ea7791350df706382ba470afc67f'], + }), + ('gap', '1.2.2', { + 'checksums': ['9c66a52b371b282b20295676bdd86a11d59a6fb2acddb19170376e1a5c65b834'], + }), + ('qrnn', '2.0.5', { + 'checksums': ['3bd83ee8bd83941f9defdab1b5573d0ceca02bf06759a67665e5b9358ff92f52'], + }), + ('TMB', '1.7.19', { + 'checksums': ['9a30063aafc2762c8cbc3564f5afa0a5127ff55a6f348a68e45ada571a82d26e'], + }), + ('glmmTMB', '1.0.2.1', { + 'checksums': ['4b0923027bbe2a304282273fa626044063c195f4eee8d2fea88d85df598765a8'], + }), + ('gmp', '0.6-2', { + 'checksums': ['6bfcb45b3f1e7da27d8773f911027355cab371d150c3dabf7dbaf8fba85b7f0e'], + }), + ('ROI', '1.0-0', { + 'checksums': ['b0d87fb4ed2137d982734f3c5cdc0305aabe6e80f95de29655d02a9e82a0a341'], + }), + ('Rglpk', '0.6-4', { + 'checksums': ['a28dbc3130b9618d6ed2ef718d2c55df8ed8c44a47161097c53fe15fa3bfbfa6'], + }), + ('ROI.plugin.glpk', '1.0-0', { + 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], + }), + ('spaMM', '3.7.2', { + 'checksums': ['2580a38b2b6165477255bb025913b3d3342c000cc2c6aba10c0748178b04f2d1'], + }), + ('qgam', '1.3.2', { + 'checksums': ['273a40d0bfdc340c049bcb85aea83acd887868d8a69c0062b8399e0b24137a52'], + }), + ('DHARMa', '0.3.3.0', { + 'checksums': ['29712e1ea88b143ce800c77d2fcb8a667bb3b4cf22a089ef32105d6935abbc88'], + }), + ('mvnfast', '0.2.5.1', { + 'checksums': ['6393f4d2c3f67ec2d633975320309b83e9c240b59e78c0d46de70ec6378870a4'], + }), + ('bridgesampling', '1.0-0', { + 'checksums': ['9e182e15ba4e0a0fefd6edc58f1939fd971dd5c53c444ca9c1820bb2c1de90ab'], + }), + ('BayesianTools', '0.1.7', { + 'checksums': ['af49389bdeb794da3c39e1d63f59e6219438ecb8613c5ef523b00c6fed5a600c'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.5', { + 'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3.1', { + 'checksums': ['052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.5', { + 'checksums': ['d042d448671355d0664d37fd64dc90932eb780e6494c479d4431d1faae2071a1'], + }), + ('Rssa', '1.0.3', { + 'checksums': ['d3dc8a22c428148b955d84b703ca0bf3993318a86b067edfe4c4de271b3054ea'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.32', { + 'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'], + }), + ('DistributionUtils', '0.6-0', { + 'checksums': ['7443d6cd154760d55b6954142908eae30385672c4f3f838dd49876ec2f297823'], + }), + ('gapfill', '0.9.6-1', { + 'checksums': ['22f04755873e34a9077bb1b1de8d16f5bc56cb8c395c4f797f9ad0b209b1b996'], + }), + ('gee', '4.13-20', { + 'checksums': ['53014cee059bd87dc22f9679dfbf18fe6813b9ab41dfe90361921159edfbf798'], + }), + ('Matching', '4.9-7', { + 'checksums': ['1956ecb5ebe1c88e2112cd277ae5c2ab4b8d8f60743e6e856a2c2e40aa05fc6d'], + }), + ('MatchIt', '4.1.0', { + 'checksums': ['b34767cbb8cfb70c6b781849d5430b11480fac43af0a2d53460a1c57c7997ba1'], + }), + ('RItools', '0.1-17', { + 'checksums': ['75654780e9ca39cb3c43acfaca74080ad74de50f92c5e36e95694aafdfdc0cea'], + }), + ('optmatch', '0.9-13', { + 'checksums': ['f8f327faa95c808773376570793bbabdbc185a6c7fcdce3b96a09c998134d0d8'], + }), + ('SPAtest', '3.1.2', { + 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], + }), + ('SKAT', '2.0.1', { + 'checksums': ['c8637cf5786b926f6bbef3f4ef1d3af5130cc0cfd9094d4835839724b2d0e8c7'], + }), + ('GillespieSSA', '0.6.1', { + 'checksums': ['272e9b6b26001d166fd7ce8d04f32831ba23c676075fbd1e922e27ba2c962052'], + }), + ('startupmsg', '0.9.6', { + 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], + }), + ('distr', '2.8.0', { + 'checksums': ['bb7df05d6b946bcdbbec2e3397c7c7e349b537cabfcbb13a34bcf6312a71ceb7'], + }), + ('distrEx', '2.8.0', { + 'checksums': ['b064cde7d63ce93ec9969c8c4463c1e327758b6f8ea7765217d77f9ba9d590bf'], + }), + ('KODAMA', '1.5', { + 'checksums': ['8ecf53732c1be2bd1e111b3c6de65b66caf28360306e683fe945dc76d4c267dd'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-2', { + 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + }), + ('dtw', '1.22-3', { + 'checksums': ['df7cf9adf613422ddb22a160597eb5f5475ab6c67c0d790092edb7f72ba98f00'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.3', { + 'checksums': ['f5eafab17f2d4a8a2a83821ad3e96ae7c26b62bbce9de414484c657383c7b42e'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-3', { + 'checksums': ['776d5456e14398e44b78b3d7db526559bb7a3537e546a29c88aa192141c756de'], + }), + ('reticulate', '1.18', { + 'checksums': ['b33f855a58f446eefbe38df8a1a4865390f5d4ebd64b2c72266baaee64628513'], + }), + ('hdf5r', '1.3.3', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['a0f83cbf21563e81dbd1a1bd8379623ed0c9c4df4e094c75013abfd7a5271545'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('pulsar', '0.3.7', { + 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], + }), + ('bayesm', '3.1-4', { + 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('gsl', '2.1-6', { + 'checksums': ['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], + }), + ('energy', '1.7-8', { + 'checksums': ['de08e8de037bb30068bbf0c1880b153a586d342304681f4ba103ab808c7f4789'], + }), + ('compositions', '2.0-1', { + 'checksums': ['84a291308faf858e5a9d9570135c2da5e57b0887f407903485fa85d09da61a0f'], + }), + ('clustree', '0.4.3', { + 'checksums': ['5ff3afc3fb3e1d20d033328935084de574250d29545c0a5b69180fe4846fbe53'], + }), + ('plotly', '4.9.3', { + 'checksums': ['d44d1a16d96de28bc2d36f1c897384215eeec44d109546c6e9c2707db0880120'], + }), + ('tweedie', '2.3.3', { + 'checksums': ['a032cad512dac37a8619e6f66cb513eb82a88a5a2ffbe91e92c2d44d1756d0d9'], + }), + ('RcppGSL', '0.3.8', { + 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], + }), + ('mvabund', '4.1.9', { + 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.2.3', { + 'checksums': ['154bf7e65452186841036a2a7f2af89664965a63040ff0bee33f8b3fab8c0e4b'], + }), + ('grpreg', '3.3.0', { + 'checksums': ['d7c93c62659bd0f0d944cc1470f13443ffdebfeac5ef21ffb604ff6acbeb455b'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('ergm', '3.11.0', { + 'checksums': ['4e5506b44badc2343be3657acbf2bca51b47d7c187ff499d5a5e70a9811fe9f2'], + }), + ('networkDynamic', '0.10.1', { + 'checksums': ['22eed8d9dea8d70877c1619eb2bc3f1ac5142ce3db6fd6eb3e0879ca56b76ca0'], + }), + ('tergm', '3.7.0', { + 'checksums': ['afd2b160bda691127f8fc57c4caff61f688cc03e71e622f8e833b2a26dc635df'], + }), + ('ergm.count', '3.4.0', { + 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], + }), + ('tsna', '0.3.1', { + 'checksums': ['bba4b5e04ba647784581a2137f653f60b4c83cfd726c399556054c5a6d2cbd95'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.5-0', { + 'checksums': ['795ffd3d62bf14d3ecb3f5307bd329cd75798cf4b270ff0e768bc71a35de0ace'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.15', { + 'checksums': ['73d20ff1abd752a9d8267eea9d97be58818554ffe072923810db576c449ecbc2'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + # Replace hardcoded CUDA compute capabilities with settings from EB + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': local_liquidSVM_sed + " && LIQUIDSVM_TARGET='empty'", + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.32.0.1', { + 'checksums': ['86161b81e4aecf0243b17cabcd1f887cf4b9104918d91c804810be603d50ab66'], + }), + ('mlegp', '3.1.8', { + 'checksums': ['eac1df085a608451828575028ca05b78dc6b5035da14cabc141bfee5ef986de9'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.6', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.2.0', { + 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.5', { + 'checksums': ['9c41ca817104ab076bfd62cccac7d024658ebf4a11dcd91654f0588868aa8d74'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0-1', { + 'checksums': ['9fc1f7432a40d8911393701ca33e2ad64356c3bd12128f01dd216399b16e3d93'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + 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'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '3.0', { + 'checksums': ['ada4e1f8cbb08ba8ff16275ec5f9a453857e0cab63b70d42753989ab4c716b7b'], + }), + ('bbmle', '1.0.23.1', { + 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('terra', '1.1-4', { + 'checksums': ['6f6929d6bc7757281c7e314b43875d79b5bcfd1174d62d3462509b82752950ef'], + }), + ('rasterVis', '0.50', { + 'checksums': 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}), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.0.1', { + 'checksums': ['a3bb9bdc7a4a79ea38482df3f8cbb6e9082332a0d894eeb4b3dc816344cec0e4'], + }), + ('maxlike', '0.1-8', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-16', { + 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.2', { + 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], + }), + ('ENMeval', '0.3.1', { + 'checksums': ['e7f20c1b4d7ede82a3aca86e3ce3fc4ae46337f812dfc171b499c2558b0183d0'], + }), + ('plotmo', '3.6.0', { + 'checksums': ['c05afcc442f9542868beea5c3c40fb93b049f9b61c42725b2a1e2bc750c241e3'], + }), + ('earth', '5.3.0', { + 'checksums': ['05ace806271a74b3ddf8718a93237fe2a8550a8659ebd87f8079c0bda5e02437'], + }), + ('mda', '0.5-2', { + 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], + }), + ('biomod2', '3.4.6', { + 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], + }), + ('poLCA', '1.4.1', { + 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], + }), + ('PermAlgo', '1.1', { + 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.12', { + 'checksums': ['9acdf912f0e7a68a5b6a7946d5ebb0c2007b3d6cd2e39075eddae2b586354e89'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-1', { + 'checksums': ['e8abadc5614f132edc3fb9cb1c82ce4dacc1315b727fbd49db7399aee24115ba'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-19', { + 'checksums': ['6c7eed2d238ab4d8ebcd624e05a68849fa57bf2929b893bcd1a0990b5fcc304d'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.4.0', { + 'checksums': ['49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.2', { + 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], + }), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '2.1', { + 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], + }), + ('lmom', '2.8', { + 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], + }), + ('gld', '2.6.2', { + 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], + }), + ('DescTools', '0.99.40', { + 'checksums': ['53954f0477eac77328efac562716c8b078e76b5ad5edf0227ba2624aa2b8c7dd'], + }), + ('orthopolynom', '1.0-5', { + 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], + }), + ('gaussquad', '1.0-2', { + 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.0', { + 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], + }), + ('tableone', '0.12.0', { + 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], + }), + ('jstable', '1.0.1', { + 'checksums': ['2e4cfce264a2353e4655d0faafc93969222d67a21c0c9cc61a2454abd99c5cdc'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.2', { + 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], + }), + ('sensemakr', '0.1.3', { + 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.3-15', { + 'checksums': ['f73ead024bc3b65bdb0c5e5cd5458845158914eb579c07be2fd697a3573ebe6f'], + }), + ('metafor', '2.4-0', { + 'checksums': ['b64a678b762e91f1e0a6360b15e79fe19159b243c9f40ad9cc0be833bb4ba9ac'], + }), + ('fmri', '1.9.6', { + 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + }), + ('AnalyzeFMRI', '1.1-23', { + 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.4', { + 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], + }), + # Specific packages for GPUs + ('OpenCL', '0.2-1', { + 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], + }), + ('RViennaCL', '1.7.1.8', { + 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], + }), +] + +moduleclass = 'lang' From 7b56c32fa223747c23f1fa5885f427e4c3517109 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Mar 2021 19:37:12 +0100 Subject: [PATCH 0497/2365] add motifmatchr extensions (+ required dependency packages) to R-bundle-Bioconductor 3.12 --- ...dle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index f227bad343..38eb0cc24c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -969,6 +969,24 @@ exts_list = [ ('Signac', '1.1.1', { 'checksums': ['ac49a45c0d6016d4239cf762c00fc1b58cbb65e05b58646de48e2f845e99b4da'], }), + ('poweRlaw', '0.70.6', { + 'checksums': ['efc091449c5c6494c1c13c85a8eb95625d1c55ffffebe86c7ea16e4abbafa191'], + }), + ('CNEr', '1.26.0', { + 'checksums': ['cc303968ea8b340ae4c1347123b025e50226dcadc04da9f91fc2fb3d44bdc463'], + }), + ('DirichletMultinomial', '1.32.0', { + 'checksums': ['536fe211d52af5a20ac6cfbbde5beca803e8e95a5e3282e7032b349f0dc51f25'], + }), + ('TFMPvalue', '0.0.8', { + 'checksums': ['6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841'], + }), + ('TFBSTools', '1.28.0', { + 'checksums': ['0a5aca444ea9eb154caaa9b91f0ddc2e5815a3c3488f8975deacde08b985825c'], + }), + ('motifmatchr', '1.12.0', { + 'checksums': ['ff98ca2efbe89692deb19156733bf06879ce2c8ed7cde601aa10bc8621b0377f'], + }), ] modextrapaths = {'R_LIBS': ''} From ebf895a04183876cdd1a62a181a4dfe21079c52b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 14 Mar 2021 12:17:14 +0100 Subject: [PATCH 0498/2365] use GCC toolchain for LAPACK, use ScaLAPACK on top of BLIS + LAPACK for goblf /2020btoolchain --- easybuild/easyconfigs/g/goblf/goblf-2020b.eb | 4 +- .../ScaLAPACK-2.1.0-gompi-2020b-bl.eb | 44 +++++++++++++++++++ 2 files changed, 46 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb diff --git a/easybuild/easyconfigs/g/goblf/goblf-2020b.eb b/easybuild/easyconfigs/g/goblf/goblf-2020b.eb index 277dd9be18..9b191e1790 100644 --- a/easybuild/easyconfigs/g/goblf/goblf-2020b.eb +++ b/easybuild/easyconfigs/g/goblf/goblf-2020b.eb @@ -24,8 +24,8 @@ dependencies = [ local_comp, ('OpenMPI', '4.0.5', '', local_comp), # part of gompi toolchain ('BLIS', '0.8.0', '', local_gcccore), - ('LAPACK', '3.9.0', '', local_gcccore), - ('ScaLAPACK', '2.1.0', '-bf', local_comp_mpi_tc), + ('LAPACK', '3.9.0', '', local_comp), + ('ScaLAPACK', '2.1.0', '-bl', local_comp_mpi_tc), ('FFTW', '3.3.8', '', local_comp_mpi_tc), ] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb new file mode 100644 index 0000000000..d909934cb8 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb @@ -0,0 +1,44 @@ +name = 'ScaLAPACK' +version = '2.1.0' +versionsuffix = '-bl' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6', # scalapack-2.1.0.tgz + 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('BLIS', '0.8.0'), + ('LAPACK', '3.9.0'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' +configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From b60731c008ef82465fbb485f79ad691dd6924c03 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sun, 14 Mar 2021 20:35:40 +0000 Subject: [PATCH 0499/2365] Replaces sanity check with hg --help --- .../Mercurial-5.7.1-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0f9233a104 --- /dev/null +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +## +# Author: Robert Mijakovic +## +easyblock = "PythonPackage" + +name = 'Mercurial' +version = '5.7.1' + +homepage = 'http://mercurial.selenic.com/' +description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects +of any size and offers an easy and intuitive interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.mercurial-scm.org/release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cb5139144ccb2ef648f36963c8606d47dea1cb0e22aa2c055d6f860ce3fde7b0'] + +dependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_commands = ["hg --help"] + +moduleclass = 'tools' From 1f599ecdd2d69497a7e1c9196ee5d67fe88ccb95 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sun, 14 Mar 2021 20:51:41 +0000 Subject: [PATCH 0500/2365] adding easyconfigs: texinfo-6.7-GCCcore-10.2.0.eb --- .../t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..92671cd1e2 --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'texinfo' +version = '6.7' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [('binutils', '2.35')] + +osdependencies = ['texlive'] + +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" + +sanity_check_paths = { + 'files': [ + 'texmf/tex/texinfo/texinfo.tex', + 'bin/install-info', 'bin/makeinfo', 'bin/pdftexi2dvi', 'bin/pod2texi', 'bin/texi2pdf' + ], + 'dirs': ['bin', 'share', 'texmf'], +} + +moduleclass = 'devel' From c9cd9a5b2f9ca3dfe704f9136ca51fa72f8011e4 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sun, 14 Mar 2021 21:22:14 +0000 Subject: [PATCH 0501/2365] adding easyconfigs: Valgrind-3.16.1-gompi-2020b.eb --- .../v/Valgrind/Valgrind-3.16.1-gompi-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-gompi-2020b.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-gompi-2020b.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-gompi-2020b.eb new file mode 100644 index 0000000000..aa520b0bb1 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-gompi-2020b.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.16.1' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'ftp://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Valgrind-3.15.0-no-MPI-1.patch'] +checksums = [ + 'c91f3a2f7b02db0f3bc99479861656154d241d2fdb265614ba918cc6720a33ca', # valgrind-3.16.1.tar.bz2 + 'e99464ad9f2d2e74c5c50d2fa1bcf8637295b11cd841102035f8601b01afd85f', # Valgrind-3.15.0-no-MPI-1.patch +] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' From f643ea7751f002077e3ccb83e8e749e7e1807751 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 15 Mar 2021 10:23:04 +0000 Subject: [PATCH 0502/2365] adding easyconfigs: ACTC-1.1-GCCcore-10.2.0.eb --- .../a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..89ab6d27b0 --- /dev/null +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'MakeCp' + +name = 'ACTC' +version = '1.1' + +homepage = 'https://sourceforge.net/projects/actc' +description = "ACTC converts independent triangles into triangle strips or fans." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a1303291629b9de6008c3c9d7b020a4b854802408fb3f8222ec492808c8b44d'] + +builddependencies = [('binutils', '2.35')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['tcsample', 'tctest', 'tctest2'], 'bin'), + (['tc.h'], 'include/ac'), + (['libactc.a'], 'lib'), + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README', +] + +sanity_check_paths = { + 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README'], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/ac'} + +moduleclass = 'lib' From 94e35ac6bf9dcd8cd171274d880f6f2e1402847a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 15 Mar 2021 12:42:32 +0200 Subject: [PATCH 0503/2365] adding easyconfigs: FLTK-1.3.5-GCCcore-10.2.0.eb, xprop-1.2.5-GCCcore-10.2.0.eb --- .../f/FLTK/FLTK-1.3.5-GCCcore-10.2.0.eb | 42 +++++++++++++++++++ .../x/xprop/xprop-1.2.5-GCCcore-10.2.0.eb | 32 ++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6cf60f80c8 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.5' + +homepage = 'https://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-1.3.4_fix-LDFLAGS.patch'] +checksums = [ + '8729b2a055f38c1636ba20f749de0853384c1d3e9d1a6b8d4d1305143e115702', # fltk-1.3.5-source.tar.gz + 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +builddependencies = [ + ('binutils', '2.35') +] + +dependencies = [ + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('xprop', '1.2.5'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b1256f2c81 --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.5' + +homepage = "https://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.x.org/archive/individual/app/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b7bf6b6be6cf23e7966a153fc84d5901c14f01ee952fbd9d930aa48e2385d670'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20201008'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' From 2dfa3a5d409688de58b202ce0232cd796d0b3ce1 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 15 Mar 2021 12:24:13 +0000 Subject: [PATCH 0504/2365] adding easyconfigs: arpack-ng-3.8.0-foss-2020b.eb --- .../a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb new file mode 100644 index 0000000000..e860127e99 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb @@ -0,0 +1,37 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = "3.8.0" + +homepage = 'https://github.com/opencollab/arpack-ng' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'opencollab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['ada5aeb3878874383307239c9235b716a8a170c6d096a6625bfd529844df003d'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Eigen', '3.3.8') +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib64/libarpack.la", "lib64/libarpack.%s" % SHLIB_EXT, "lib64/libparpack.la", "lib64/libparpack.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'numlib' From cb683af2000f81f6e213c546865024e19c9daea9 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 15 Mar 2021 13:58:13 +0100 Subject: [PATCH 0505/2365] delly: style --- .../m/maze/maze-20170124-foss-2020b.eb | 31 +++++++---------- .../s/suave/suave-20160529-foss-2020b.eb | 33 ++++++++----------- 2 files changed, 24 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb b/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb index bba584205d..5eb3c020b0 100644 --- a/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb +++ b/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'maze' version = '20170124' @@ -10,6 +10,15 @@ substring matches are computed with MUMmer3 and visualised.""" toolchain = {'name': 'foss', 'version': '2020b'} +source_urls = ['https://github.com/dellytools/maze/archive'] +sources = ['106803d350719188181ce39cbb5c832822b724da.tar.gz'] +patches = [('maze-setup-py-python3.patch', 1)] +checksums = [ + # 106803d350719188181ce39cbb5c832822b724da.tar.gz + 'aac74021b5f3652723d593f1983a417e8db73147079d06dad9a18acdfdb00f93', + 'd2b9245d7169e13127ee28dbdd54101f768d2e53cab59f3bc1a70479089f278c', # maze-setup-py-python3.patch +] + dependencies = [ ('Python', '3.8.6'), ('MUMmer', '4.0.0beta2'), @@ -19,25 +28,7 @@ dependencies = [ ] use_pip = True - -exts_default_options = {'source_urls': [PYPI_SOURCE]} -exts_list = [ - ('Click', '7.0', { - 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], - }), - (name, version, { - 'patches': [('maze-setup-py-python3.patch', 1)], - 'source_tmpl': '106803d350719188181ce39cbb5c832822b724da.tar.gz', - 'source_urls': ['https://github.com/dellytools/maze/archive'], - 'checksums': [ - # 106803d350719188181ce39cbb5c832822b724da.tar.gz - 'aac74021b5f3652723d593f1983a417e8db73147079d06dad9a18acdfdb00f93', - '6d8d127582463c366c41e1fff737f8d24469397657e0a7a04c1516640d3b97f4', # maze-setup-py-python3.patch - ], - }), -] - -sanity_pip_check = True +download_dep_fail = True sanity_check_paths = { 'files': ['bin/maze_server', 'bin/extract_reference_slices'], diff --git a/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb b/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb index 8a156ae761..53530368e6 100644 --- a/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb +++ b/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'suave' version = '20160529' @@ -11,6 +11,15 @@ comparison).""" toolchain = {'name': 'foss', 'version': '2020b'} +source_urls = ['https://github.com/dellytools/suave/archive'] +sources = ['45e4963d1a2c84cc0acdfaa603f29df10ff2ce49.tar.gz'] +patches = [('suave-setup-py.patch', 1)] +checksums = [ + # 45e4963d1a2c84cc0acdfaa603f29df10ff2ce49.tar.gz + 'f585f27adcf1f3a8aeaead2e5f190f6f0d23522cf6bbe1c3388f4c3270d0fb9c', + 'aed388bae77cdb1178c4f7ad5284756dfde38f62b6739c07d88f90ed9e5a60f7', # suave-setup-py.patch +] + dependencies = [ ('Python', '3.8.6'), ('Flask', '1.1.2'), @@ -19,26 +28,8 @@ dependencies = [ ] use_pip = True - -exts_default_options = {'source_urls': [PYPI_SOURCE]} -exts_list = [ - ('Click', '7.0', { - 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], - }), - (name, version, { - 'modulename': 'suave_server', - 'patches': [('suave-setup-py-python3.patch', 1)], - 'source_tmpl': '45e4963d1a2c84cc0acdfaa603f29df10ff2ce49.tar.gz', - 'source_urls': ['https://github.com/dellytools/suave/archive'], - 'checksums': [ - # 45e4963d1a2c84cc0acdfaa603f29df10ff2ce49.tar.gz - 'f585f27adcf1f3a8aeaead2e5f190f6f0d23522cf6bbe1c3388f4c3270d0fb9c', - '47b404c0150a117936b3e18aa479012b5f055eea7d85e663c9b44e0f8bfe8247', # suave-setup-py-python3.patch - ], - }), -] - sanity_pip_check = True +download_dep_fail = True sanity_check_paths = { 'files': ['bin/suave_server', 'bin/suave_bam_to_h5'], @@ -47,4 +38,6 @@ sanity_check_paths = { sanity_check_commands = ['suave_server --help'] +options = {'modulename': 'suave_server'} + moduleclass = 'bio' From 3bc362d608bb7a4be232f2e964ce79c849956276 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Mar 2021 14:06:38 +0100 Subject: [PATCH 0506/2365] add sanity check command for Elk --- easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb b/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb index 4cb91d01d7..c1b6581087 100644 --- a/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb +++ b/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb @@ -57,4 +57,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = ["elk | grep '^Elk code version %(version)s'"] + moduleclass = 'phys' From cb7b76366bb82cad103a5f15e5f8ba636a2c1edf Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 15 Mar 2021 16:13:22 +0100 Subject: [PATCH 0507/2365] delly: style --- easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb b/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb index 5eb3c020b0..b8301fe060 100644 --- a/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb +++ b/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb @@ -29,6 +29,7 @@ dependencies = [ use_pip = True download_dep_fail = True +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/maze_server', 'bin/extract_reference_slices'], From 66f5d6bda3a1692514d43770250d1adf80b41c52 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 15 Mar 2021 15:28:45 +0000 Subject: [PATCH 0508/2365] Solves too long line --- .../easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb index e860127e99..6a206a117b 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb @@ -30,7 +30,8 @@ preconfigopts = "sh bootstrap && " configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' sanity_check_paths = { - 'files': ["lib64/libarpack.la", "lib64/libarpack.%s" % SHLIB_EXT, "lib64/libparpack.la", "lib64/libparpack.%s" % SHLIB_EXT], + 'files': ["lib64/libarpack.la", "lib64/libarpack.%s" % SHLIB_EXT, + "lib64/libparpack.la", "lib64/libparpack.%s" % SHLIB_EXT], 'dirs': [] } From 06774ab477f12e051229416c9388238af2408485 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Mar 2021 19:03:07 +0100 Subject: [PATCH 0509/2365] use LAPACK as LAPACK library in ScaLAPACK used in goblf/2020b --- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb index d909934cb8..b95684c3a0 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb @@ -31,7 +31,7 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' -configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DLAPACK_LIBRARIES="$EBROOTLAPACK/lib/liblapack.a" ' configopts += '-DCMAKE_C_COMPILER=mpicc ' configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' From 7885c86a2d18aca15b27a6382b3e95c7efc99867 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 15 Mar 2021 11:09:22 -0700 Subject: [PATCH 0510/2365] {bio}[GCC/10.2.0] Arriba 2.1.0 --- .../a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..2eea4c45f1 --- /dev/null +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'Arriba' +version = '2.1.0' + +github_account = 'suhrig' +homepage = 'https://github.com/%(github_account)s/%(namelower)s' +description = """Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. + It was developed for the use in a clinical research setting. Therefore, short runtimes and high + sensitivity were important design criteria.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] +checksums = ['21c46121e00cf84ad471b2b22fca722d37e55bbdf9e7118978dc250754a264bb'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('STAR', '2.7.7a'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +postinstallcmds = ['mkdir %(installdir)s/database'] +files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', 'LICENSE', + 'README.md', 'run_%(namelower)s.sh'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [('%(namelower)s', '-h')] + +moduleclass = 'bio' From be9e04312f1e7cfbf233e2f2d6b831de24de5bd7 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 15 Mar 2021 18:26:18 +0000 Subject: [PATCH 0511/2365] Update easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb --- .../easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb index 0f9233a104..d930cd3469 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb @@ -6,7 +6,7 @@ easyblock = "PythonPackage" name = 'Mercurial' version = '5.7.1' -homepage = 'http://mercurial.selenic.com/' +homepage = 'https://www.mercurial-scm.org' description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. """ From eeb2d807f4e1dd2c050787f9c1c7a047ffc0a9c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Mar 2021 20:43:09 +0100 Subject: [PATCH 0512/2365] adding easyconfigs: GetOrganelle-1.7.4-pre2-foss-2020b.eb, Bowtie2-2.4.2-GCC-10.2.0.eb, SPAdes-3.15.2-GCC-10.2.0.eb --- .../b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb | 36 +++++++++++++++ .../GetOrganelle-1.7.4-pre2-foss-2020b.eb | 44 ++++++++++++++++++ .../s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb | 46 +++++++++++++++++++ 3 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..2a3ee99cd4 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.4.2' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e'] + +dependencies = [ + ('tbb', '2020.3'), + ('zlib', '1.2.11'), +] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb new file mode 100644 index 0000000000..095a77b88c --- /dev/null +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonPackage' + +name = 'GetOrganelle' +local_commit = '3476ad9' +version = '1.7.4-pre2' + +homepage = 'https://github.com/Kinggerm/GetOrganelle' +description = """This toolkit assemblies organelle genome from genomic skimming data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['ee3dc807e0fb59c1788717a155238115d7a860191f686ef2c5a5b685aa2a2948'] + +dependencies = [ + ('Python', '3.8.6'), + ('Bandage', '0.8.1', '_Centos', True), + ('SciPy-bundle', '2020.11'), + ('sympy', '1.7.1'), + ('SPAdes', '3.15.2'), + ('Bowtie2', '2.4.2'), + ('BLAST+', '2.11.0'), + ('Perl', '5.32.0'), + ('matplotlib', '3.3.3') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': False} + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_commands = ["get_organelle_from_reads.py -h"] + +sanity_check_paths = { + 'files': ['bin/check_annotations.py', 'bin/get_organelle_from_reads.py', 'bin/slim_graph.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..c12ae57556 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'CMakeMake' + +name = 'SPAdes' +version = '3.15.2' + +homepage = 'http://cab.spbu.ru/software/spades/' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['e93b43951a814dc7bd6a246e1e863bbad6aac4bfe1928569402c131b2af99d0d'] + +builddependencies = [ + ('CMake', '3.18.4'), +] +dependencies = [ + ('Python', '3.8.6'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('libreadline', '8.0'), +] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', + 'spades-ionhammer', 'spades-kmercount', 'spades.py']], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s.py', '--test')] + +moduleclass = 'bio' From ee25ec74dcf2efff042cf40167e17bf775e6ba4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Mar 2021 20:53:16 +0100 Subject: [PATCH 0513/2365] use https for homepage in SPAdes easyconfig --- easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb index c12ae57556..d1300d60a1 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb @@ -12,7 +12,7 @@ easyblock = 'CMakeMake' name = 'SPAdes' version = '3.15.2' -homepage = 'http://cab.spbu.ru/software/spades/' +homepage = 'https://cab.spbu.ru/software/spades/' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '10.2.0'} From ee3f6d76553b59ad9bbfb98c9018f45f111d77ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Mar 2021 20:56:30 +0100 Subject: [PATCH 0514/2365] add DMCfun extension for R v4.0.3 + v4.0.4 --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 21 +++++++++++++++++++ .../easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 21 +++++++++++++++++++ .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 21 +++++++++++++++++++ 3 files changed, 63 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 559545c064..b27365ac40 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2782,6 +2782,27 @@ exts_list = [ ('rnetcarto', '0.2.4', { 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], }), + ('DEoptim', '2.2-5', { + 'checksums': ['ae12dedcd4a43994e811e7285f8c12bfdb688e7c99d65515cf7e8cb6db13955a'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2013.9-1', { + 'checksums': ['1a1a399682a06a5fea3934985ebb1334005676c6a2a22d06f3c91c3923432908'], + }), + ('Rvmmin', '2018-4.17', { + 'checksums': ['d53ba7ab06596a47990caf101a50935b2b34402f9dd8414f098a873026ff1f56'], + }), + ('Rcgmin', '2013-2.21', { + 'checksums': ['a824a09c32d7565a3e30607c71333506d5b7197478fbe8b43f8a77dad6c12f0a'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '1.3.0', { + 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index eb09ea2bb5..4ac9ced88b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2792,6 +2792,27 @@ exts_list = [ ('rnetcarto', '0.2.4', { 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], }), + ('DEoptim', '2.2-5', { + 'checksums': ['ae12dedcd4a43994e811e7285f8c12bfdb688e7c99d65515cf7e8cb6db13955a'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2013.9-1', { + 'checksums': ['1a1a399682a06a5fea3934985ebb1334005676c6a2a22d06f3c91c3923432908'], + }), + ('Rvmmin', '2018-4.17', { + 'checksums': ['d53ba7ab06596a47990caf101a50935b2b34402f9dd8414f098a873026ff1f56'], + }), + ('Rcgmin', '2013-2.21', { + 'checksums': ['a824a09c32d7565a3e30607c71333506d5b7197478fbe8b43f8a77dad6c12f0a'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '1.3.0', { + 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 7ed6463d54..e3afe51d73 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2817,6 +2817,27 @@ exts_list = [ ('rnetcarto', '0.2.4', { 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], }), + ('DEoptim', '2.2-5', { + 'checksums': ['ae12dedcd4a43994e811e7285f8c12bfdb688e7c99d65515cf7e8cb6db13955a'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2013.9-1', { + 'checksums': ['1a1a399682a06a5fea3934985ebb1334005676c6a2a22d06f3c91c3923432908'], + }), + ('Rvmmin', '2018-4.17', { + 'checksums': ['d53ba7ab06596a47990caf101a50935b2b34402f9dd8414f098a873026ff1f56'], + }), + ('Rcgmin', '2013-2.21', { + 'checksums': ['a824a09c32d7565a3e30607c71333506d5b7197478fbe8b43f8a77dad6c12f0a'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '1.3.0', { + 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], + }), ] moduleclass = 'lang' From 1d4b2eebeed740da9b69690a206c7f0290d363ea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 16 Mar 2021 09:50:30 +0200 Subject: [PATCH 0515/2365] Fix BEEF homepage --- easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb index 1eb3a345b2..0de4a51f65 100644 --- a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'BEEF' version = '0.1.1' -homepage = 'svn://suncatls1.slac.stanford.edu/beef' +homepage = 'https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software' description = """BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at From eb35f6d7ec8a1dfbda80cdf4ab58e8d3100b58d9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 16 Mar 2021 10:01:10 +0000 Subject: [PATCH 0516/2365] Use official project name (initial capital) --- .../Octopus-vcf-0.7.1-foss-2020b.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb new file mode 100644 index 0000000000..410a43d89c --- /dev/null +++ b/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMakeCp' + +# To avoid a naming clash +name = 'Octopus-vcf' +version = '0.7.1' + +homepage = 'https://github.com/luntergroup/octopus' +description = """Octopus is a mapping-based variant caller that implements several calling models within + a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a + tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities + in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in + reasonable time.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/luntergroup/octopus/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b544121cb132634a1156e79c0a2ff19abacd3fb4ad5b711dec9dc664b6fcf49a'] + +dependencies = [ + ('CMake', '3.18.4'), + ('Boost', '1.74.0'), + ('HTSlib', '1.11'), + ('GMP', '6.2.0'), + ('Python', '3.8.6'), + ('git', '2.28.0', '-nodocs'), +] + +configopts = '-DHTSlib_NO_SYSTEM_PATHS=TRUE -DHTSLIB_ROOT=$EBROOTHTSLIB ' + +separate_build_dir = True + +preinstallopts = 'if [ ! -d %(installdir)s/bin ]; then mkdir %(installdir)s/bin; fi' + +files_to_copy = [ + (['%(builddir)s/easybuild_obj/src/octopus'], 'bin'), + 'doc', 'lib', 'LICENSE', 'logo.png', 'README.md', + 'resources', 'scripts', 'test' +] + +sanity_check_commands = ['octopus -h'] + +sanity_check_paths = { + 'files': ['bin/octopus'], + 'dirs': ['doc', 'lib', 'resources'] +} + +moduleclass = 'bio' From 261cf2549b5a246f04b05cac2741f8fc06de3635 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 16 Mar 2021 12:44:01 +0200 Subject: [PATCH 0517/2365] adding easyconfigs: PLUMED-2.7.0-foss-2020b.eb --- .../p/PLUMED/PLUMED-2.7.0-foss-2020b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb new file mode 100644 index 0000000000..a7856a3a21 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.7.0' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['b23399a3300ce3ae080e81263274ab8551e00217c3f37cb33cb7e37954fe8572'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python i' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From dff6f1fd17d78ee9756c745e539a1229e112cb43 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 16 Mar 2021 11:19:07 +0000 Subject: [PATCH 0518/2365] Moves Extrae from foss to gompi. --- .../e/Extrae/Extrae-3.8.0-gompi-2020b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-3.8.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.0-gompi-2020b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.0-gompi-2020b.eb new file mode 100644 index 0000000000..732bba271d --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.0-gompi-2020b.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +name = 'Extrae' +version = '3.8.0' + +homepage = 'https://www.bsc.es/computer-sciences/performance-tools' +description = """Extrae is the core instrumentation package developed by +the Performance Tools group at BSC. Extrae is capable of instrumenting +applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 +using different instrumentation approaches. The information gathered by +Extrae typically includes timestamped events of runtime calls, +performance counters and source code references. Besides, Extrae +provides its own API to allow the user to manually instrument his or her +application.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] +checksums = ['b9bd863655ab0e1dd83213eec5ca85612ef35269f219039a75f088331b49572f'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.74.0'), + ('libunwind', '1.4.0'), + ('libxml2', '2.9.10'), + ('libdwarf', '20201201'), + ('PAPI', '6.0.0'), +] + +moduleclass = 'perf' From bfd84239c7fc30a318886639bda4ac0bbf6fb651 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 16 Mar 2021 11:24:24 +0000 Subject: [PATCH 0519/2365] Draft: VMD-1.9.4a51-foss --- .../v/VMD/VMD-1.9.4a51-foss-2020b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb new file mode 100644 index 0000000000..8df549ceb3 --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -0,0 +1,59 @@ +## +# Author: Robert Mijakovic +## +name = 'VMD' +version = '1.9.4a51' + +homepage = 'https://www.ks.uiuc.edu/Research/vmd' +description = """VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular + systems using 3-D graphics and built-in scripting.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', + 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', + 'https://webclu.bio.wzw.tum.de/stride/' +] +sources = [ + 'vmd-%(version)s.src.tar.gz', + {'filename': 'stride.tar.gz', 'extract_cmd': "tar -C vmd-%(version)s/lib/stride -xf %s"}, +] +patches = [ + ('VMD-1.9.3_plugins.patch'), + ('VMD-1.9.3_surf_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_surf_bad_printfs.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_MAX_AT_IN_RES.patch', 'vmd-%(version)s'), + ('VMD-%(version)s_configure.patch', 'vmd-%(version)s'), + ('VMD-%(version)s_extra_colors.patch', 'vmd-%(version)s'), +] +checksums = [ + 'b1c40b21111f5bab56d43d5e442c468d327159b07915af2ec175ba6b12842e5c', # vmd-1.9.4a51.src.tar.gz + '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz + '85760d6ae838e2b09801e34b36b484532383f7aaf2e8634b3ef808002a92baa3', # VMD-1.9.3_plugins.patch + 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch + 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch + 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch + 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch + '53af80c866a9221559b4882bfc9e7de8a5a5388b4a2c5cc91d6d55100660dd2f', # VMD-1.9.4_configure.patch + '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4_extra_colors.patch +] + +dependencies = [ + ('Tcl', '8.6.11'), + ('Tk', '8.6.11'), + ('FLTK', '1.3.5'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('Mesa', '20.2.1'), + ('netCDF', '4.7.4'), + ('FFmpeg', '4.3.1'), + ('ImageMagick', '7.0.10-35'), + ('ACTC', '1.1'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), +] + +moduleclass = 'vis' From 44ad5f29f8b87107db4ecaac97b074b305e7aee5 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 16 Mar 2021 11:27:25 +0000 Subject: [PATCH 0520/2365] Downgrades Tk and Tcl dependencies. --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb index 8df549ceb3..aa3ec91eea 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -41,8 +41,8 @@ checksums = [ ] dependencies = [ - ('Tcl', '8.6.11'), - ('Tk', '8.6.11'), + ('Tcl', '8.6.10'), + ('Tk', '8.6.10'), ('FLTK', '1.3.5'), ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), From c3026e64520c62a9d2f84df6bb536c4c5ff3e1d4 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 16 Mar 2021 12:15:07 +0000 Subject: [PATCH 0521/2365] =?UTF-8?q?Adds=20POV-Ray=20as=20suggested=20by?= =?UTF-8?q?=20=C3=85ke.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb index aa3ec91eea..51b8837861 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -54,6 +54,7 @@ dependencies = [ ('ACTC', '1.1'), ('zlib', '1.2.11'), ('libpng', '1.6.37'), + ('POV-Ray', '3.0.7.8'), ] moduleclass = 'vis' From f090033fda36200266ec6ff8c9d297477e5b93cc Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 16 Mar 2021 12:41:04 +0000 Subject: [PATCH 0522/2365] Fixes POV-Ray dependency version. --- .../v/VMD/VMD-1.9.4a51-foss-2020b.eb | 2 +- .../v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 62 +++++++++++++++++++ 2 files changed, 63 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb index 51b8837861..703d55ce3f 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -54,7 +54,7 @@ dependencies = [ ('ACTC', '1.1'), ('zlib', '1.2.11'), ('libpng', '1.6.37'), - ('POV-Ray', '3.0.7.8'), + ('POV-Ray', '3.7.0.8'), ] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb new file mode 100644 index 0000000000..94ac3280ac --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -0,0 +1,62 @@ +## +# Author: Robert Mijakovic +## +name = 'VMD' +version = '1.9.4a51' + +homepage = 'https://www.ks.uiuc.edu/Research/vmd' +description = """VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular + systems using 3-D graphics and built-in scripting.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', + 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', + 'https://webclu.bio.wzw.tum.de/stride/' +] +sources = [ + 'vmd-%(version)s.src.tar.gz', + {'filename': 'stride.tar.gz', 'extract_cmd': "tar -C vmd-%(version)s/lib/stride -xf %s"}, +] +patches = [ + ('VMD-1.9.3_plugins.patch'), + ('VMD-1.9.3_surf_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_surf_bad_printfs.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_MAX_AT_IN_RES.patch', 'vmd-%(version)s'), + ('VMD-%(version)s_configure.patch', 'vmd-%(version)s'), + ('VMD-%(version)s_extra_colors.patch', 'vmd-%(version)s'), +] +checksums = [ + 'b1c40b21111f5bab56d43d5e442c468d327159b07915af2ec175ba6b12842e5c', # vmd-1.9.4a51.src.tar.gz + '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz + '85760d6ae838e2b09801e34b36b484532383f7aaf2e8634b3ef808002a92baa3', # VMD-1.9.3_plugins.patch + 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch + 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch + 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch + 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch + '53af80c866a9221559b4882bfc9e7de8a5a5388b4a2c5cc91d6d55100660dd2f', # VMD-1.9.4_configure.patch + '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4_extra_colors.patch +] + +dependencies = [ + ('Tcl', '8.6.10'), + ('Tk', '8.6.10'), + ('FLTK', '1.3.5'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('Mesa', '20.2.1'), + ('netCDF', '4.7.4'), + ('FFmpeg', '4.3.1'), + ('ImageMagick', '7.0.10-35'), + ('ACTC', '1.1'), + ('OptiX', '6.5.0', '', True), + + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('POV-Ray', '3.7.0.8'), +] + +moduleclass = 'vis' From 5cefed29a57385070d487bdb5cc20a57e3851c65 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 16 Mar 2021 13:04:28 +0000 Subject: [PATCH 0523/2365] Adds the missing dependency, netCDF with gompic toolchain. --- .../n/netCDF/netCDF-4.7.4-gompic-2020b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb new file mode 100644 index 0000000000..7fe6fa75d9 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## +name = 'netCDF' +version = '4.7.4' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompic', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['netCDF-%(version)s_fix-ocdebug.patch'] +checksums = [ + '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b', # v4.7.4.tar.gz + '94c9883005f189a4551947e04191a68199cf4cdcada4b2d313115720fb4690e9', # netCDF-4.7.4_fix-ocdebug.patch +] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('cURL', '7.72.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From 2922c1e1853e8538effec636d3477500e3174265 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 16 Mar 2021 16:09:17 +0200 Subject: [PATCH 0524/2365] Fix typo --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb index a7856a3a21..05666961bc 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -27,7 +27,7 @@ dependencies = [ ] preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' -configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python i' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' From f15807de3404957caee3f3ccd2d7a3e71edac1a7 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 16 Mar 2021 18:09:54 +0100 Subject: [PATCH 0525/2365] Update easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb index 94ac3280ac..b7e405c0a6 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -53,7 +53,6 @@ dependencies = [ ('ImageMagick', '7.0.10-35'), ('ACTC', '1.1'), ('OptiX', '6.5.0', '', True), - ('zlib', '1.2.11'), ('libpng', '1.6.37'), ('POV-Ray', '3.7.0.8'), From 9309f29af2932b0e58bdea20c221ed63359c2174 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 16 Mar 2021 17:24:37 +0000 Subject: [PATCH 0526/2365] Adds compute_80 and sm_80. --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb | 2 +- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb index 703d55ce3f..10015c6588 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -36,7 +36,7 @@ checksums = [ 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch - '53af80c866a9221559b4882bfc9e7de8a5a5388b4a2c5cc91d6d55100660dd2f', # VMD-1.9.4_configure.patch + '5afd42629fa7a1a9835e6479caca30995ea284a62e54b0c75a9dbfbaef98418c', # VMD-1.9.4_configure.patch '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4_extra_colors.patch ] diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb index b7e405c0a6..c5061caf58 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -36,7 +36,7 @@ checksums = [ 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch - '53af80c866a9221559b4882bfc9e7de8a5a5388b4a2c5cc91d6d55100660dd2f', # VMD-1.9.4_configure.patch + '5afd42629fa7a1a9835e6479caca30995ea284a62e54b0c75a9dbfbaef98418c', # VMD-1.9.4_configure.patch '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4_extra_colors.patch ] From 0056c7f418ee9c15edac29210b274d0c3b2cc73b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Mar 2021 19:12:50 +0100 Subject: [PATCH 0527/2365] rename 'manta' to 'Manta' --- .../b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 1 - .../manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb | 69 ------------------- 2 files changed, 70 deletions(-) delete mode 100644 easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index 7e7244dd47..9445b5ae8b 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -19,7 +19,6 @@ checksums = [ 'ee61e889ce9473ad82b69c9a8cbe1bf9650d633b74fdf7e4f4a4825aa990feca', ] -# patch of a missing include file that has been fixed in 1.75.0 https://github.com/boostorg/serialization/issues/219 dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb deleted file mode 100644 index aef74b24d0..0000000000 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb +++ /dev/null @@ -1,69 +0,0 @@ -## -# Authors:: Denis Kristak -## -easyblock = 'CMakeMake' - -name = 'manta' -version = '1.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Illumina/manta' -description = """ -Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. -It is optimized for analysis of germline variation in small sets of individuals and -somatic variation in tumor/normal sample pairs. Manta discovers, assembles and -scores large-scale SVs, medium-sized indels and large insertions within a -single efficient workflow. -""" - -toolchain = {'name': 'GCC', 'version': '10.2.0'} - -github_account = 'Illumina' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['76ce7c4a95a3b92cb16381f9a3b091afa234948ae6f028982abbd49e21206421'] - -builddependencies = [ - ('CMake', '3.18.4'), - ('Doxygen', '1.8.20'), -] - -dependencies = [ - ('Python', '2.7.18'), - ('Boost', '1.74.0'), - ('zlib', '1.2.11'), -] - -buildopts = "FLAGS='-I$EBROOTPYTHON/include -L$EBROOTPYTHON/lib -lpython ' " - -# following are necessary should anyone try to make manta compatible with python3 -# making included pyflow compatible with python3 -# preinstallopts = "sed -i 's/0755/0o755/g' ./redist/pyflow-*/src/pyflow.py && " -# preinstallopts += "sed -i 's/DataDirException, e/DataDirException(e)/g' ./redist/pyflow-*/src/pyflow.py && " -# preinstallopts += "sed -i 's/raise Exception(\"pyflow module has only been tested for python versions \ -# \[2.4,3.0)/pass #/g' ./redist/pyflow-*/src/pyflow.py && " -# preinstallopts += "sed -i 's/raise Exception(\"Manta does not currently support python3/pass #/g' \ -# ../manta-%(version)s/src/python/lib/makeRunScript.py && " - -local_binaries = ['CheckSVLoci', 'DumpSVLoci', 'EstimateSVLoci', 'GenerateSVCandidates', 'GetAlignmentStats', - 'GetChromDepth', 'MergeAlignmentStats', 'MergeSVLoci', 'SummarizeAlignmentStats', 'SummarizeSVLoci', - 'TestAssembler'] - -sanity_check_paths = { - 'files': [ - ['bin/%s' % x for x in ['configManta.py', 'runMantaWorkflowDemo.py']] + - ['libexec/%s' % x for x in ['denovo_scoring.py', 'extractSmallIndelCandidates.py']], - ], - 'dirs': ['libexec'], -} - -sanity_check_commands = [ - 'python %(installdir)s/bin/runMantaWorkflowDemo.py' -] - -modextrapaths = { - 'PATH': 'libexec', - 'PYTHONPATH': 'lib/python', -} - -moduleclass = 'bio' From 131a7858958fb952e11e28b957a13be452f9eb05 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 16 Mar 2021 18:50:50 +0000 Subject: [PATCH 0528/2365] CMake and git are build deps --- .../o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb index 410a43d89c..06da9ef94e 100644 --- a/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb @@ -17,13 +17,16 @@ source_urls = ['https://github.com/luntergroup/octopus/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['b544121cb132634a1156e79c0a2ff19abacd3fb4ad5b711dec9dc664b6fcf49a'] -dependencies = [ +builddependencies = [ ('CMake', '3.18.4'), + ('git', '2.28.0', '-nodocs'), +] + +dependencies = [ ('Boost', '1.74.0'), ('HTSlib', '1.11'), ('GMP', '6.2.0'), ('Python', '3.8.6'), - ('git', '2.28.0', '-nodocs'), ] configopts = '-DHTSlib_NO_SYSTEM_PATHS=TRUE -DHTSLIB_ROOT=$EBROOTHTSLIB ' From 7168c9b895ea5f19b36e3b0d551662e15d280129 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Mar 2021 21:08:08 +0100 Subject: [PATCH 0529/2365] stick to 'manta' software name, to be consistent with existing easyconfigs --- .../manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..aef74b24d0 --- /dev/null +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,69 @@ +## +# Authors:: Denis Kristak +## +easyblock = 'CMakeMake' + +name = 'manta' +version = '1.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Illumina/manta' +description = """ +Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. +It is optimized for analysis of germline variation in small sets of individuals and +somatic variation in tumor/normal sample pairs. Manta discovers, assembles and +scores large-scale SVs, medium-sized indels and large insertions within a +single efficient workflow. +""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'Illumina' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['76ce7c4a95a3b92cb16381f9a3b091afa234948ae6f028982abbd49e21206421'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('Boost', '1.74.0'), + ('zlib', '1.2.11'), +] + +buildopts = "FLAGS='-I$EBROOTPYTHON/include -L$EBROOTPYTHON/lib -lpython ' " + +# following are necessary should anyone try to make manta compatible with python3 +# making included pyflow compatible with python3 +# preinstallopts = "sed -i 's/0755/0o755/g' ./redist/pyflow-*/src/pyflow.py && " +# preinstallopts += "sed -i 's/DataDirException, e/DataDirException(e)/g' ./redist/pyflow-*/src/pyflow.py && " +# preinstallopts += "sed -i 's/raise Exception(\"pyflow module has only been tested for python versions \ +# \[2.4,3.0)/pass #/g' ./redist/pyflow-*/src/pyflow.py && " +# preinstallopts += "sed -i 's/raise Exception(\"Manta does not currently support python3/pass #/g' \ +# ../manta-%(version)s/src/python/lib/makeRunScript.py && " + +local_binaries = ['CheckSVLoci', 'DumpSVLoci', 'EstimateSVLoci', 'GenerateSVCandidates', 'GetAlignmentStats', + 'GetChromDepth', 'MergeAlignmentStats', 'MergeSVLoci', 'SummarizeAlignmentStats', 'SummarizeSVLoci', + 'TestAssembler'] + +sanity_check_paths = { + 'files': [ + ['bin/%s' % x for x in ['configManta.py', 'runMantaWorkflowDemo.py']] + + ['libexec/%s' % x for x in ['denovo_scoring.py', 'extractSmallIndelCandidates.py']], + ], + 'dirs': ['libexec'], +} + +sanity_check_commands = [ + 'python %(installdir)s/bin/runMantaWorkflowDemo.py' +] + +modextrapaths = { + 'PATH': 'libexec', + 'PYTHONPATH': 'lib/python', +} + +moduleclass = 'bio' From 979b1afb69d1adf73d2cd0fb27a19f7d4e259722 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 16 Mar 2021 21:17:35 -0700 Subject: [PATCH 0530/2365] {bio}[GCC/10.2.0] RevBayes 1.1.1 --- .../r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..b055c17afc --- /dev/null +++ b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +# easybuild easyconfig +# +# John Dey +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +easyblock = 'CmdCp' + +name = 'RevBayes' +version = '1.1.1' + +homepage = 'https://revbayes.github.io/' + +description = """RevBayes provides an interactive environment for statistical computation in + phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in + evolutionary biology, particularly phylogenetics.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/revbayes/revbayes/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['d61293fceac817d8203ed1e828661d76c73fa16bf04458a50a37057e99fd40c0'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Boost', '1.74.0'), + ('Java', '11', '', True), +] + +start_dir = 'projects/cmake' +local_cmd = './build.sh -DCMAKE_CXX_FLAGS="-pthread" -DBoost_NO_BOOST_CMAKE=ON' +cmds_map = [('', local_cmd)] + +files_to_copy = [(['projects/cmake/rb'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/rb'], + 'dirs': [], +} + +moduleclass = 'bio' From 49e4a2f821a480ec80d1410d0c53775fc11dd22e Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 17 Mar 2021 11:47:47 +0000 Subject: [PATCH 0531/2365] version updated to latest --- .../k/kallisto/kallisto-0.46.2-foss-2020b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb new file mode 100644 index 0000000000..aa268d4e37 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.46.2' + +homepage = 'https://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'pachterlab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2'] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), +] + +dependencies = [('HDF5', '1.10.7')] + +preconfigopts = "cd ../%(name)s-%(version)s/ext/htslib/ && autoreconf && cd - &&" + +parallel = 1 + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' From 4fc5f81eff47bbf22d5eefb143eb79a93ba6246c Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 17 Mar 2021 13:17:11 +0000 Subject: [PATCH 0532/2365] adding easyconfigs: AOCC-3.0.0-GCCcore-10.2.0.eb --- .../a/AOCC/AOCC-3.0.0-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-3.0.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-3.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-3.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..18edf3ece0 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-3.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'AOCC' +version = '3.0.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = [ + '4ff269b1693856b9920f57e3c85ce488c8b81123ddc88682a3ff283979362227', # aocc-compiler-3.0.0.tar +] + +dependencies = [ + ('binutils', '2.35'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +moduleclass = 'compiler' From 24f09a2a2f56cc46ee970b863020a9e05c706cb5 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 17 Mar 2021 13:41:59 +0000 Subject: [PATCH 0533/2365] adding easyconfigs: OSU-Micro-Benchmarks-5.7-gompi-2020b.eb, OSU-Micro-Benchmarks-5.7-gompic-2020b.eb --- .../OSU-Micro-Benchmarks-5.7-gompi-2020b.eb | 28 ++++++++++++++++++ .../OSU-Micro-Benchmarks-5.7-gompic-2020b.eb | 29 +++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb new file mode 100644 index 0000000000..f569964b49 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb @@ -0,0 +1,28 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.7' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb new file mode 100644 index 0000000000..a3c2312f7d --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.7' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' +configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From faa95f6a372d82f768d06ce4cfc60a712e943ff9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 17 Mar 2021 19:02:07 +0200 Subject: [PATCH 0534/2365] adding easyconfigs: GLFW-3.3.3-GCCcore-10.2.0.eb --- .../g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..58d27f55b0 --- /dev/null +++ b/easybuild/easyconfigs/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'GLFW' +version = '3.3.3' + +homepage = 'https://www.glfw.org' +description = """GLFW is an Open Source, multi-platform library for OpenGL, +OpenGL ES and Vulkan development on the desktop""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['aa9922b55a464d5bab58fcbe5a619f517d54e3dc122361c116de573670006a7a'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20201008'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['include/GLFW/glfw3.h', 'include/GLFW/glfw3native.h', + 'lib/libglfw3.a', 'lib/libglfw.%s' % SHLIB_EXT , 'lib/pkgconfig/glfw3.pc'], + 'dirs': ['include/GLFW', 'lib/cmake/glfw3', 'lib/pkgconfig'], +} + +moduleclass = 'vis' From 8910b2f8e014c9145d69a065cdbdd1414ad5762e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Mar 2021 18:16:44 +0100 Subject: [PATCH 0535/2365] consistently include 'new_archive' source URL in Qt5 easyconfigs (fixes #12421) --- easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb index ad095ebda2..d9eed72478 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb @@ -12,7 +12,8 @@ toolchainopts = {'vectorize': False} source_urls = [ 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', - 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', ] sources = ['qt-everywhere-src-%(version)s.tar.xz'] patches = [ From c37182e25160b86bbe17c7eb2502d282dd930682 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 18 Mar 2021 07:41:10 +0000 Subject: [PATCH 0536/2365] adding easyconfigs: SAMtools-1.12-GCC-9.3.0.eb, SAMtools-1.12-GCC-10.2.0.eb --- .../s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb new file mode 100644 index 0000000000..4501b991b2 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +## + +name = 'SAMtools' +version = '1.12' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6da3770563b1c545ca8bdf78cf535e6d1753d6383983c7929245d5dba2902dcb'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.72.0'), +] + +moduleclass = 'bio' From 7a4bf4e80fe39df55687a4d6dc3e17a198eed8f0 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 18 Mar 2021 08:56:41 +0100 Subject: [PATCH 0537/2365] adding easyconfigs: Boost.Python-1.74.0-GCC-10.2.0.eb, PyCUDA-2020.1-fosscuda-2020b.eb --- .../Boost.Python-1.74.0-GCC-10.2.0.eb | 27 ++++++++++++ .../p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb | 44 +++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..b9d56af993 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.74.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.71.0_fix-Python3.patch'] +checksums = [ + 'afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5', # boost_1_74_0.tar.gz + '60e3aede2f444a3855f4efed94d1de5c2887983876e0fae21f6ca5cfdc53ea96', # Boost-1.71.0_fix-Python3.patch +] + +multi_deps = {'Python': ['3.8.6', '2.7.18']} + +dependencies = [('Boost', version)] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..57530f7332 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'PyCUDA' +version = '2020.1' + +homepage = 'https://mathema.tician.de/software/pycuda' +description = "PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost.Python', '1.74.0'), + ('Mako', '1.1.3'), +] + +local_preinstallopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost " +local_preinstallopts += "--boost-lib-dir=$EBROOTBOOST/lib --no-use-shipped-boost " +local_preinstallopts += "--boost-python-libname=boost_python38 && " + +sanity_pip_check = True +use_pip = True +download_dep_fail = True + +exts_default_options = { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s'], +} + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.2', { + 'checksums': ['50f2d5b2196a18950fa1397d5ad7ea52daa5985e6196bfd06ba608a7caf93d07'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['effa3b99b55af67f3afba9b0d1b64b4a0add4dd6a33bdd6786df1aa4cc8761a5'], + }), +] + +moduleclass = 'lang' From 7ee5e14320b83ced4667eef989c6065eed5530fd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 18 Mar 2021 10:34:04 +0100 Subject: [PATCH 0538/2365] Remove download_dep_fail (default for PythonBundle) --- easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb index 57530f7332..796d97e202 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -21,7 +21,6 @@ local_preinstallopts += "--boost-python-libname=boost_python38 && " sanity_pip_check = True use_pip = True -download_dep_fail = True exts_default_options = { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', From 85af6efc130581e52e09277a9908a35b6f4fa5dc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 18 Mar 2021 11:34:23 +0200 Subject: [PATCH 0539/2365] Fix style --- easybuild/easyconfigs/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb index 58d27f55b0..f3e6e7ecec 100644 --- a/easybuild/easyconfigs/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb @@ -31,7 +31,7 @@ configopts = [ sanity_check_paths = { 'files': ['include/GLFW/glfw3.h', 'include/GLFW/glfw3native.h', - 'lib/libglfw3.a', 'lib/libglfw.%s' % SHLIB_EXT , 'lib/pkgconfig/glfw3.pc'], + 'lib/libglfw3.a', 'lib/libglfw.%s' % SHLIB_EXT, 'lib/pkgconfig/glfw3.pc'], 'dirs': ['include/GLFW', 'lib/cmake/glfw3', 'lib/pkgconfig'], } From b7c0d8e10011d53e66892e4b33ec7a050f591d20 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 18 Mar 2021 11:20:13 -0700 Subject: [PATCH 0540/2365] {lib}[GCCcore-10.2.0] libtasn1-4.16.0 --- .../libtasn1-4.16.0-GCCcore-10.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.16.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.16.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.16.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c422aeee5a --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.16.0-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.16.0' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and + some other packages. It was written by Fabio Fiorina, and has been shipped as + part of GnuTLS for some time but is now a proper GNU package.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['0e0fb0903839117cb6e3b56e68222771bebf22ad7fc2295a0ed7d576e8d4329d'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 2c265a72d7d5dd9e2500e4902dddb7c0a7002205 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 19 Mar 2021 10:58:26 +0100 Subject: [PATCH 0541/2365] Use variable templates for sources --- .../p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb index 796d97e202..2ca01eff24 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -4,7 +4,7 @@ name = 'PyCUDA' version = '2020.1' homepage = 'https://mathema.tician.de/software/pycuda' -description = "PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python." +description = 'PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.' toolchain = {'name': 'fosscuda', 'version': '2020b'} @@ -15,16 +15,16 @@ dependencies = [ ('Mako', '1.1.3'), ] -local_preinstallopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost " -local_preinstallopts += "--boost-lib-dir=$EBROOTBOOST/lib --no-use-shipped-boost " -local_preinstallopts += "--boost-python-libname=boost_python38 && " +local_preinstallopts = './configure.py --cuda-root="$EBROOTCUDA" --boost-inc-dir="$EBROOTBOOST/include/boost" ' +local_preinstallopts += '--boost-lib-dir="$EBROOTBOOST/lib" --no-use-shipped-boost ' +local_preinstallopts += '--boost-python-libname=boost_python38 && ' sanity_pip_check = True use_pip = True exts_default_options = { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s'], + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'source_urls': [PYPI_SOURCE], } exts_list = [ From 37f5da68387493d386c6f5519e67de87f4b9c73a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 19 Mar 2021 11:05:32 +0100 Subject: [PATCH 0542/2365] Use PYPI_LOWER_SOURCE --- easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb index 2ca01eff24..d7b079235c 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -24,7 +24,7 @@ use_pip = True exts_default_options = { 'source_tmpl': SOURCELOWER_TAR_GZ, - 'source_urls': [PYPI_SOURCE], + 'source_urls': [PYPI_LOWER_SOURCE], } exts_list = [ From 898cb21c4ca4098a58a81b7c3447aaaae7983313 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 19 Mar 2021 11:16:49 +0100 Subject: [PATCH 0543/2365] Revert to PYPI_SOURCE --- easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb index d7b079235c..2ca01eff24 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -24,7 +24,7 @@ use_pip = True exts_default_options = { 'source_tmpl': SOURCELOWER_TAR_GZ, - 'source_urls': [PYPI_LOWER_SOURCE], + 'source_urls': [PYPI_SOURCE], } exts_list = [ From 9c8722e88b758c5c9a3c0c5545c0112563704488 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Mar 2021 11:48:23 +0000 Subject: [PATCH 0544/2365] adding easyconfigs: iVar-1.3.1-GCC-9.3.0.eb, iVar-1.3.1-GCC-10.2.0.eb --- .../i/iVar/iVar-1.3.1-GCC-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/i/iVar/iVar-1.3.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/i/iVar/iVar-1.3.1-GCC-10.2.0.eb b/easybuild/easyconfigs/i/iVar/iVar-1.3.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..9ff54171ea --- /dev/null +++ b/easybuild/easyconfigs/i/iVar/iVar-1.3.1-GCC-10.2.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'iVar' +version = '1.3.1' + +homepage = 'https://github.com/andersen-lab/ivar' +description = """ +iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. +""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'andersen-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a5fb33e8e8fffedbb0836cb7c2f8b19d50f7f90112a9dca1f6a8e9f322056e6f'] + +builddependencies = [('Autotools', '20200321')] +dependencies = [ + ('HTSlib', '1.11'), +] + +preconfigopts = './autogen.sh &&' + +sanity_check_paths = { + 'files': ['bin/ivar'], + 'dirs': [], +} + +sanity_check_commands = ['ivar version'] + +moduleclass = 'bio' From f3a6f93426cac7454da1d3842ca66b8c74125cff Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Fri, 19 Mar 2021 13:59:29 +0000 Subject: [PATCH 0545/2365] adding easyconfigs: Keras-2.4.3-foss-2020b.eb, Theano-1.1.2-foss-2020b-PyMC.eb, mkl-service-2.3.0-foss-2020b.eb --- .../k/Keras/Keras-2.4.3-foss-2020b.eb | 39 ++++++++++++++++++ .../t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb | 41 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb new file mode 100644 index 0000000000..8a7e4f90ee --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'Keras' +version = '2.4.3' + +homepage = 'https://keras.io/' +description = """ +Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Theano', '1.1.2', '-PyMC'), + ('PyYAML', '5.3.1'), + ('h5py', '3.1.0'), + ('TensorFlow', '2.4.1'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('Keras_Applications', '1.0.8', { + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'checksums': ['fedd729b52572fb108a98e3d97e1bac10a81d3917d2103cc20ab2a5f03beb973'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb new file mode 100644 index 0000000000..bd33ad40df --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.1.2' +versionsuffix = '-PyMC' + +homepage = 'https://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/T/Theano%(versionsuffix)s'] +sources = ['Theano-PyMC-%(version)s.tar.gz'] +checksums = ['5da6c2242ea72a991c8446d7fe7d35189ea346ef7d024c890397011114bf10fc'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('mkl-service', '2.3.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] + +sanity_check_paths = { + 'files': ['bin/theano-cache'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +local_blas_warning = "Using NumPy C-API based implementation for BLAS functions" +sanity_check_commands = [ + # make sure that warning about falling back to (slow) NumPy C-API for BLAS functions is *not* printed + # mkl-service dependency is required to ensure this doesn't happen + "python -c 'import theano.tensor' 2>&1 | grep '%s'; test $? != 0" % local_blas_warning, +] + +moduleclass = 'math' From 34aad0de0c34bb8f3ffba824f757301e06dbfbca Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 19 Mar 2021 13:02:47 -0700 Subject: [PATCH 0546/2365] update LibSoup --- .../LibSoup/LibSoup-2.72.0-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibSoup/LibSoup-2.72.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.72.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.72.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7481e75050 --- /dev/null +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.72.0-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MesonNinja' + +name = 'LibSoup' +version = '2.72.0' + +homepage = 'https://wiki.gnome.org/Projects/libsoup' +description = """libsoup is an HTTP client/server library for GNOME. It +uses GObjects and the glib main loop, to integrate well with GNOME +applications, and also has a synchronous API, for use in threaded +applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'cstd': 'gnu11'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['170c3f8446b0f65f8e4b93603349172b1085fb8917c181d10962f02bb85f5387'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.66.1'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('libxml2', '2.9.10'), + ('SQLite', '3.33.0'), + ('GLib', '2.66.1'), + ('libpsl', '0.21.1'), + ('cURL', '7.72.0'), +] + +# uncomment for checking TLS support +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +# remove option -Dtls_check=false for checking TLS support +configopts = '-Dgssapi=disabled -Dvapi=disabled -Dtls_check=false ' + +sanity_check_paths = { + 'files': ['lib/libsoup-2.4.%s' % SHLIB_EXT, 'lib/libsoup-gnome-2.4.%s' % SHLIB_EXT], + 'dirs': ['include/libsoup-2.4/libsoup', 'include/libsoup-gnome-2.4/libsoup', 'lib/pkgconfig'] +} + +moduleclass = 'lib' From 318265aef0d87394469d6dae3be99308ae3101d1 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 19 Mar 2021 13:40:56 -0700 Subject: [PATCH 0547/2365] add libpsl to LibSoup --- .../l/libpsl/libpsl-0.21.1-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..56cfaf83bd --- /dev/null +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libpsl' +version = '0.21.1' + +homepage = 'https://rockdaboot.github.io/libpsl' +description = "C library for the Public Suffix List" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/rockdaboot/%(name)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ac6ce1e1fbd4d0254c4ddb9d37f1fa99dec83619c1253328155206b896210d4c'] + +builddependencies = [ + ('binutils', '2.35'), + ('libtool', '2.4.6'), + ('Autotools', '20200321'), + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['bin/psl', 'lib/libpsl.a'], + 'dirs': [] +} + +moduleclass = 'lib' From 53c402b4771fd209b113080b066ad8672559cc17 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 19 Mar 2021 14:04:12 -0700 Subject: [PATCH 0548/2365] {lib}[GCCcore 10.2.0] jbigkit 2.1 --- .../j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5d3338697b --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +# EasyBuild easyconfig +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' + +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932', # jbigkit-2.1.tar.gz + '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce', # jbigkit-2.1_libpath.patch + '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696', # jbigkit-2.1_shlib.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' From 03036e5b85ea9a1c123101557880950f12b50723 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 19 Mar 2021 14:48:49 -0700 Subject: [PATCH 0549/2365] {lib}[SYSTEM] Catc2 2.13.4 --- .../easyconfigs/c/Catch2/Catch2-2.13.4.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/Catch2/Catch2-2.13.4.eb diff --git a/easybuild/easyconfigs/c/Catch2/Catch2-2.13.4.eb b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.4.eb new file mode 100644 index 0000000000..eb0b2d7e30 --- /dev/null +++ b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.4.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Catch2' +version = '2.13.4' + +homepage = 'https://github.com/catchorg/Catch2' +description = """A modern, C++-native, header-only, + test framework for unit-tests, TDD and BDD + - using C++11, C++14, C++17 and later + (or C++03 on the Catch1.x branch) +""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/catchorg/Catch2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('GCCcore', '10.2.0'), # required to a access CMake when using hierarchical module naming scheme + ('binutils', '2.35', '', ('GCCcore', '10.2.0')), # to make CMake compiler health check pass on old systems + ('CMake', '3.18.4', '', ('GCCcore', '10.2.0')), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/catch2', 'lib64/cmake'], +} + +moduleclass = 'lib' From 4c4be9f71ff212d645df67be59ea31199c04612c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 22 Mar 2021 10:44:12 +0100 Subject: [PATCH 0550/2365] adding easyconfigs: Ratatosk-0.4-GCC-10.2.0.eb --- .../r/Ratatosk/Ratatosk-0.4-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ratatosk/Ratatosk-0.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/r/Ratatosk/Ratatosk-0.4-GCC-10.2.0.eb b/easybuild/easyconfigs/r/Ratatosk/Ratatosk-0.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..bb1a332b58 --- /dev/null +++ b/easybuild/easyconfigs/r/Ratatosk/Ratatosk-0.4-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'Ratatosk' +version = '0.4' + +homepage = 'https://github.com/DecodeGenetics/Ratatosk' + +description = "Phased hybrid error correction of long reads using colored de Bruijn graphs" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [ + {'source_urls': ['https://github.com/DecodeGenetics/Ratatosk/archive'], + 'download_filename': 'dc9a884.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'source_urls': ['https://github.com/pmelsted/bifrost/archive'], + 'download_filename': '53286c1.tar.gz', 'filename': 'Bifrost-1.0.5.tar.gz', + 'extract_cmd': 'tar -C Ratatosk-*/Bifrost --strip-components=1 -xf %s'}, +] +checksums = [ + 'd810e588c3a64a24c9f83712d0475fb9f516d76fc96aee5c16f7c84fde327cc5', # Ratatosk-0.4.tar.gz + '0a74136aefc35d7cd7a91a77a71b9d72bbfb98b35bdab48c60368dcaf6016c39', # Bifrost-1.0.5.tar.gz +] + +dependencies = [('zlib', '1.2.11')] + +builddependencies = [('CMake', '3.18.4')] + +sanity_check_paths = { + 'files': ['bin/Ratatosk'], + 'dirs': [], +} + +sanity_check_commands = ['Ratatosk --help'] + +moduleclass = 'bio' From 40777640bd7412596f9ef4243ad102c20b676c23 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 22 Mar 2021 18:03:27 +0200 Subject: [PATCH 0551/2365] adding easyconfigs: igraph-0.9.0-fosscuda-2020b.eb, python-igraph-0.9.0-fosscuda-2020b.eb, PyCairo-1.18.2-GCCcore-10.2.0.eb, leidenalg-0.8.2-fosscuda-2020b-Python-3.8.6.eb, hyperopt-0.2.5-fosscuda-2020b-Python-3.8.6-Java-1.8.eb, Spark-3.1.1-fosscuda-2020b.eb, Hadoop-2.10.0-GCCcore-10.2.0-native.eb, Arrow-0.16.0-fosscuda-2020b-Python-3.8.6.eb --- .../python-igraph-0.9.0-fosscuda-2020b.eb | 47 ++++++++++++++++ .../s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 53 +++++++++++++++++++ 2 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..4b3e4b7083 --- /dev/null +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'python-igraph' +version = '0.9.0' + +homepage = 'https://igraph.org/python' +description = """Python interface to the igraph high performance graph library, primarily aimed at complex network + research and analysis.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +osdependencies = [('zlib-devel', 'zlib1g-dev')] + +dependencies = [ + ('Python', '3.8.6'), + ('igraph', '0.9.0'), + ('PyCairo', '1.18.2'), + ('Clang', '11.0.1'), + ('libxml2', '2.9.10'), + ('pkg-config', '0.29.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('texttable', '1.6.2', { + 'checksums': ['eff3703781fbc7750125f50e10f001195174f13825a92a45e9403037d539b4f4'], + }), + (name, version, { + 'buildopts': '--use-pkg-config', + 'modulename': 'igraph', + 'checksums': ['7aa1d77fa02e27475eb4f14503f3cb342c3ed8990d9224640fd29c70797f2dd6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/igraph'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# cairo must be available for proper plotting support +sanity_check_commands = ["python -c 'from igraph.drawing.utils import find_cairo; cairo = find_cairo(); cairo.Context'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..c3f74c2564 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '3.1.1' +local_python_versionsuffix = '-Python-%(pyver)s' +local_java_versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' +] +sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] +checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] + +dependencies = [ + ('Python', '3.8.6'), + ('Java', '1.8', '', True), + ('Hadoop', '2.10.0', '-native'), + ('Arrow', '0.16.0', local_python_versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py4j', '0.10.7', { + 'source_tmpl': 'py4j-%(version)s.zip', + 'checksums': ['721189616b3a7d28212dfb2e7c6a1dd5147b03105f1fc37ff2432acd0e863fa5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyspark', 'bin/spark-shell'], + 'dirs': ['python'] +} + +sanity_check_commands = [ + "pyspark -h", + "python -c 'import pyspark'", +] + +modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} + +modextravars = {'SPARK_HOME': '%(installdir)s'} + +moduleclass = 'devel' From dd8688848cf7faec250ff66ac284dc18e3e6c569 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 22 Mar 2021 18:15:09 +0200 Subject: [PATCH 0552/2365] adding easyconfigs: PyMC3-3.11.1-fosscuda-2020b-Python-3.8.6.eb, Theano-1.1.2-fosscuda-2020b-PyMC.eb, netcdf4-python-1.5.5.1-fosscuda-2020b.eb, xarray-0.16.2-fosscuda-2020b.eb, libgpuarray-0.7.6-fosscuda-2020b-Python-3.8.6.eb, cuDNN-8.1.1.33-CUDA-11.1.1.eb, PyMC3-3.11.1-fosscuda-2020b-Python-3.8.6.eb, PyTables-3.6.1-fosscuda-2020b.eb, pyro-api-0.1.2-fosscuda-2020b-Python-3.8.6.eb, pyro-ppl-1.5.2-fosscuda-2020b-Python-3.8.6.eb --- .../netcdf4-python-1.5.5.1-fosscuda-2020b.eb | 50 +++++++++++++++++++ .../PyTables/PyTables-3.6.1-fosscuda-2020b.eb | 48 ++++++++++++++++++ .../Theano-1.1.2-fosscuda-2020b-PyMC.eb | 43 ++++++++++++++++ .../x/xarray/xarray-0.16.2-fosscuda-2020b.eb | 27 ++++++++++ 4 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..b91d0032cf --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.5.5.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('netCDF', '4.7.4'), + ('cURL', '7.72.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('cftime', '1.4.1', { + 'checksums': ['7c55540bc164746c3c4f86a07c9c7b9ed4dfb0b0d988348ec63cec065c58766d'], + }), + (name, version, { + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': ['d957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..c7970b0bda --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.6.1' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-libs.patch'] +checksums = [ + '4cea86bab5bcb5423a07c7951b8c65e24b674e0dcec0e448d434829eff5f18d0', # v3.6.1.tar.gz + '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.6.1-fix-libs.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # provides numexpr + ('HDF5', '1.10.7'), + ('LZO', '2.10'), + ('Blosc', '1.21.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb new file mode 100644 index 0000000000..fe599301e3 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.1.2' +versionsuffix = '-PyMC' + +homepage = 'https://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/T/Theano%(versionsuffix)s'] +sources = ['Theano-PyMC-%(version)s.tar.gz'] +checksums = ['5da6c2242ea72a991c8446d7fe7d35189ea346ef7d024c890397011114bf10fc'] + +dependencies = [ + ('Python', '3.8.6'), + ('libgpuarray', '0.7.6', '-Python-3.8.6'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] + + +sanity_check_paths = { + 'files': ['bin/theano-cache'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +local_blas_warning = "Using NumPy C-API based implementation for BLAS functions" +sanity_check_commands = [ + # make sure that warning about falling back to (slow) NumPy C-API for BLAS functions is *not* printed + # mkl-service dependency is required to ensure this doesn't happen + "python -c 'import theano.tensor' 2>&1 | grep '%s'; test $? != 0" % local_blas_warning, +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..29b10a1398 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.16.2' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['38e8439d6c91bcd5b7c0fca349daf8e0643ac68850c987262d53526e9d7d01e4'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'data' From e553ba899f305e1cfd6121429b447fcb13be4953 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 22 Mar 2021 18:20:19 +0200 Subject: [PATCH 0553/2365] adding easyconfigs: cell2location-v0.05-alpha-fosscuda-2020b-Python-3.8.6.eb, dill-0.3.3-fosscuda-2020b.eb, IPython-7.21.0-fosscuda-2020b-Python-3.7.4.eb, netCDF-4.7.4-fosscuda-2020b.eb, request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb, Seaborn-0.11.1-fosscuda-2020b-Python-3.8.6.eb, statsmodels-0.12.1-fosscuda-2020b.eb, umap-learn-0.4.6-fosscuda-2020b-Python-3.8.6.eb --- ...st-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb | 29 +++++++++++++++++ .../statsmodels-0.12.1-fosscuda-2020b.eb | 31 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb b/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb new file mode 100644 index 0000000000..d017c751df --- /dev/null +++ b/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Binary' + +name = 'request' +version = '2.88.1' +local_nodejsver = '12.19.0' +versionsuffix = '-nodejs-%s' % local_nodejsver + +homepage = 'https://github.com/request/request/' +description = """Request is designed to be the simplest way possible to make http calls. + It supports HTTPS and follows redirects by default.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/request/request/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6506ec33a673f6a5542a950be65b02b23c8e8cda21847c19ee67dee4fdc7adc4'] + +dependencies = [ + ('nodejs', local_nodejsver), +] + +install_cmd = 'npm install --prefix %(installdir)s -g v%(version)s.tar.gz' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/node_modules/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..a4311e6cf5 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.12.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + (name, version, { + 'checksums': ['a271b4ccec190148dccda25f0cbdcbf871f408fc1394a10a7dc1af4a62b91c8e'], + }), +] + +moduleclass = 'math' From 7d8665d2a16e96d67d8ad7e98f68c9bd8d7b0aa8 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 22 Mar 2021 10:23:23 -0700 Subject: [PATCH 0554/2365] add checksum --- easybuild/easyconfigs/c/Catch2/Catch2-2.13.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Catch2/Catch2-2.13.4.eb b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.4.eb index eb0b2d7e30..f1be3f1c7c 100644 --- a/easybuild/easyconfigs/c/Catch2/Catch2-2.13.4.eb +++ b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.4.eb @@ -14,7 +14,7 @@ toolchain = SYSTEM source_urls = ['https://github.com/catchorg/Catch2/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = [] +checksums = ['e7eb70b3d0ac2ed7dcf14563ad808740c29e628edde99e973adad373a2b5e4df'] # using CMake built with GCCcore to avoid relying on the system compiler to build it builddependencies = [ From d78110eee5b001fb390551817803eda3a9a89c38 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 23 Mar 2021 09:33:10 +0000 Subject: [PATCH 0555/2365] Update all htslib-related tools to 1.12 --- .../b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb | 38 +++++++++++++++++++ .../h/HTSlib/HTSlib-1.12-GCC-10.2.0.eb | 37 ++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.12-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb new file mode 100644 index 0000000000..d04a72ec26 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.12' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7a0e6532b1495b9254e38c6698d955e5176c1ee08b760dfea2235ee161a024f5'] + +dependencies = [ + ('zlib', '1.2.11'), + ('HTSlib', '1.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('GSL', '2.6'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['libexec/bcftools'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.12-GCC-10.2.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.12-GCC-10.2.0.eb new file mode 100644 index 0000000000..9e08f3401e --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.12-GCC-10.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.12' + +homepage = "https://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2280141b46e953ba4ae01b98335a84f8e6ccbdb6d5cdbab7f70ee4f7e3b6f4ca'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.72.0'), +] + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From a15cbdde6f03c27e2615184af96ca6c7d7ee7f41 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 23 Mar 2021 11:16:20 +0100 Subject: [PATCH 0556/2365] Remove source_urls = [PYPI_SOURCE] from 2020b ECs This is no longer required as it became the default with easybuilders/easybuild-easyblocks#2364 --- .../a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb | 1 - .../a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb | 1 - easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb | 2 -- easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb | 2 -- easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb | 2 -- easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb | 2 -- easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb | 1 - easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb | 2 -- easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb | 2 -- easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb | 2 -- easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb | 2 -- easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb | 1 - easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb | 1 - easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb | 1 - .../easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb | 1 - .../easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb | 1 - .../easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb | 1 - easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb | 2 -- easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb | 2 -- easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb | 1 - .../Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb | 2 -- easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb | 1 - easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb | 1 - easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb | 1 - easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb | 1 - .../i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb | 1 - easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb | 1 - easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb | 1 - easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb | 2 -- easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb | 2 -- easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb | 1 - .../easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb | 1 - .../easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb | 1 - .../easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb | 1 - .../easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb | 2 -- .../n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb | 2 -- easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb | 1 - .../easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb | 1 - easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb | 1 - easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb | 2 -- easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb | 1 - easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb | 1 - .../easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb | 1 - easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb | 2 -- .../easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb | 2 -- .../easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb | 2 -- .../easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb | 1 - .../PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb | 2 -- .../PyTorch-Geometric-1.6.3-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb | 1 - .../easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb | 2 -- .../s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb | 2 -- .../s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb | 2 -- .../s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb | 2 -- .../s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb | 2 -- .../easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb | 1 - .../easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb | 1 - .../s/scikit-build/scikit-build-0.11.1-foss-2020b.eb | 5 ----- .../s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb | 5 ----- .../s/scikit-image/scikit-image-0.18.1-foss-2020b.eb | 2 -- .../s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb | 2 -- .../s/scikit-image/scikit-image-0.18.1-intel-2020b.eb | 2 -- .../s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb | 1 - .../s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb | 1 - .../s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb | 1 - .../s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb | 1 - easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb | 2 -- .../s/statsmodels/statsmodels-0.12.1-intel-2020b.eb | 2 -- easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb | 1 - .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 1 - .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 1 - .../tensorflow-probability-0.12.1-foss-2020b.eb | 2 -- .../tensorflow-probability-0.12.1-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb | 1 - 79 files changed, 125 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb index 6601e03e9d..aadacfddca 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb @@ -12,7 +12,6 @@ dynamics within the Campos Atomic Simulation Environment (ASE).""" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True, 'openmp': False} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['b6c03c790ba4c9f0d231659078c26ce8193fa21314bf2fe4adaa7899d5cd9dbe'] diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb index ad8a03e528..bf5397af7f 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb @@ -12,7 +12,6 @@ dynamics within the Campos Atomic Simulation Environment (ASE).""" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True, 'openmp': False} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['b6c03c790ba4c9f0d231659078c26ce8193fa21314bf2fe4adaa7899d5cd9dbe'] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb index d78de78cef..5f6282b086 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb @@ -24,8 +24,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ase', version, { 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb index 6f5ab3edf2..743f7822aa 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb @@ -24,8 +24,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ase', version, { 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb index 82de3ea825..9fd13e7e5b 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb @@ -28,8 +28,6 @@ sanity_pip_check = True # ase-ext) using Intel compilers on top of Python built with GCC. check_ldshared = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ase', version, { 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb index 355fed1b39..6376980043 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb @@ -24,8 +24,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ase', version, { 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb index 2f564e84aa..f128fd8021 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb @@ -24,8 +24,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ase', version, { 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb index c29ffe0592..56fba957d6 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb @@ -28,8 +28,6 @@ sanity_pip_check = True # ase-ext) using Intel compilers on top of Python built with GCC. check_ldshared = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ase', version, { 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb index 830df127df..e2262d8d25 100644 --- a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb @@ -8,7 +8,6 @@ description = "Exploratory analysis of Bayesian models with Python" toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['bb0730ab62223a44ec99072b12f9e9f24521a36e6b7ba2624df9f9908eba1d82'] diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb index 99b3dce72e..59ace9b78d 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb index a9bd000902..8e06a02627 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb index eb38b5693d..d3c12b132a 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb index bd28417815..c1d37aafe9 100644 --- a/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('fsspec', '0.8.7', { 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb index 5294364004..530ef90ea3 100644 --- a/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('fsspec', '0.8.7', { 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb index da0afcc593..1436265c5c 100644 --- a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('fsspec', '0.8.7', { 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], diff --git a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb index 56e8729639..4ddcccb74e 100644 --- a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb @@ -11,7 +11,6 @@ for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers a toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['1d2fcf58006c82548a16004e607d4518613d49e4a2f02a3797703eee2b39c6d8'] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb index 8fdc6c36cb..1dd3ad51a4 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb @@ -11,7 +11,6 @@ description = """GPAW is a density-functional theory (DFT) Python code based on toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'usempi': True, 'openmp': False} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb index e34fb5f250..8264ef0a7f 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -11,7 +11,6 @@ description = """GPAW is a density-functional theory (DFT) Python code based on toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'usempi': True, 'openmp': False} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb index 6776283e38..77370423b3 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb @@ -13,7 +13,6 @@ description = """GPAW is a density-functional theory (DFT) Python code based on toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'usempi': True, 'openmp': False} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb index a2cc1f7494..f8f2758be1 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb @@ -13,7 +13,6 @@ description = """GPAW is a density-functional theory (DFT) Python code based on toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'usempi': True, 'openmp': False} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), diff --git a/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb index a131fffa61..1fe9874788 100644 --- a/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb @@ -8,7 +8,6 @@ description = "GPyTorch is a Gaussian process library implemented using PyTorch. toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['9bc7aea1dee188b69ff181e3406aabf6fedfa4446b834ed6adf68b94b6ebebd5'] diff --git a/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb index 881669d3f1..3492441af2 100644 --- a/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('smart_open', '4.1.2', { 'checksums': ['4bbb6233364fc1173cc0af6b7a56ed76fce32509514f1978a995a5835f3177f1'], diff --git a/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb index 8de87c4e0c..20eab35edc 100644 --- a/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb +++ b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('smart_open', '4.1.2', { 'checksums': ['4bbb6233364fc1173cc0af6b7a56ed76fce32509514f1978a995a5835f3177f1'], diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb index be07f7b05f..0c2f4b1d60 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb @@ -11,7 +11,6 @@ description = """HTSeq is a Python library to facilitate processing and analysis toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['abd13b48021340fea783a9dff110534c19a306b54182501e1aa7b324d458b080'] diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb index 7d4084ab69..de3f87c495 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb @@ -28,8 +28,6 @@ preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_W parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cloudpickle', '1.5.0', { 'checksums': ['820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82'], diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb index a14cc3f059..140b138358 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb index dd5d5e8161..59473c4bdb 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'fosscuda', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb index 8da1824847..591338dd64 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2'] diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb index 1bc2912405..f6bb27ac98 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb @@ -11,7 +11,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'intelcuda', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2'] diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb index ad59b47535..c13fa13ed4 100644 --- a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb @@ -9,7 +9,6 @@ description = """imbalanced-learn is a Python package offering a number of re-sa toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['da59de0d1c0fa66f62054dd9a0a295a182563aa1abbb3bf9224a3678fcfe8fa4'] diff --git a/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb b/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb index 6dfe84c1af..f5feb4ef74 100644 --- a/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb +++ b/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb @@ -11,7 +11,6 @@ description = "Joyplots in Python with matplotlib & pandas" toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['55d268386a1d2d974aa90cbf6dcca3ad943d17075987dfb8c4a772852fbe79c7'] diff --git a/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb b/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb index d6ef6c36bf..bae0931936 100644 --- a/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb @@ -23,7 +23,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ ('amply', '0.1.4', { 'checksums': ['cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38'], diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb index 279267dba9..a9fa73da54 100644 --- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ ] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb index ee69963428..0b9e574190 100644 --- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ ] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], diff --git a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb index 8b2c592db4..4d89465bea 100644 --- a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb @@ -9,7 +9,6 @@ cellular electrophysiology.""" toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['393ebc85413bd1b573909736caeadd9d7757f41cceb7bd29f3b30f5107237cba'] diff --git a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb index cfa973108a..f6ff4874bc 100644 --- a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb @@ -11,7 +11,6 @@ description = "Comparing runs of Oxford Nanopore sequencing data and alignments" toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e8af09f3f9462b045e1c7abe8d4110ea4aaf10e4a1ba0152ad27c1331eb9e389'] diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb index 56f58aee1c..d8059101c3 100644 --- a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb @@ -11,7 +11,6 @@ description = "Plotting suite for long read sequencing data and alignments" toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['caf69a5789625e746814238cb4f0d510ed6768a094566e8f1dcaa77933c4d6fd'] diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb index 4ea32dc852..896f9805cf 100644 --- a/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb @@ -11,7 +11,6 @@ description = "Functions to extract information from Oxford Nanopore sequencing toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f6993855d5f1aa1e9271c61e39184b22fccd6a90e634ca88d2684ff85c8c22e5'] diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb index cc6a8ed547..86a33153d9 100644 --- a/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Python-Deprecated', '1.1.0', { 'modulename': 'deprecated', diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb index 07b7940a68..28dd6ccebe 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cftime', '1.2.0', { 'checksums': ['ff0a175edda260357ff7d24a32bbe0a8c72eafd5f6a404ce487127f9d01836db'], diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb index 17140eeadb..4b5d73a3cd 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb @@ -9,7 +9,6 @@ and study of the structure, dynamics, and functions of complex networks.""" toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb index 5ed249495d..b7466845d8 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb @@ -9,7 +9,6 @@ and study of the structure, dynamics, and functions of complex networks.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb index bad27695d3..49cf679c99 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb @@ -9,7 +9,6 @@ and study of the structure, dynamics, and functions of complex networks.""" toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] diff --git a/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb index 15e646e2da..0f17be0040 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb @@ -22,8 +22,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('llvmlite', '0.35.0', { 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], diff --git a/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb index 91d83aab01..be5572c9dd 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb @@ -22,8 +22,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('llvmlite', '0.35.0', { 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb index c472741ff9..7e14731b26 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb @@ -8,7 +8,6 @@ description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['3ceb38ffd86e29774e759486f2961599c8ed847459c68727493cadeaf115a38a'] diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb index 94bfa61bf5..c1cb9119b5 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb @@ -8,7 +8,6 @@ description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['3ceb38ffd86e29774e759486f2961599c8ed847459c68727493cadeaf115a38a'] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb index 2ca01eff24..07596366dc 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -24,7 +24,6 @@ use_pip = True exts_default_options = { 'source_tmpl': SOURCELOWER_TAR_GZ, - 'source_urls': [PYPI_SOURCE], } exts_list = [ diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb index 9bf535a3dd..fd9f3d7d32 100644 --- a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('typing_extensions', '3.7.4.3', { 'checksums': ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'], diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb index ba1007e107..3ea1d13273 100644 --- a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb @@ -17,8 +17,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb index 0e233b347c..8bf189b529 100644 --- a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb @@ -17,8 +17,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb index cf6cdc10a9..fdc220d285 100644 --- a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb @@ -9,7 +9,6 @@ description = """Python interface to Stan, a package for Bayesian inference toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038'] diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb index 307b6dd2f8..ac1c2f2460 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb @@ -20,8 +20,6 @@ dependencies = [ ('ASE', '3.20.1'), ] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb index bd807a939a..f68754b35b 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb @@ -20,8 +20,6 @@ dependencies = [ ('ASE', '3.20.1'), ] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb b/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb index 1d15a6c810..7b5a085266 100644 --- a/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb +++ b/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb @@ -11,7 +11,6 @@ description = "Tools for plotting Oxford Nanopore and other long-read data" toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['0a5f4fab1cabf7a9dbe5ec0d21be1e2ab0fabc78c8a74453006b63677bcc038f'] diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb index 56a123630c..37ad133e5d 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('numpy', '1.20.1', { 'sources': ['numpy-%(version)s.zip'], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb index 4e8b17e249..96f8870c01 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - # order is important! exts_list = [ ('numpy', '1.19.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb index 3b06eb52b6..d120637e07 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - # order is important! exts_list = [ ('numpy', '1.19.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb index 9d3c3bddbc..1f87241aa7 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - # order is important! exts_list = [ ('numpy', '1.19.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb index d254373f04..804efa8e74 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - # order is important! exts_list = [ ('numpy', '1.19.4', { diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb index 8829db33c7..0c2f044494 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb @@ -13,7 +13,6 @@ description = """ Seaborn is a Python visualization library based on matplotlib. toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d1a0c9d6bd1bc3cadb0364b8f06540f51322a670cf8438d0fde1c1c7317adc0'] diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb index 25396ba969..cf633da88f 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb @@ -13,7 +13,6 @@ description = """ Seaborn is a Python visualization library based on matplotlib. toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'] diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb index 01be14e317..755057a371 100755 --- a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb @@ -16,11 +16,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], -} - exts_list = [ ('distro', '1.5.0', { 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb index e74ec50f16..b3b51a2d4b 100755 --- a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb @@ -16,11 +16,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], -} - exts_list = [ ('distro', '1.5.0', { 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb index e922ae4b1e..ae0e8510b8 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('PyWavelets', '1.1.1', { 'modulename': 'pywt', diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb index 2eaefc8afe..bb3613e276 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('PyWavelets', '1.1.1', { 'modulename': 'pywt', diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb index f1d0c9f2b5..d92ee21ee4 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb @@ -19,8 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('PyWavelets', '1.1.1', { 'modulename': 'pywt', diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb index daedc9ec68..5d67c894a4 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb @@ -11,7 +11,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb index f4d14cdcf2..52fc2890fd 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb @@ -11,7 +11,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb index 043cb44f29..b851222523 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb @@ -11,7 +11,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb index 76e425daff..5b5729dd0a 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb @@ -11,7 +11,6 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'intelcuda', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] diff --git a/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb index 350f3a7677..251b68a8ce 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('hdf5plugin', '2.3.1', { 'checksums': ['2f6d886012c37bf7e8e002173dd6b16e6879b8e0e9f7d2f2ef9f79db97ed28d2'], diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb index 2e655bfefd..2b3ea0cbc3 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb @@ -17,8 +17,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('patsy', '0.5.1', { 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb index 35b84aecb0..f1c552b054 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb @@ -11,7 +11,6 @@ description = """SymPy is a Python library for symbolic mathematics. It aims to toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a3de9261e97535b83bb8607b0da2c7d03126650fafea2b2789657b229c246b2e'] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index bc90bd7090..1e90ae6d02 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -44,7 +44,6 @@ dependencies = [ ] exts_default_options = { - 'source_urls': [PYPI_SOURCE], 'sanity_pip_check': True, } use_pip = True diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 7650e2d84c..c832a52b75 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -46,7 +46,6 @@ dependencies = [ ] exts_default_options = { - 'source_urls': [PYPI_SOURCE], 'sanity_pip_check': True, } use_pip = True diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb index 703eaf3b6b..021eaa0106 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb @@ -24,8 +24,6 @@ dependencies = [ ('dm-tree', '0.1.5'), ] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb index 77a2363663..3bd4385f27 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb @@ -24,8 +24,6 @@ dependencies = [ ('dm-tree', '0.1.5'), ] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb index 98f20a0441..805300f989 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb @@ -10,7 +10,6 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['38e8439d6c91bcd5b7c0fca349daf8e0643ac68850c987262d53526e9d7d01e4'] From b0cb6011db8d886cd34da0d83b2f479152602981 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 23 Mar 2021 11:24:54 +0100 Subject: [PATCH 0557/2365] Fix URL of netcdf --- .../n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb index 28dd6ccebe..01db361cc5 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb @@ -9,8 +9,6 @@ description = """Python/numpy interface to netCDF.""" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), # for numpy From 25047578c566863d35e82351cf3d7450f04e3d0c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 23 Mar 2021 11:33:31 +0100 Subject: [PATCH 0558/2365] Remove source_urls = [PYPI_SOURCE] from 2020 ECs at GCC level This is no longer required as it became the default with easybuilders/easybuild-easyblocks#2364 --- .../easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb | 2 -- easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb | 1 - .../h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb | 1 - .../h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb | 1 - .../easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb | 2 -- .../easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb | 2 -- .../easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb | 2 -- easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 1 - .../easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb | 1 - .../easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 1 - .../p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb | 1 - .../easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb | 2 -- .../p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb | 2 -- easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb | 1 - .../easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb | 2 -- easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb | 1 - .../typing-extensions-3.7.4.3-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb | 1 - 28 files changed, 35 deletions(-) diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb index 482cdae8b9..a7a6526bca 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb @@ -19,7 +19,6 @@ reading, writing, simulation, processing and manipulation of phylogenetic trees toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101'] diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb index a047c7fe01..2ec06598b3 100644 --- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb @@ -10,7 +10,6 @@ allows to apply a function to each "leaf" preserving the overall structure.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['a951d2239111dfcc468071bc8ff792c7b1e3192cab5a3c94d33a8b2bda3127fa'] diff --git a/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb index d9084f7f06..923379d86b 100644 --- a/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb @@ -21,8 +21,6 @@ builddependencies = [('binutils', '2.35')] use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} - exts_list = [ ('itsdangerous', '1.1.0', { 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb index dad396aedb..6291abd1fc 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb @@ -8,7 +8,6 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['8951bcfc61c0f40102b92a4777daf9eb85445b537c4d09086deb0e097190bef0'] diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb index b5e6c59197..4779ef3e22 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb @@ -11,7 +11,6 @@ description = """Hypothesis is an advanced testing library for Python. It lets y toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['f8c281355aaba1da696e40f1488c2bb47c42660424f5750daea45a85e2d047b3'] diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb index 6a08263f91..6b59173187 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb @@ -10,7 +10,6 @@ description = """Hypothesis is an advanced testing library for Python. It lets y toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a74e127a865fde12b853cc00f5f52a3a1601d2a1c311b3ffc8de92a4c06778f7'] diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb index 99ddf43c2b..e96de73689 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb @@ -22,8 +22,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('ipython_genutils', '0.2.0', { 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb index 941bc4ae31..36fecff59c 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -24,8 +24,6 @@ osdependencies = [OS_PKG_OPENSSL_DEV] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('certipy', '0.1.3', { 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb index 4633201883..ce2bcb29a8 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb @@ -21,8 +21,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('json5', '0.9.5', { 'checksums': ['703cfee540790576b56a92e1c6aaa6c4b0d98971dc358ead83812aa4d06bdb96'], diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb index 12c3d7ed2a..ce0683e82d 100644 --- a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb @@ -8,7 +8,6 @@ description = "Fast static image export for web-based visualization libraries wi toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = ['kaleido-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'] checksums = ['8d0403b1eb21080e09d6d728c1ea7170fd4763c415fe89dfea6edf35ec36f8e7'] diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb index 31000e33a4..dbd3721ba1 100644 --- a/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb @@ -8,7 +8,6 @@ description = """The lxml XML toolkit is a Pythonic binding for the C libraries toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['cd11c7e8d21af997ee8079037fff88f16fda188a9776eb4b81c7e4c9c0a7d7fc'] diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb index 7ac3876f78..d4c483239b 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb @@ -8,7 +8,6 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['8195c8c1400ceb53496064314c6736719c6f25e7479cd24c77be3d9361cddc27'] diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb index deecc4136f..660814b8cc 100644 --- a/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb @@ -8,7 +8,6 @@ description = "Meson is a cross-platform build system designed to be both as fas toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['6bed2a25a128bbabe97cf40f63165ebe800e4fcb46db8ab7ef5c2b5789f092a5'] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index ccc0793115..9304f308f9 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -9,7 +9,6 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e'] diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index b4d46a0f4f..ee4425b49c 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -22,7 +22,6 @@ dependencies = [ ] exts_default_options = { - 'source_urls': [PYPI_SOURCE], 'use_pip': True } diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb index f51c02e2fa..8d15298523 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb @@ -19,7 +19,6 @@ description = """PyOpenGL is the most common cross platform Python binding to Op toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4107ba0d0390da5766a08c242cf0cf3404c377ed293c5f6d701e457c57ba3424'] diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb index ded1c9a677..3035aed1cc 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb @@ -8,7 +8,6 @@ description = """PyYAML is a YAML parser and emitter for the Python programming toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index ac42a9c106..8882252086 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -31,7 +31,6 @@ osdependencies = [OS_PKG_OPENSSL_DEV] exts_default_options = { 'download_dep_fail': True, 'sanity_pip_check': True, - 'source_urls': [PYPI_SOURCE], 'use_pip': True, } diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 4371dc3f09..80a005ae19 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -41,7 +41,6 @@ installopts = " && ln -s %(installdir)s/bin/pip3 %(installdir)s/bin/pip" exts_default_options = { 'download_dep_fail': True, 'sanity_pip_check': True, - 'source_urls': [PYPI_SOURCE], 'use_pip': True, } diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb index de70590971..58bed1af99 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb @@ -9,7 +9,6 @@ description = """pkgconfig is a Python module to interface with the pkg-config c toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f'] diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb index 6366976289..cd0c9c372f 100644 --- a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb @@ -16,8 +16,6 @@ dependencies = [('Python', '3.8.6')] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('retrying', '1.3.3', { 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb index 596b4a4cb3..cfd093a102 100644 --- a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb @@ -38,8 +38,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('apipkg', '1.5', { 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb index 6dd7277e0d..863392420b 100644 --- a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb @@ -9,7 +9,6 @@ It provides support for PyQt5, PyQt4, PySide2 and PySide.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2db72c44b55d0fe1407be8fba35c838ad0d6d3bb81f23007886dc1fc0f459c8d'] diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb index 530c2fc18d..26585354a2 100644 --- a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb @@ -11,7 +11,6 @@ such as inline figures, proper multiline editing with syntax highlighting, graph toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['404994edfe33c201d6bd0c4bd501b00c16125071573c938533224992bea0b30f'] diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb index 9034563c84..2c05582ea3 100644 --- a/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb @@ -13,8 +13,6 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -exts_default_options = {'source_urls': [PYPI_SOURCE]} - use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb index 9dc227ef7a..faa6ef0376 100644 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb @@ -8,7 +8,6 @@ description = """A fast, extensible progress bar for Python and CLI""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['11d544652edbdfc9cc41aa4c8a5c166513e279f3f2d9f1a9e1c89935b51de6ff'] diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb index 87343f80b2..444c6ce3c6 100644 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb @@ -8,7 +8,6 @@ description = 'Typing Extensions – Backported and Experimental Type Hints for toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = ['typing_extensions-%(version)s.tar.gz'] checksums = ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'] diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb index 91ac3e247d..a98f29a352 100644 --- a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb @@ -13,7 +13,6 @@ of a convolutional neural network.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] From 3c654b5051d8cdd089110c084fa5938fef67ce1a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 23 Mar 2021 11:40:05 +0100 Subject: [PATCH 0559/2365] Revert changes for the Python core ECs --- easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index 8882252086..ac42a9c106 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -31,6 +31,7 @@ osdependencies = [OS_PKG_OPENSSL_DEV] exts_default_options = { 'download_dep_fail': True, 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], 'use_pip': True, } diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 80a005ae19..4371dc3f09 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -41,6 +41,7 @@ installopts = " && ln -s %(installdir)s/bin/pip3 %(installdir)s/bin/pip" exts_default_options = { 'download_dep_fail': True, 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], 'use_pip': True, } From 281599162c7d0e365a1df76b0d1d2d9171a6ad90 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 23 Mar 2021 14:56:15 +0200 Subject: [PATCH 0560/2365] updated java version+versionsuffix --- .../a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 63 +++++++++++++++++++ .../s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 10 +-- 2 files changed, 68 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..8dbd35330f --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -0,0 +1,63 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '0.17.1' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings)), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + 'http://apache.belnet.be/arrow/arrow-%(version)s/', + 'https://www-eu.apache.org/dist/arrow/arrow-%(version)s/', +] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Autotools', '20200321'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('pkg-config', '0.29.2'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('Boost', '1.74.0'), +] + +separate_build_dir = True +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/python/development.html +configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index c3f74c2564..a8b68ba100 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -1,9 +1,9 @@ +# Author: Denis Krišťák (INUITS) + easyblock = 'Tarball' name = 'Spark' version = '3.1.1' -local_python_versionsuffix = '-Python-%(pyver)s' -local_java_versionsuffix = '-Java-%(javaver)s' homepage = 'https://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" @@ -18,9 +18,9 @@ checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] dependencies = [ ('Python', '3.8.6'), - ('Java', '1.8', '', True), - ('Hadoop', '2.10.0', '-native'), - ('Arrow', '0.16.0', local_python_versionsuffix), + ('Java', '11', '', True), + # ('Hadoop', '2.10.0', '-native'), + ('Arrow', '0.17.1'), ] exts_defaultclass = 'PythonPackage' From 282fd852a88ebe38b0ebff3ee9ca8718fec0c3b7 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 23 Mar 2021 16:11:07 +0200 Subject: [PATCH 0561/2365] turn on sanity_pip_check, removed python versionsuffix --- .../libgpuarray-0.7.6-fosscuda-2020b.eb | 50 +++++++++++++++++ .../netcdf4-python-1.5.5.1-fosscuda-2020b.eb | 2 + .../p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb | 53 +++++++++++++++++++ .../PyTables/PyTables-3.6.1-fosscuda-2020b.eb | 2 + .../pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb | 37 +++++++++++++ .../pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb | 51 ++++++++++++++++++ .../Theano-1.1.2-fosscuda-2020b-PyMC.eb | 2 + .../x/xarray/xarray-0.16.2-fosscuda-2020b.eb | 2 + 8 files changed, 199 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb new file mode 100644 index 0000000000..c585aaf524 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -0,0 +1,50 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'CMakeMake' + +name = 'libgpuarray' +version = '0.7.6' + +homepage = 'http://deeplearning.net/software/libgpuarray/' +description = "Library to manipulate tensors on the GPU." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Mako', '1.1.3'), + ('NCCL', '2.8.3', '-CUDA-11.1.1', True), +] + +build_type = 'Release' + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} +exts_list = [ + (name, version, { + 'buildcmd': 'build_ext', + 'modulename': 'pygpu', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], + 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgpuarray.%s' % SHLIB_EXT, 'lib/libgpuarray-static.a'], + 'dirs': ['include/gpuarray', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb index b91d0032cf..a16fa1c427 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb @@ -1,3 +1,5 @@ +# Author: Denis Krišťák (INUITS) + easyblock = 'PythonBundle' name = 'netcdf4-python' diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..9de026b36b --- /dev/null +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb @@ -0,0 +1,53 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyMC3' +version = '3.11.1' + +homepage = 'https://docs.pymc.io/' +description = """Probabilistic Programming in Python: +Bayesian Modeling and Probabilistic Machine Learning with Theano""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('Theano', '1.1.2', '-PyMC'), + ('matplotlib', '3.3.3'), + ('h5py', '3.1.0'), + ('tqdm', '4.56.2'), + ('netcdf4-python', '1.5.5.1'), + ('xarray', '0.16.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('typing_extensions', '3.7.4.3', { + 'checksums': ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'], + }), + ('arviz', '0.11.1', { + 'checksums': ['bb0730ab62223a44ec99072b12f9e9f24521a36e6b7ba2624df9f9908eba1d82'], + }), + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + ('dill', '0.3.3', { + 'source_tmpl': 'dill-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('fastprogress', '1.0.0', { + 'checksums': ['89e28ac1d2a5412aab18ee3f3dfd1ee8b5c1f2f7a44d0add0d0d4f69f0191bfe'], + }), + ('pymc3', version, { + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + 'checksums': ['501d48b9f5d033678de7a5918b9d055a6806adf84fe16a5a9d65eaa2dc71acd8'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb index c7970b0bda..3213dd286e 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb @@ -1,3 +1,5 @@ +# Author: Denis Krišťák (INUITS) + easyblock = 'PythonPackage' name = 'PyTables' diff --git a/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..9446b6a61d --- /dev/null +++ b/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb @@ -0,0 +1,37 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'pyro-api' +version = '0.1.2' + +homepage = 'https://bitbucket.org/petsc/petsc4py' +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'pyroapi'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'from pyroapi import distributions as dist'", + "python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'" +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..5de019d038 --- /dev/null +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb @@ -0,0 +1,51 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'pyro-ppl' +version = '1.5.2' + +homepage = 'https://bitbucket.org/petsc/petsc4py' +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8a93af3a007ac507a8b50fd1165dbb355182d17df29d3b5bc498b02b479fdb27'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('pyro-api', '0.1.2'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), +] + +download_dep_fail = True +use_pip = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), +] + +options = {'modulename': 'pyro'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb index fe599301e3..cfde98335b 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb @@ -1,3 +1,5 @@ +# Author: Denis Krišťák (INUITS) + easyblock = 'PythonPackage' name = 'Theano' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb index 29b10a1398..0496a7fe61 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb @@ -1,3 +1,5 @@ +# Author: Denis Krišťák (INUITS) + easyblock = 'PythonPackage' name = 'xarray' From 0be13e94ab54a89b150ede8b1294ca7c44eb1163 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 23 Mar 2021 16:35:46 +0200 Subject: [PATCH 0562/2365] turn on sanity_pip_check, removed python versionsuffix --- .../easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb | 4 ++-- .../easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb | 4 ++-- .../easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb index 9446b6a61d..6785b9e1a1 100644 --- a/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb @@ -5,8 +5,8 @@ easyblock = 'PythonPackage' name = 'pyro-api' version = '0.1.2' -homepage = 'https://bitbucket.org/petsc/petsc4py' -description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." +homepage = 'https://github.com/pyro-ppl/pyro-api' +description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch." toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb index 5de019d038..b2cf1dd9eb 100644 --- a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb @@ -5,8 +5,8 @@ easyblock = 'PythonPackage' name = 'pyro-ppl' version = '1.5.2' -homepage = 'https://bitbucket.org/petsc/petsc4py' -description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." +homepage = 'https://github.com/pyro-ppl/pyro' +description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch." toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb index cfde98335b..cb87a9010a 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb @@ -18,7 +18,7 @@ checksums = ['5da6c2242ea72a991c8446d7fe7d35189ea346ef7d024c890397011114bf10fc'] dependencies = [ ('Python', '3.8.6'), - ('libgpuarray', '0.7.6', '-Python-3.8.6'), + ('libgpuarray', '0.7.6'), ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), ('SciPy-bundle', '2020.11'), ] From e6c65eeb577fd0907573fc1527e4d0e8df54fe14 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 23 Mar 2021 16:33:52 +0100 Subject: [PATCH 0563/2365] Use pip to install pkgconfig 1.5.1 --- .../p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb index de70590971..f7ba3e761c 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb @@ -20,8 +20,8 @@ dependencies = [ ('pkg-config', '0.29.2'), ] -# Due to poetry doing the actual build of pkgconfig we need use_pip=False -use_pip = False +use_pip = True download_dep_fail = True +sanity_pip_check = True moduleclass = 'devel' From e69b36219bbf34d1b76071e083d061ae6fbc80e2 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 23 Mar 2021 17:41:10 +0200 Subject: [PATCH 0564/2365] changes acc. to tests --- .../r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb | 2 ++ .../s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb b/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb index d017c751df..a7e257c4ff 100644 --- a/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb +++ b/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb @@ -1,3 +1,5 @@ +# Author: Denis Krišťák (INUITS) + easyblock = 'Binary' name = 'request' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb index a4311e6cf5..b2aa71b3e1 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb @@ -1,3 +1,5 @@ +# Author: Denis Krišťák (INUITS) + easyblock = 'PythonBundle' name = 'statsmodels' From 3def1546244fbeb870c226229ba3fbe074e4dd82 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 23 Mar 2021 17:46:27 +0200 Subject: [PATCH 0565/2365] changes acc. to tests --- .../Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb | 27 ++++++++++++++ .../umap-learn-0.4.6-fosscuda-2020b.eb | 37 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..e87b55d020 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb @@ -0,0 +1,27 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.11.1' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb new file mode 100644 index 0000000000..9850c3ee38 --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb @@ -0,0 +1,37 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'umap-learn' +version = '0.4.6' + +homepage = 'https://pypi.org/project/umap-learn/' +description = """Uniform Manifold Approximation and Projection (UMAP) is a +dimension reduction technique that can be used for visualisation similarly to t-SNE, +but also for general non-linear dimension reduction.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('numba', '0.52.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'umap'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 0c57e209828bca54b4b872fb052d49a69e42be86 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 23 Mar 2021 17:07:11 +0100 Subject: [PATCH 0566/2365] Revert change for pkgconfig due to pip issue --- .../p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb index 58bed1af99..de70590971 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb @@ -9,6 +9,7 @@ description = """pkgconfig is a Python module to interface with the pkg-config c toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f'] From a9da855c736b336b8dce52626a2fdae74c50be8a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 23 Mar 2021 19:11:59 +0200 Subject: [PATCH 0567/2365] adding easyconfigs: SIMPLE-3.0.0-foss-2020b.eb --- .../s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb new file mode 100644 index 0000000000..b09d8da89c --- /dev/null +++ b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb @@ -0,0 +1,73 @@ +#Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/03 +easyblock = 'CMakeMake' + +name = 'SIMPLE' +version = '3.0.0' + +homepage = 'http://simplecryoem.com/' +description = """Single-particle IMage Processing Linux Engine SIMPLE is an open-source software +package for analysis of cryogenic transmission electron microscopy (cryo-EM) +movies of single-particles (Single-Particle Analysis, SPA).""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts={'openmp': True, 'opt': True} + +source_urls=[GITHUB_SOURCE] +github_account='hael' +sources = ["v%(version)s.tar.gz"] +checksums = ['9cf98d042b918170e3a9b92148c7081d35e0ef1c9fa8b6ea16cf2bd476945dd7'] + +builddependencies = [('CMake', '3.18.4')] +dependencies=[ +('XZ','5.2.5'), +('LibTIFF','4.1.0'), +('jbigkit','2.1'), +] +preconfigopts="" +preconfigopts+='sed -i "s/unset (OpenMP_Fortran_FLAGS CACHE)/#&/g" ../*/cmake/Modules/ZSetParallelLibrary.cmake &&' #Avoid calling FindOpenMP_Fortran.cmake. + +configopts=" -DFFTW_DIR=$EBROOTFFTW " +configopts+="-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include " +configopts+="-DJBIG_LIBRARY=$EBROOTJBIGKIT/lib/libjbig.so " +configopts+="-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib64/libjpeg.so " +configopts+="-DLZMA_LIBRARY=$EBROOTXZ/lib/liblzma.so " +configopts+="-DUSE_OPENMP=ON " +configopts+="-DUSE_MPI=OFF " +configopts+="-DSIMPLE_BUILD_TESTS=ON " +configopts+="-DOpenMP_Fortran_FLAGS=$CFLAGS " +configopts+="-DCMAKE_SHARED_LINKER_FLAGS=-fopenmp " +configopts=[configopts+'-DBUILD_SHARED_LIBS=OFF',configopts+'-DBUILD_SHARED_LIBS=ON'] + +buildopts='all single_exec' +separate_build_dir = True + +modextravars = { + 'SIMPLE_QSYS': 'local', + 'SIMPLE_PATH': '%(installdir)s', + 'SIMPLE_EMAIL': "my.name@uni.edu" +} + +modextrapaths = {'PATH': 'scripts'} + +postinstallcmds=[ #move some stuff and clean up +"cp %(builddir)s/easybuild*/bin/{simple*,single_exec,quant_exec} %(installdir)s/bin/ -pP " +"&& cp -rpP %(builddir)s/easybuild*/{gui_data,tutorials}/ %(installdir)s " +'&& rm -rf %(installdir)s/bin/simple_test_*' +'&& cp %(builddir)s/SIMPLE*/{doc,LICENSE,src/inc} %(installdir)s -rpP' +'&& cd %(installdir)s/lib && ln -s libSIMPLE%(version)s.so libSIMPLE.so' +] +docpaths=["doc"] +runtest='test' +runtest=False +pretestopts='. add2.bashrc && export LD_LIBRARY_PATH=%(builddir)s/lib:$LD_LIBRARY_PATH && ' +sanity_check_paths = { + 'files': ['LICENSE', + 'bin/simple_exec','bin/simple', + 'lib/libSIMPLE%(version)s.a', + 'lib/libSIMPLE%s.%s' % (version,SHLIB_EXT), + 'lib/simple/simple_varlist.txt'], + 'dirs': ['scripts','doc','inc','gui_data'] +} + + +moduleclass = 'bio' From cd875f7e6a62a8cf06971b887630df0d19182603 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 23 Mar 2021 19:40:48 +0200 Subject: [PATCH 0568/2365] Fix tests --- .../easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb index b09d8da89c..a868ea394e 100644 --- a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb @@ -10,7 +10,7 @@ package for analysis of cryogenic transmission electron microscopy (cryo-EM) movies of single-particles (Single-Particle Analysis, SPA).""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts={'openmp': True, 'opt': True} +toolchainopts={'openmp': True, 'opt': False} #simple_test_units fails with opt=True source_urls=[GITHUB_SOURCE] github_account='hael' @@ -51,22 +51,22 @@ modextrapaths = {'PATH': 'scripts'} postinstallcmds=[ #move some stuff and clean up "cp %(builddir)s/easybuild*/bin/{simple*,single_exec,quant_exec} %(installdir)s/bin/ -pP " -"&& cp -rpP %(builddir)s/easybuild*/{gui_data,tutorials}/ %(installdir)s " +"&& cp -rpP %(builddir)s/easybuild*/gui_data/ %(installdir)s " '&& rm -rf %(installdir)s/bin/simple_test_*' '&& cp %(builddir)s/SIMPLE*/{doc,LICENSE,src/inc} %(installdir)s -rpP' '&& cd %(installdir)s/lib && ln -s libSIMPLE%(version)s.so libSIMPLE.so' ] docpaths=["doc"] runtest='test' -runtest=False -pretestopts='. add2.bashrc && export LD_LIBRARY_PATH=%(builddir)s/lib:$LD_LIBRARY_PATH && ' +#runtest=False +pretestopts='. add2.bashrc && export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:$LD_LIBRARY_PATH && ' sanity_check_paths = { 'files': ['LICENSE', 'bin/simple_exec','bin/simple', 'lib/libSIMPLE%(version)s.a', 'lib/libSIMPLE%s.%s' % (version,SHLIB_EXT), 'lib/simple/simple_varlist.txt'], - 'dirs': ['scripts','doc','inc','gui_data'] + 'dirs': ['scripts','doc','inc','gui_data','tutorials'] } From 5f91becb9328d0f68cebcd9464654ab6e6b8d4c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Mar 2021 19:56:40 +0100 Subject: [PATCH 0569/2365] adding easyconfigs: VTK-9.0.1-foss-2020b.eb --- .../easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 101 ++++++++++++++++++ 1 file changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb new file mode 100644 index 0000000000..a772a853ae --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -0,0 +1,101 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '9.0.1' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + '1b39a5e191c282861e7af4101eaa8585969a2de05f5646c9199a161213a622c7', # VTK-9.0.1.tar.gz + '3f8bfdadd66e0b541bc5580340481abf92bec100b09d787283632ab590b1ce1c', # VTKData-9.0.1.tar.gz + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('XZ', '5.2.5'), + ('HDF5', '1.10.7'), + ('netCDF', '4.7.4'), + ('libGLU', '9.0.1'), + ('X11', '20201008'), +] + +separate_build_dir = True + +# Third party modules +configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " +configopts += "-DVTK_USE_SYSTEM_LZMA=ON " +configopts += "-DVTK_USE_SYSTEM_HDF5=ON " +configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " +configopts += "-DVTK_USE_SYSTEM_PNG=ON " +# OpenGL +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON " +# note: specifying full Python version leads to problems (see https://gitlab.kitware.com/vtk/vtk/-/issues/17934) +configopts += "-DVTK_PYTHON_VERSION=3 " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +# Other +configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + ('python', "-c 'import %(namelower)s'"), + ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), +] + + +moduleclass = 'vis' From edaa78018117324a6c9fa4cdd7eb138b0d76820f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Mar 2021 21:05:43 +0100 Subject: [PATCH 0570/2365] {bio}[foss/2020b] carputils v20210322, openCARP v5.0, meshtool v16, meshalyzer v2.2 w/ Python 3.8.6 --- .../freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb | 43 +++++++++++++++++++ .../gengetopt-2.23-GCCcore-10.2.0.eb | 27 ++++++++++++ .../g/glew/glew-2.1.0-GCCcore-10.2.0.eb | 36 ++++++++++++++++ .../m/meshalyzer/meshalyzer-2.2-foss-2020b.eb | 41 ++++++++++++++++++ .../m/meshtool/meshtool-16-GCC-10.2.0.eb | 25 +++++++++++ 5 files changed, 172 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/meshalyzer/meshalyzer-2.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2896975b44 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.2.1' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['freeglut-%(version)s_fix-GCC-10.patch'] +checksums = [ + 'd4000e02102acaf259998c870e25214739d1f16f67f99cb35e4f46841399da68', # freeglut-3.2.1.tar.gz + '9c7b0f7131fe550f828415f984eb8e25d8e0a897005f3bfbe1437c4c5259a0e5', # freeglut-3.2.1_fix-GCC-10.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..27bd0e0e7a --- /dev/null +++ b/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'gengetopt' +version = '2.23' + +homepage = 'https://www.gnu.org/software/gengetopt/gengetopt.html' +description = "Gengetopt is a tool to write command line option parsing code for C programs." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['b941aec9011864978dd7fdeb052b1943535824169d2aa2b0e7eae9ab807584ac'] + +builddependencies = [ + ('binutils', '2.35'), + ('makeinfo', '6.7'), +] + +sanity_check_paths = { + 'files': ['bin/gengetopt'], + 'dirs': ['share'], +} + +sanity_check_commands = ["gengetopt --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bee02ca561 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'glew' +version = '2.1.0' + +homepage = 'http://glew.sourceforge.net/' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Mesa', '20.2.1')] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all' + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': ['', ] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/meshalyzer/meshalyzer-2.2-foss-2020b.eb b/easybuild/easyconfigs/m/meshalyzer/meshalyzer-2.2-foss-2020b.eb new file mode 100644 index 0000000000..04d794caa9 --- /dev/null +++ b/easybuild/easyconfigs/m/meshalyzer/meshalyzer-2.2-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'meshalyzer' +version = '2.2' + +homepage = 'https://git.opencarp.org/openCARP/meshalyzer' +description = "Graphical program for display time dependent data on 3D finite elment meshes" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://git.opencarp.org/openCARP/%(name)s/-/archive/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['meshalyzer-2.0_fix-VTK-linking.patch'] +checksums = [ + '635a4d6a5febfaabc9792a3bbde0215d1b838d342d428e29487be3efc5dc595b', # meshalyzer-2.2.tar.gz + '23f55c2290ea9b62440bdf8e0c1006116438beb7c4b7065b8cf136387a537e0f', # meshalyzer-2.0_fix-VTK-linking.patch +] + +local_vtk_majmin_ver = '9.0' +dependencies = [ + ('libpng', '1.6.37'), + ('FLTK', '1.3.5'), + ('glew', '2.1.0'), + ('freeglut', '3.2.1'), + ('HDF5', '1.10.7'), + ('VTK', '%s.1' % local_vtk_majmin_ver), +] + +buildopts = 'HDF5_ROOT=$EBROOTHDF5 LIB_EXT=".so" ' +buildopts += 'VTK_INCDIR=$EBROOTVTK/include/vtk-%s/ VTK_LIBDIR=$EBROOTVTK/lib' % local_vtk_majmin_ver + +files_to_copy = [(['meshalyzer'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/meshalyzer'], + 'dirs': [], +} + +sanity_check_commands = ["meshalyzer --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb b/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb new file mode 100644 index 0000000000..cc3f7d844b --- /dev/null +++ b/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'meshtool' +version = '16' + +homepage = 'https://bitbucket.org/aneic/meshtool' +description = """Meshtool is a comand-line tool written in C++. It is designed to apply various manipulations to +volumetric meshes.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://bitbucket.org/aneic/meshtool/get/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['822e715b363603dfe320b4b530ad4a77cc5ecd0ccb692d77e01b6ecfe7da9d38'] + +files_to_copy = [(['meshtool'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/meshtool'], + 'dirs': [], +} + +sanity_check_commands = ["meshtool help"] + +moduleclass = 'tools' From 978d2de8a22f3e3025db8e6be1a7fdc75257c863 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 24 Mar 2021 11:39:53 +0200 Subject: [PATCH 0571/2365] fix style --- .../s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb | 91 ++++++++++--------- 1 file changed, 49 insertions(+), 42 deletions(-) diff --git a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb index a868ea394e..b29c83f032 100644 --- a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb @@ -1,4 +1,4 @@ -#Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/03 +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/03 easyblock = 'CMakeMake' name = 'SIMPLE' @@ -10,64 +10,71 @@ package for analysis of cryogenic transmission electron microscopy (cryo-EM) movies of single-particles (Single-Particle Analysis, SPA).""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts={'openmp': True, 'opt': False} #simple_test_units fails with opt=True +toolchainopts = {'openmp': True, 'opt': False} # simple_test_units fails with opt=True -source_urls=[GITHUB_SOURCE] -github_account='hael' +source_urls = [GITHUB_SOURCE] +github_account = 'hael' sources = ["v%(version)s.tar.gz"] checksums = ['9cf98d042b918170e3a9b92148c7081d35e0ef1c9fa8b6ea16cf2bd476945dd7'] builddependencies = [('CMake', '3.18.4')] -dependencies=[ -('XZ','5.2.5'), -('LibTIFF','4.1.0'), -('jbigkit','2.1'), -] -preconfigopts="" -preconfigopts+='sed -i "s/unset (OpenMP_Fortran_FLAGS CACHE)/#&/g" ../*/cmake/Modules/ZSetParallelLibrary.cmake &&' #Avoid calling FindOpenMP_Fortran.cmake. - -configopts=" -DFFTW_DIR=$EBROOTFFTW " -configopts+="-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include " -configopts+="-DJBIG_LIBRARY=$EBROOTJBIGKIT/lib/libjbig.so " -configopts+="-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib64/libjpeg.so " -configopts+="-DLZMA_LIBRARY=$EBROOTXZ/lib/liblzma.so " -configopts+="-DUSE_OPENMP=ON " -configopts+="-DUSE_MPI=OFF " -configopts+="-DSIMPLE_BUILD_TESTS=ON " -configopts+="-DOpenMP_Fortran_FLAGS=$CFLAGS " -configopts+="-DCMAKE_SHARED_LINKER_FLAGS=-fopenmp " -configopts=[configopts+'-DBUILD_SHARED_LIBS=OFF',configopts+'-DBUILD_SHARED_LIBS=ON'] - -buildopts='all single_exec' +dependencies = [ + ('XZ', '5.2.5'), + ('LibTIFF', '4.1.0'), + ('jbigkit', '2.1'), ] + +# Avoid using problematic FindOpenMP_Fortran.cmake; +# Instead OpenMP_Fortran_FLAGS will be set in configopts. +preconfigopts = 'sed -i "s/unset (OpenMP_Fortran_FLAGS CACHE)/#&/g" ../*/cmake/Modules/ZSetParallelLibrary.cmake &&' + +configopts = " -DFFTW_DIR=$EBROOTFFTW " +configopts += "-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include " +configopts += "-DJBIG_LIBRARY=$EBROOTJBIGKIT/lib/libjbig.so " +configopts += "-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib64/libjpeg.so " +configopts += "-DLZMA_LIBRARY=$EBROOTXZ/lib/liblzma.so " +configopts += "-DUSE_OPENMP=ON " +configopts += "-DUSE_MPI=OFF " +configopts += "-DSIMPLE_BUILD_TESTS=ON " +configopts += "-DOpenMP_Fortran_FLAGS=$CFLAGS " +configopts += "-DCMAKE_SHARED_LINKER_FLAGS=-fopenmp " +configopts = [configopts + '-DBUILD_SHARED_LIBS=OFF', configopts + '-DBUILD_SHARED_LIBS=ON'] + +buildopts = 'all single_exec' separate_build_dir = True modextravars = { 'SIMPLE_QSYS': 'local', 'SIMPLE_PATH': '%(installdir)s', - 'SIMPLE_EMAIL': "my.name@uni.edu" + 'SIMPLE_EMAIL': "my.name@uni.edu" } modextrapaths = {'PATH': 'scripts'} -postinstallcmds=[ #move some stuff and clean up -"cp %(builddir)s/easybuild*/bin/{simple*,single_exec,quant_exec} %(installdir)s/bin/ -pP " -"&& cp -rpP %(builddir)s/easybuild*/gui_data/ %(installdir)s " -'&& rm -rf %(installdir)s/bin/simple_test_*' -'&& cp %(builddir)s/SIMPLE*/{doc,LICENSE,src/inc} %(installdir)s -rpP' -'&& cd %(installdir)s/lib && ln -s libSIMPLE%(version)s.so libSIMPLE.so' -] -docpaths=["doc"] -runtest='test' -#runtest=False -pretestopts='. add2.bashrc && export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:$LD_LIBRARY_PATH && ' +postinstallcmds = [ + # "make install" misses some required directories. + "cp %(builddir)s/easybuild_obj/bin/{simple*,single_exec,quant_exec} %(installdir)s/bin/ -pP " + "&& cp -rpP %(builddir)s/easybuild_obj/{gui_data,tutorials}/ %(installdir)s " + '&& cp %(builddir)s/SIMPLE*/{doc,LICENSE,src/inc} %(installdir)s -rpP' + '&& cd %(installdir)s/lib && ln -s libSIMPLE%(version)s.so libSIMPLE.so' + # "test binaries are only required for "make test". + '&& rm -rf %(installdir)s/bin/simple_test_*'] + + +runtest = 'test' +# required for shared build tests: +pretestopts = '. add2.bashrc && export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:$LD_LIBRARY_PATH && ' + sanity_check_paths = { 'files': ['LICENSE', - 'bin/simple_exec','bin/simple', - 'lib/libSIMPLE%(version)s.a', - 'lib/libSIMPLE%s.%s' % (version,SHLIB_EXT), - 'lib/simple/simple_varlist.txt'], - 'dirs': ['scripts','doc','inc','gui_data','tutorials'] + 'bin/simple_exec', + 'bin/simple', + 'lib/libSIMPLE%(version)s.a', + 'lib/libSIMPLE%s.%s' % (version, SHLIB_EXT), + 'lib/simple/simple_varlist.txt'], + 'dirs': ['scripts', 'gui_data', 'tutorials', # req. at runtime + 'doc', 'inc', ] } +docpaths = ["doc"] moduleclass = 'bio' From a6fb953dac497fc317db9c3991caac6658dd1cea Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 24 Mar 2021 12:02:05 +0200 Subject: [PATCH 0572/2365] fix hompage URL to https --- easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb index b29c83f032..ad6d123006 100644 --- a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb @@ -4,7 +4,7 @@ easyblock = 'CMakeMake' name = 'SIMPLE' version = '3.0.0' -homepage = 'http://simplecryoem.com/' +homepage = 'https://simplecryoem.com/' description = """Single-particle IMage Processing Linux Engine SIMPLE is an open-source software package for analysis of cryogenic transmission electron microscopy (cryo-EM) movies of single-particles (Single-Particle Analysis, SPA).""" From 67c255c39e1a2033c4025b59e5aeab1d34895e35 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 24 Mar 2021 12:28:36 +0200 Subject: [PATCH 0573/2365] fix redefinition of configopts --- .../s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb index ad6d123006..88f6ba8acf 100644 --- a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb @@ -27,17 +27,17 @@ dependencies = [ # Instead OpenMP_Fortran_FLAGS will be set in configopts. preconfigopts = 'sed -i "s/unset (OpenMP_Fortran_FLAGS CACHE)/#&/g" ../*/cmake/Modules/ZSetParallelLibrary.cmake &&' -configopts = " -DFFTW_DIR=$EBROOTFFTW " -configopts += "-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include " -configopts += "-DJBIG_LIBRARY=$EBROOTJBIGKIT/lib/libjbig.so " -configopts += "-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib64/libjpeg.so " -configopts += "-DLZMA_LIBRARY=$EBROOTXZ/lib/liblzma.so " -configopts += "-DUSE_OPENMP=ON " -configopts += "-DUSE_MPI=OFF " -configopts += "-DSIMPLE_BUILD_TESTS=ON " -configopts += "-DOpenMP_Fortran_FLAGS=$CFLAGS " -configopts += "-DCMAKE_SHARED_LINKER_FLAGS=-fopenmp " -configopts = [configopts + '-DBUILD_SHARED_LIBS=OFF', configopts + '-DBUILD_SHARED_LIBS=ON'] +local_configopts = " -DFFTW_DIR=$EBROOTFFTW " +local_configopts += "-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include " +local_configopts += "-DJBIG_LIBRARY=$EBROOTJBIGKIT/lib/libjbig.so " +local_configopts += "-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib64/libjpeg.so " +local_configopts += "-DLZMA_LIBRARY=$EBROOTXZ/lib/liblzma.so " +local_configopts += "-DUSE_OPENMP=ON " +local_configopts += "-DUSE_MPI=OFF " +local_configopts += "-DSIMPLE_BUILD_TESTS=ON " +local_configopts += "-DOpenMP_Fortran_FLAGS=$CFLAGS " +local_configopts += "-DCMAKE_SHARED_LINKER_FLAGS=-fopenmp " +configopts = [local_configopts + '-DBUILD_SHARED_LIBS=OFF', local_configopts + '-DBUILD_SHARED_LIBS=ON'] buildopts = 'all single_exec' separate_build_dir = True From 46f3f8dd2abf071e2f0594a2f9641b51a0b455dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Mar 2021 16:27:59 +0100 Subject: [PATCH 0574/2365] adding easyconfigs: Clang-11.0.1-gcccuda-2020b.eb --- .../c/Clang/Clang-11.0.1-gcccuda-2020b.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb new file mode 100644 index 0000000000..ef7462a07f --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb @@ -0,0 +1,71 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '11.0.1' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'gcccuda', 'version': '2020b'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', + 'clang-tools-extra-%(version)s.src.tar.xz', +] +checksums = [ + 'ccd87c254b6aebc5077e4e6977d08d4be888e7eb672c6630a26a15d58b59b528', # llvm-11.0.1.src.tar.xz + '73f572c2eefc5a155e01bcd84815751d722a4d3925f53c144acfb93eeb274b4d', # clang-11.0.1.src.tar.xz + '087be3f1116e861cd969c9b0b0903c27028b52eaf45157276f50a9c2500687fc', # compiler-rt-11.0.1.src.tar.xz + '08dfce0e7b168d621f6c64b6b60a25300acb9337345ab0014c4f64a053c5b9ea', # polly-11.0.1.src.tar.xz + '4d15a21b90e7de2f01296503f6e4b16c50197fbe9c82e7e81f9c07e28bd82ca7', # openmp-11.0.1.src.tar.xz + '60ba0da01a391078dcc437fee629f3bf7e30e06467a3a060b4a2a3aa661308b7', # lld-11.0.1.src.tar.xz + '9fd5f669621ffea88a2b93e3d99f3a958b5defb954f71bf754709b63275f5e3d', # libcxx-11.0.1.src.tar.xz + '4a697056a5c08621a8380dcaf3836525835aa76b3008d9e8f27abf9270bf683f', # libcxxabi-11.0.1.src.tar.xz + '2ca211dd8cc396a919709a9bc35af11b7d425df0c608d85ba6629242893516c9', # clang-tools-extra-11.0.1.src.tar.xz +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.35'), + ('hwloc', '2.2.0'), + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), + ('GMP', '6.2.0'), + ('Z3', '4.8.10'), +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Python', '3.8.6'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True +build_extra_clang_tools = True + +skip_all_tests = True + +moduleclass = 'compiler' From f6c0fdf743462ec79220013a032d85fdc0a3e687 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 24 Mar 2021 18:30:56 +0200 Subject: [PATCH 0575/2365] replace .so by SHLIB_EXT --- .../easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb index 88f6ba8acf..c0bbf80440 100644 --- a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb @@ -29,9 +29,9 @@ preconfigopts = 'sed -i "s/unset (OpenMP_Fortran_FLAGS CACHE)/#&/g" ../*/cmake/M local_configopts = " -DFFTW_DIR=$EBROOTFFTW " local_configopts += "-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include " -local_configopts += "-DJBIG_LIBRARY=$EBROOTJBIGKIT/lib/libjbig.so " -local_configopts += "-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib64/libjpeg.so " -local_configopts += "-DLZMA_LIBRARY=$EBROOTXZ/lib/liblzma.so " +local_configopts += "-DJBIG_LIBRARY=$EBROOTJBIGKIT/lib/libjbig.%s " % SHLIB_EXT +local_configopts += "-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib64/libjpeg.%s " % SHLIB_EXT +local_configopts += "-DLZMA_LIBRARY=$EBROOTXZ/lib/liblzma.%s " % SHLIB_EXT local_configopts += "-DUSE_OPENMP=ON " local_configopts += "-DUSE_MPI=OFF " local_configopts += "-DSIMPLE_BUILD_TESTS=ON " @@ -55,9 +55,9 @@ postinstallcmds = [ "cp %(builddir)s/easybuild_obj/bin/{simple*,single_exec,quant_exec} %(installdir)s/bin/ -pP " "&& cp -rpP %(builddir)s/easybuild_obj/{gui_data,tutorials}/ %(installdir)s " '&& cp %(builddir)s/SIMPLE*/{doc,LICENSE,src/inc} %(installdir)s -rpP' - '&& cd %(installdir)s/lib && ln -s libSIMPLE%(version)s.so libSIMPLE.so' + + '&& cd %(installdir)s/lib ' + '&& ln -s libSIMPLE%s.%s libSIMPLE.%s' % (version, SHLIB_EXT, SHLIB_EXT) # "test binaries are only required for "make test". - '&& rm -rf %(installdir)s/bin/simple_test_*'] + + '&& rm -rf %(installdir)s/bin/simple_test_*'] runtest = 'test' From 066ebffe6862d84d0b92c7dbc8873df9072404a7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 24 Mar 2021 16:57:42 +0000 Subject: [PATCH 0576/2365] Update SIMPLE-3.0.0-foss-2020b.eb Remove unnecessary plus signs --- easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb index c0bbf80440..4cded3c94b 100644 --- a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb @@ -55,9 +55,9 @@ postinstallcmds = [ "cp %(builddir)s/easybuild_obj/bin/{simple*,single_exec,quant_exec} %(installdir)s/bin/ -pP " "&& cp -rpP %(builddir)s/easybuild_obj/{gui_data,tutorials}/ %(installdir)s " '&& cp %(builddir)s/SIMPLE*/{doc,LICENSE,src/inc} %(installdir)s -rpP' - + '&& cd %(installdir)s/lib ' + '&& ln -s libSIMPLE%s.%s libSIMPLE.%s' % (version, SHLIB_EXT, SHLIB_EXT) + '&& cd %(installdir)s/lib ' + '&& ln -s libSIMPLE%s.%s libSIMPLE.%s' % (version, SHLIB_EXT, SHLIB_EXT) # "test binaries are only required for "make test". - + '&& rm -rf %(installdir)s/bin/simple_test_*'] + '&& rm -rf %(installdir)s/bin/simple_test_*'] runtest = 'test' From bbaa6ba1a8f9c20173f0e8450e14844bcdf3bb18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Mar 2021 18:21:49 +0100 Subject: [PATCH 0577/2365] {bio}[GCC/10.2.0,iccifort/2020.4.304] pybedtools v0.8.2 + BEDTools v2.30.0 w/ Python 3.8.6 --- .../b/BEDTools/BEDTools-2.30.0-GCC-10.2.0.eb | 43 +++++++++++++++++++ .../BEDTools-2.30.0-iccifort-2020.4.304.eb | 43 +++++++++++++++++++ .../BamTools-2.5.1-iccifort-2020.4.304.eb | 21 +++++++++ .../pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb | 26 +++++++++++ .../pybedtools-0.8.2-iccifort-2020.4.304.eb | 26 +++++++++++ 5 files changed, 159 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..ba9d1d085d --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-10.2.0.eb @@ -0,0 +1,43 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.30.0' + +homepage = "https://bedtools.readthedocs.io/" +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8'] + +builddependencies = [('Python', '3.8.6')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.1'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..4564f1bb57 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-iccifort-2020.4.304.eb @@ -0,0 +1,43 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.30.0' + +homepage = "https://bedtools.readthedocs.io/" +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8'] + +builddependencies = [('Python', '3.8.6')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.1'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..ad901666a4 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb @@ -0,0 +1,21 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'BamTools' +version = '2.5.1' + +homepage = 'https://github.com/pezmaster31/%(namelower)s' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pezmaster31/bamtools/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..bbc0a46ba7 --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pybedtools' +version = '0.8.2' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['a184a36099458627e7ef52ea88218f7c00dc9c505b4256ece9ede58b1efa8771'] + +dependencies = [ + ('Python', '3.8.6'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.16.0.1'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..e95f035888 --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pybedtools' +version = '0.8.2' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['a184a36099458627e7ef52ea88218f7c00dc9c505b4256ece9ede58b1efa8771'] + +dependencies = [ + ('Python', '3.8.6'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.16.0.1'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' From c8241a0787df3d45a9d79acd5f575c3c0b0c973a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Mar 2021 18:25:06 +0100 Subject: [PATCH 0578/2365] adding easyconfigs: SAMtools-1.11-iccifort-2020.4.304.eb, HTSlib-1.11-iccifort-2020.4.304.eb --- .../HTSlib/HTSlib-1.11-iccifort-2020.4.304.eb | 37 +++++++++++++++++++ .../SAMtools-1.11-iccifort-2020.4.304.eb | 35 ++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.11-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.11-iccifort-2020.4.304.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.11-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..6716a07996 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.11-iccifort-2020.4.304.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.11' + +homepage = "https://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['cffadd9baa6fce27b8fe0b01a462b489f06a5433dfe92121f667f40f632538d7'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.72.0'), +] + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..1c73a42bfa --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb @@ -0,0 +1,35 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +## + +name = 'SAMtools' +version = '1.11' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['e283cebd6c1c49f0cf8a3ca4fa56e1d651496b4d2e42f80ab75991a9ece4e5b6'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.72.0'), +] + +moduleclass = 'bio' From 9f7dbe5d6d8a08da93b8797298f4ef5b8b9a0d58 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Mar 2021 18:31:08 +0100 Subject: [PATCH 0579/2365] remove source_urls from pybedtools 0.8.2 easyconfigs, no longer needed (used by default now in PythonPackage) --- .../easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb | 1 - .../p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb index bbc0a46ba7..c37bdeea0d 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb @@ -8,7 +8,6 @@ description = "pybedtools wraps and extends BEDTools and offers feature-level ma toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a184a36099458627e7ef52ea88218f7c00dc9c505b4256ece9ede58b1efa8771'] diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb index e95f035888..33f837b9ad 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb @@ -8,7 +8,6 @@ description = "pybedtools wraps and extends BEDTools and offers feature-level ma toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a184a36099458627e7ef52ea88218f7c00dc9c505b4256ece9ede58b1efa8771'] From 7868a218f39985eebbc66281bc048df4e8010576 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Mar 2021 18:32:23 +0100 Subject: [PATCH 0580/2365] adding easyconfigs: Kent_tools-411-GCC-10.2.0.eb --- .../k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb new file mode 100644 index 0000000000..f9110e0bf8 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '411' + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +checksums = ['17e0562aceeca488fddf1ec83a4de933ac43ba45eeeaedd0e5070a7fb3a000e7'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +dependencies = [ + ('MariaDB', '10.5.8'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('util-linux', '2.36'), +] + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'bio' From ee10c47ad73f35ce2500ac96c138a90e9f3923c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Mar 2021 18:33:33 +0100 Subject: [PATCH 0581/2365] adding easyconfigs: segemehl-0.3.4-GCC-10.2.0.eb --- .../s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..cfa7f2dfd9 --- /dev/null +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = "segemehl" +version = "0.3.4" + +homepage = 'https://www.bioinf.uni-leipzig.de/Software/segemehl/' +description = """segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping + and split read mapping.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] + +dependencies = [ + ('HTSlib', '1.11'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +buildopts = 'all' + +files_to_copy = [(["haarz.x", "segemehl.x"], "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["haarz.x", "segemehl.x"]], + 'dirs': [] +} + +moduleclass = 'bio' From 17a7f4fd0003542e8d8b35a600e4139dba8c850d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Mar 2021 18:34:04 +0100 Subject: [PATCH 0582/2365] adding easyconfigs: segemehl-0.3.4-iccifort-2020.4.304.eb --- .../segemehl-0.3.4-iccifort-2020.4.304.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..7a0308a476 --- /dev/null +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = "segemehl" +version = "0.3.4" + +homepage = 'https://www.bioinf.uni-leipzig.de/Software/segemehl/' +description = """segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping + and split read mapping.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] + +dependencies = [ + ('HTSlib', '1.11'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +buildopts = 'all' + +files_to_copy = [(["haarz.x", "segemehl.x"], "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["haarz.x", "segemehl.x"]], + 'dirs': [] +} + +moduleclass = 'bio' From 3dee4cd0d07bdf396177a3e9f6a87f667f696456 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Mar 2021 19:47:06 +0100 Subject: [PATCH 0583/2365] adding easyconfigs: BWA-0.7.17-GCC-10.2.0.eb, BWA-0.7.17-iccifort-2020.4.304.eb --- .../b/BWA/BWA-0.7.17-GCC-10.2.0.eb | 39 +++++++++++++++++++ .../b/BWA/BWA-0.7.17-iccifort-2020.4.304.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb new file mode 100644 index 0000000000..48f02d3037 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman, Big Data Institute, University of Oxford +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +dependencies = [ + ('Perl', '5.32.0'), + ('zlib', '1.2.11'), +] + +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..d3c453af6d --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-iccifort-2020.4.304.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman, Big Data Institute, University of Oxford +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +dependencies = [ + ('Perl', '5.32.0'), + ('zlib', '1.2.11'), +] + +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' + +moduleclass = 'bio' From 8e4eebd726dcf9a31987aa37dd9d65723293993c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 25 Mar 2021 10:43:05 +0100 Subject: [PATCH 0584/2365] adding easyconfigs: Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb --- ...vod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..fe80381811 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.21.3' +local_pt_version = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('flatbuffers', '1.12.0'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('PyTorch', local_pt_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + 'checksums': ['dee8b2387b1ec9f54fe1737a95b992a52ce20cb3f1a4388017215fae14978f95'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From dee1299490145d65231c08d0b422845703d49669 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 25 Mar 2021 14:58:42 +0200 Subject: [PATCH 0585/2365] more style fixes. opt=true --- .../easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb index 4cded3c94b..020040b808 100644 --- a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb @@ -10,7 +10,7 @@ package for analysis of cryogenic transmission electron microscopy (cryo-EM) movies of single-particles (Single-Particle Analysis, SPA).""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'openmp': True, 'opt': False} # simple_test_units fails with opt=True +toolchainopts = {'openmp': True, 'opt': True} source_urls = [GITHUB_SOURCE] github_account = 'hael' @@ -52,11 +52,10 @@ modextrapaths = {'PATH': 'scripts'} postinstallcmds = [ # "make install" misses some required directories. - "cp %(builddir)s/easybuild_obj/bin/{simple*,single_exec,quant_exec} %(installdir)s/bin/ -pP " - "&& cp -rpP %(builddir)s/easybuild_obj/{gui_data,tutorials}/ %(installdir)s " + 'cp %(builddir)s/easybuild_obj/bin/{simple*,single_exec,quant_exec} %(installdir)s/bin/ -pP ' + '&& cp -rpP %(builddir)s/easybuild_obj/{gui_data,tutorials}/ %(installdir)s ' '&& cp %(builddir)s/SIMPLE*/{doc,LICENSE,src/inc} %(installdir)s -rpP' - '&& cd %(installdir)s/lib ' + '&& ln -s libSIMPLE%s.%s libSIMPLE.%s' % (version, SHLIB_EXT, SHLIB_EXT) - # "test binaries are only required for "make test". + '&& cd %(installdir)s/lib ' + '&& ln -s libSIMPLE%s.%s libSIMPLE.%s' % (version, SHLIB_EXT, SHLIB_EXT) + '&& rm -rf %(installdir)s/bin/simple_test_*'] @@ -75,6 +74,6 @@ sanity_check_paths = { 'doc', 'inc', ] } -docpaths = ["doc"] +docpaths = ['doc'] moduleclass = 'bio' From a778f5df50af0fc92fbfa656613865e4bf306226 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 16:47:56 +0100 Subject: [PATCH 0586/2365] fix source URLs in Arrow 0.x easyconfigs --- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index 0fb5b5532b..d5c0491c4c 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -9,10 +9,7 @@ description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [ - 'http://apache.belnet.be/arrow/arrow-%(version)s/', - 'https://www-eu.apache.org/dist/arrow/arrow-%(version)s/', -] +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] patches = ['Arrow-0.16.0_fix-intel.patch'] checksums = [ From 48d9220171d555e4fa162f0539e09863b7817e8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 17:13:47 +0100 Subject: [PATCH 0587/2365] update to igraph 0.9.1, CMake is just a build dep --- .../i/igraph/igraph-0.9.1-fosscuda-2020b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.9.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.9.1-fosscuda-2020b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.9.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..28cd22238a --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.9.1-fosscuda-2020b.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'CMakeMake' + +name = 'igraph' +version = '0.9.1' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['1902810650e8f9d98feefa3eca735db5a879416d00a08f68aad2ca07964cee9f'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('GLPK', '4.65'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), +] + +configopts = "--with-external-blas --with-external-lapack --with-external-glpk" + +# extra folder `igraph` is wrong, since all other software expects it to be in ./include folder directly +postinstallcmds = [ + 'mv %(installdir)s/include/igraph/* %(installdir)s/include/ && rmdir %(installdir)s/include/igraph ', +] + +sanity_check_paths = { + 'files': ['include/igraph%s.h' % x for x in ['', '_blas', '_constants', '_lapack', '_types', '_version']], + 'dirs': [], +} + +moduleclass = 'lib' From 1e70200539b7d0c2523baf56cc95fd808f93e051 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 21:03:08 +0100 Subject: [PATCH 0588/2365] fix source URL for Arrow 0.17.1 with fosscuda/2020b --- .../a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 5 +-- .../leidenalg-0.8.3-fosscuda-2020b.eb | 44 +++++++++++++++++++ .../PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb | 44 +++++++++++++++++++ 3 files changed, 89 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 8dbd35330f..dff73a9b59 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -11,10 +11,7 @@ description = """Apache Arrow (incl. PyArrow Python bindings)), a cross-language toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [ - 'http://apache.belnet.be/arrow/arrow-%(version)s/', - 'https://www-eu.apache.org/dist/arrow/arrow-%(version)s/', -] +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] checksums = ['cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2'] diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..06b16f79b4 --- /dev/null +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'leidenalg' +version = '0.8.3' + +homepage = 'https://github.com/vtraag/leidenalg' +description = """Implementation of the Leiden algorithm for various quality +functions to be used with igraph in Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('PyYAML', '5.3.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('igraph', '0.9.0'), + ('python-igraph', '0.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ddt', '1.4.2', { + 'checksums': ['64a67366a2715e636b88694cc6075cc02db292f01098b8e385397c894d395378'], + }), + (name, version, { + 'checksums': ['84c2fa673390b62986e51258cbe048a49c163e516ee791b372c2779c928d8e7e'], + 'buildopts': '--use-pkg-config', + 'runtest': "python setup.py test", + 'testopts': '--use-pkg-config', + }), +] + +sanity_check_commands = ["python -c 'import leidenalg; import igraph as ig; " + "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), " + "leidenalg.ModularityVertexPartition)'"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7839c97765 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'PyCairo' +version = '1.18.2' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dcb853fd020729516e8828ad364084e752327d4cff8505d20b13504b32b16531'] + +multi_deps = {'Python': ['3.8.6', '2.7.18']} + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('cairo', '1.16.0'), +] + +# PyGTK needs PyCairo installed by pip +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# Don't build a wheel or the pkg-cfg file won't be installed +installopts = '--no-binary=%(namelower)s' + +sanity_check_paths = { + 'files': ['%s/%s.%s' % (p, n, e) + for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')] for n in ['py3cairo', 'pycairo']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +options = {'modulename': 'cairo'} + +moduleclass = 'vis' From 6baef97f2926d4ee943fa44dd48b22764d61e813 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 21:04:42 +0100 Subject: [PATCH 0589/2365] avoid use protobuf built with system toolchain for Hadoop + don't copy native libraries twice (lib/ + lib64/) --- .../protobuf/protobuf-2.5.0-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2bfabbaa61 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '2.5.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c55aa3dc538e6fd5eaf732f4eb6b98bdcb7cedb5b91d3b5bdcf29c98c293f58e'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From ce8e8eb0f8b62393ae4d45a46e98743a4be519f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 21:06:28 +0100 Subject: [PATCH 0590/2365] bump igraph dep to 0.9.1 in leidenalg 0.8.3 easyconfig --- .../easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb index 06b16f79b4..7011c0085c 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb @@ -18,7 +18,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), - ('igraph', '0.9.0'), + ('igraph', '0.9.1'), ('python-igraph', '0.9.0'), ] From b4eb0fe702b4a9b33d197cc6aff123a1bb7d3e9b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 21:08:25 +0100 Subject: [PATCH 0591/2365] update PyCairo to 1.20.0, only depend on Python 3.8.6, remove pyproject.toml to retain header files and pkg-config file --- .../p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb index 7839c97765..a4dcd75516 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb @@ -3,18 +3,15 @@ easyblock = 'PythonPackage' name = 'PyCairo' -version = '1.18.2' +version = '1.20.0' homepage = 'https://pycairo.readthedocs.io/' description = """Python bindings for the cairo library""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['dcb853fd020729516e8828ad364084e752327d4cff8505d20b13504b32b16531'] - -multi_deps = {'Python': ['3.8.6', '2.7.18']} +checksums = ['5695a10cb7f9ae0d01f665b56602a845b0a8cb17e2123bfece10c2e58552468c'] builddependencies = [ ('binutils', '2.35'), @@ -22,6 +19,7 @@ builddependencies = [ ] dependencies = [ + ('Python', '3.8.6'), ('cairo', '1.16.0'), ] @@ -30,12 +28,14 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +# remove pyproject.toml, which causes trouble (header files and .pc file are not installed) +preinstallopts = "rm pyproject.toml && " + # Don't build a wheel or the pkg-cfg file won't be installed installopts = '--no-binary=%(namelower)s' sanity_check_paths = { - 'files': ['%s/%s.%s' % (p, n, e) - for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')] for n in ['py3cairo', 'pycairo']], + 'files': ['%s/py3cairo.%s' % (p, e) for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')]], 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], } From e26752cb9bc1910a00a7c4d4772e8c708a7dc0dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 21:09:37 +0100 Subject: [PATCH 0592/2365] bump dependencies for python-igraph 0.9.0 + add patch to fix installation --- .../python-igraph-0.9.0-fosscuda-2020b.eb | 28 +++++++++++-------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb index 4b3e4b7083..5b5c25791f 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb @@ -9,30 +9,34 @@ description = """Python interface to the igraph high performance graph library, toolchain = {'name': 'fosscuda', 'version': '2020b'} -osdependencies = [('zlib-devel', 'zlib1g-dev')] +builddependencies = [ + ('pkg-config', '0.29.2'), +] dependencies = [ ('Python', '3.8.6'), - ('igraph', '0.9.0'), - ('PyCairo', '1.18.2'), + ('igraph', '0.9.1'), + ('PyCairo', '1.20.0'), ('Clang', '11.0.1'), ('libxml2', '2.9.10'), - ('pkg-config', '0.29.2'), + ('zlib', '1.2.11'), ] use_pip = True -sanity_pip_check = True - -exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ - ('texttable', '1.6.2', { - 'checksums': ['eff3703781fbc7750125f50e10f001195174f13825a92a45e9403037d539b4f4'], + ('texttable', '1.6.3', { + 'checksums': ['ce0faf21aa77d806bbff22b107cc22cce68dc9438f97a2df32c93e9afa4ce436'], }), (name, version, { - 'buildopts': '--use-pkg-config', + 'installopts': '--install-option="--use-pkg-config" --install-option="--static"', 'modulename': 'igraph', - 'checksums': ['7aa1d77fa02e27475eb4f14503f3cb342c3ed8990d9224640fd29c70797f2dd6'], + 'patches': ['python-igraph-%(version)s_fix-igraph-libs.patch'], + 'checksums': [ + '7aa1d77fa02e27475eb4f14503f3cb342c3ed8990d9224640fd29c70797f2dd6', # python-igraph-0.9.0.tar.gz + # python-igraph-0.9.0_fix-igraph-libs.patch + '7af7a6e6a8b982ced7cdd939d82a98829512088744bebad34c714a3c4803f126', + ], }), ] @@ -44,4 +48,6 @@ sanity_check_paths = { # cairo must be available for proper plotting support sanity_check_commands = ["python -c 'from igraph.drawing.utils import find_cairo; cairo = find_cairo(); cairo.Context'"] +sanity_pip_check = True + moduleclass = 'lib' From 051dff8bfead7190119d2eaa44332f446e50162b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 21:11:10 +0100 Subject: [PATCH 0593/2365] update py4j extension in Spark 3.1.1 easyconfig to latest version --- .../s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index a8b68ba100..5558a5352f 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -24,15 +24,13 @@ dependencies = [ ] exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} exts_list = [ - ('py4j', '0.10.7', { - 'source_tmpl': 'py4j-%(version)s.zip', - 'checksums': ['721189616b3a7d28212dfb2e7c6a1dd5147b03105f1fc37ff2432acd0e863fa5'], + ('py4j', '0.10.9.2', { + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], + 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], + 'download_dep_fail': True, + 'use_pip': True, }), ] From 0bc561f24238db89153260af44792c5b338d1c70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 21:30:15 +0100 Subject: [PATCH 0594/2365] fix typo --- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index dff73a9b59..5f6def8751 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -6,7 +6,7 @@ name = 'Arrow' version = '0.17.1' homepage = 'https://arrow.apache.org' -description = """Apache Arrow (incl. PyArrow Python bindings)), a cross-language development platform +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} From dba26527a3d1219a45eeb8d33cfd2432aa267b3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 21:34:28 +0100 Subject: [PATCH 0595/2365] strip out default source URL in PythonPackage easyconfigs --- .../netcdf4-python-1.5.5.1-fosscuda-2020b.eb | 2 -- .../easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb | 2 -- .../p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb | 6 ------ .../p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb | 7 ------- .../easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb | 1 - 5 files changed, 18 deletions(-) diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb index a16fa1c427..502f67a862 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('cftime', '1.4.1', { 'checksums': ['7c55540bc164746c3c4f86a07c9c7b9ed4dfb0b0d988348ec63cec065c58766d'], diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb index 9de026b36b..5114a27aba 100644 --- a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb @@ -25,8 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('typing_extensions', '3.7.4.3', { 'checksums': ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'], diff --git a/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb index 6785b9e1a1..380ab5a451 100644 --- a/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb @@ -10,7 +10,6 @@ description = "Pyro is a flexible, scalable deep probabilistic programming libra toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'] @@ -24,11 +23,6 @@ sanity_pip_check = True options = {'modulename': 'pyroapi'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = [ "python -c 'from pyroapi import distributions as dist'", "python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'" diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb index b2cf1dd9eb..7ad051a7bc 100644 --- a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb @@ -10,7 +10,6 @@ description = "Pyro is a flexible, scalable deep probabilistic programming libra toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['8a93af3a007ac507a8b50fd1165dbb355182d17df29d3b5bc498b02b479fdb27'] @@ -28,7 +27,6 @@ use_pip = True exts_defaultclass = 'PythonPackage' exts_default_options = { - 'source_urls': [PYPI_SOURCE], 'sanity_pip_check': True, 'download_dep_fail': True, 'use_pip': True, @@ -43,9 +41,4 @@ exts_list = [ options = {'modulename': 'pyro'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb index 0496a7fe61..00d0c4eb93 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb @@ -12,7 +12,6 @@ description = """xarray (formerly xray) is an open source project and Python pac toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['38e8439d6c91bcd5b7c0fca349daf8e0643ac68850c987262d53526e9d7d01e4'] From 990cbd54bfbe557ebc9a9f484fee8abc098b0d58 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 21:54:04 +0100 Subject: [PATCH 0596/2365] add missing patch for netcdf4-python 1.5.5.1 to avoid diskless tests --- .../netcdf4-python-1.5.5.1-fosscuda-2020b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb index 502f67a862..1753ec88f9 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb @@ -28,9 +28,14 @@ exts_list = [ 'checksums': ['7c55540bc164746c3c4f86a07c9c7b9ed4dfb0b0d988348ec63cec065c58766d'], }), (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], - 'checksums': ['d957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd'], + 'checksums': [ + 'd957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd', # netCDF4-1.5.5.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], }), ] From d192e59c47597df77a7ddc7f39a9bde8d2741576 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 22:33:18 +0100 Subject: [PATCH 0597/2365] enable download_dep_fail and use_pip via exts_default_options in Spark 3.1.1 easyconfig --- easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index 5558a5352f..d006f6a932 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -24,13 +24,15 @@ dependencies = [ ] exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} exts_list = [ ('py4j', '0.10.9.2', { 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], - 'download_dep_fail': True, - 'use_pip': True, }), ] From 88747142c37fe7d3b0ea741d4b853b7f34d2ac79 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 22:47:54 +0100 Subject: [PATCH 0598/2365] use PythonBundle easyblock for pyro-ppl easyconfig --- .../pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb | 23 ++++++------------- 1 file changed, 7 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb index 7ad051a7bc..ec240437e2 100644 --- a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb @@ -1,6 +1,6 @@ # Author: Denis Krišťák (INUITS) -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'pyro-ppl' version = '1.5.2' @@ -10,9 +10,6 @@ description = "Pyro is a flexible, scalable deep probabilistic programming libra toolchain = {'name': 'fosscuda', 'version': '2020b'} -sources = [SOURCE_TAR_GZ] -checksums = ['8a93af3a007ac507a8b50fd1165dbb355182d17df29d3b5bc498b02b479fdb27'] - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -21,24 +18,18 @@ dependencies = [ ('tqdm', '4.56.2'), ] -download_dep_fail = True use_pip = True -exts_defaultclass = 'PythonPackage' - -exts_default_options = { - 'sanity_pip_check': True, - 'download_dep_fail': True, - 'use_pip': True, -} - exts_list = [ - ('opt-einsum', '3.3.0', { - 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + ('opt_einsum', '3.3.0', { 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), + (name, version, { + 'checksums': ['8a93af3a007ac507a8b50fd1165dbb355182d17df29d3b5bc498b02b479fdb27'], + 'modulename': 'pyro', + }), ] -options = {'modulename': 'pyro'} +sanity_pip_check = True moduleclass = 'tools' From 62f25d5516a1ce1b34db839ed651d252423f1580 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Mar 2021 22:48:45 +0100 Subject: [PATCH 0599/2365] drop duplicate empty line in Theano easyconfig --- .../easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb index cb87a9010a..c7c4aba1c1 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb @@ -29,7 +29,6 @@ sanity_pip_check = True fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] - sanity_check_paths = { 'files': ['bin/theano-cache'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 24613de3d6a7b555ae1edb4adfc9edf06e6ea283 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Mar 2021 14:14:49 +0100 Subject: [PATCH 0600/2365] use correct configure options for VTK 9.0.1, remove unused HDF5 + netCDF dependencies, check for vtkMPI.h to catch building VTK without MPI support --- .../easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 20 ++++--------------- 1 file changed, 4 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb index a772a853ae..38253852e8 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -42,32 +42,20 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('XZ', '5.2.5'), - ('HDF5', '1.10.7'), - ('netCDF', '4.7.4'), ('libGLU', '9.0.1'), ('X11', '20201008'), ] separate_build_dir = True -# Third party modules -configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " -configopts += "-DVTK_USE_SYSTEM_LZMA=ON " -configopts += "-DVTK_USE_SYSTEM_HDF5=ON " -configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " -configopts += "-DVTK_USE_SYSTEM_PNG=ON " # OpenGL -configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python -configopts += "-DVTK_WRAP_PYTHON=ON " -# note: specifying full Python version leads to problems (see https://gitlab.kitware.com/vtk/vtk/-/issues/17934) -configopts += "-DVTK_PYTHON_VERSION=3 " -configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 " # Other -configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DVTK_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " @@ -87,7 +75,7 @@ local_vtk_exec += ['vtkpython'] local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_vtk_exec] + + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], } From ea92d8947b0f294067b61e75ba155824a71aa2ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Mar 2021 14:18:44 +0100 Subject: [PATCH 0601/2365] add missing Bison build dependency for leidenalg 0.8.3 --- .../easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb index 7011c0085c..f0e29a156c 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ ('pkg-config', '0.29.2'), ('PyYAML', '5.3.1'), + ('Bison', '3.7.1'), ] dependencies = [ From b266ac3bfce738f9ef995cb2e0e1604bef5273a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Mar 2021 18:07:37 +0100 Subject: [PATCH 0602/2365] use correct configure option to enable MPI support in VTK 9.x: -DVTK_USE_MPI=ON --- easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb index 38253852e8..090ed4ff9e 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -55,7 +55,7 @@ configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 " # Other -configopts += "-DVTK_MPI=ON " +configopts += "-DVTK_USE_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " From d2d4e0799af618bbccfc7f745b9dfd06697a5342 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Mar 2021 11:31:32 +0200 Subject: [PATCH 0603/2365] make sure that VTK 9.0.1 links to libpython by configuring with -DVTK_PYTHON_OPTIONAL_LINK=OFF --- easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb index 090ed4ff9e..b4161f95ea 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -53,7 +53,7 @@ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python -configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 " +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " # Other configopts += "-DVTK_USE_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" @@ -81,8 +81,11 @@ sanity_check_paths = { } sanity_check_commands = [ - ('python', "-c 'import %(namelower)s'"), - ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, ] From 7f0f4020865105bc1a6dda7c798cc720f18e90e5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 29 Mar 2021 12:54:39 +0200 Subject: [PATCH 0604/2365] [SciPy-bundle] Fix numpy tests on PPC --- .../s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb | 7 ++++++- .../s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb index 96f8870c01..168b6741d2 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb @@ -21,8 +21,13 @@ use_pip = True # order is important! exts_list = [ ('numpy', '1.19.4', { + 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512'], + 'checksums': [ + '141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512', # numpy-1.19.4.zip + # numpy-1.16.2_relax-long-complex-test.patch + '450d088992d46cc8e4c218eee47294e82e67760a51fdeae95ae0eb5bcdf1eefc', + ], }), ('scipy', '1.5.4', { 'checksums': ['4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b'], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb index d120637e07..18d8d34673 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb @@ -21,8 +21,13 @@ use_pip = True # order is important! exts_list = [ ('numpy', '1.19.4', { + 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512'], + 'checksums': [ + '141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512', # numpy-1.19.4.zip + # numpy-1.16.2_relax-long-complex-test.patch + '450d088992d46cc8e4c218eee47294e82e67760a51fdeae95ae0eb5bcdf1eefc', + ], }), ('scipy', '1.5.4', { 'checksums': ['4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b'], From f8c02b0bbed07a8a03a2931f7e94311ea8853b9f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 29 Mar 2021 13:28:50 +0200 Subject: [PATCH 0605/2365] Enable pip check --- .../s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb | 3 +-- .../s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb index 168b6741d2..a7f3b33fba 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb @@ -17,6 +17,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True # order is important! exts_list = [ @@ -52,6 +53,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb index 18d8d34673..c12d4981d1 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb @@ -17,6 +17,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True # order is important! exts_list = [ @@ -52,6 +53,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lang' From 1445e5accf1b268d0d251a6c199e9a01e194afd9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 29 Mar 2021 18:32:25 +0200 Subject: [PATCH 0606/2365] Don't download hwloc during FIRESTARTER build --- .../f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb index 349652c2ec..c7a0866a3d 100644 --- a/easybuild/easyconfigs/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb @@ -12,25 +12,22 @@ between the cores and multiple levels of the memory hierarchy.""" toolchain = {'name': 'gcccuda', 'version': '2020b'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/tud-zih-energy/FIRESTARTER/releases/download/v2.0/'] -sources = ['FIRESTARTER_%(version)s.tar.gz'] +source_urls = ['https://github.com/tud-zih-energy/FIRESTARTER/releases/download/v%(version)s/'] +sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['a3b09ac4ec29c3d24750bf161c58abe6b9c2f86d56f046d2657be72daf63b673'] -start_dir = 'sources' - -# Iterations don't work otherwise -unpack_options = ' && mkdir easybuild_obj' -separate_build_dir = True +start_dir = 'sources' builddependencies = [ ('binutils', '2.35'), ('CMake', '3.18.4'), + ('hwloc', '2.2.0'), ] # All configopts, including default values configopts = '-DFIRESTARTER_BUILD_TYPE=FIRESTARTER_CUDA' configopts += ' -DFIRESTARTER_LINK_STATIC=ON' -configopts += ' -DFIRESTARTER_BUILD_HWLOC=ON' +configopts += ' -DFIRESTARTER_BUILD_HWLOC=OFF' configopts += ' -DFIRESTARTER_THREAD_AFFINITY=ON' files_to_copy = [(['FIRESTARTER'], 'bin')] From 07bbeee690a081d2e68519e787c7f8f3db1e126a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 30 Mar 2021 11:13:33 +0200 Subject: [PATCH 0607/2365] Update patches for changes in numpy 1.19 --- .../s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb | 6 +++--- .../s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb index a7f3b33fba..7266b75a30 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb @@ -22,12 +22,12 @@ sanity_pip_check = True # order is important! exts_list = [ ('numpy', '1.19.4', { - 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], + 'patches': ['numpy-1.19.4_skip-ppc-long-complex-test.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': [ '141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512', # numpy-1.19.4.zip - # numpy-1.16.2_relax-long-complex-test.patch - '450d088992d46cc8e4c218eee47294e82e67760a51fdeae95ae0eb5bcdf1eefc', + # numpy-1.19.4_skip-ppc-long-complex-test.patch + '31f4e64c9335edc1ae5a99cf22adf43147f3526847cca79d0e16a863a8c4da32', ], }), ('scipy', '1.5.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb index c12d4981d1..4505176611 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb @@ -22,12 +22,12 @@ sanity_pip_check = True # order is important! exts_list = [ ('numpy', '1.19.4', { - 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], + 'patches': ['numpy-1.19.4_skip-ppc-long-complex-test.patch'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': [ '141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512', # numpy-1.19.4.zip - # numpy-1.16.2_relax-long-complex-test.patch - '450d088992d46cc8e4c218eee47294e82e67760a51fdeae95ae0eb5bcdf1eefc', + # numpy-1.19.4_skip-ppc-long-complex-test.patch + '31f4e64c9335edc1ae5a99cf22adf43147f3526847cca79d0e16a863a8c4da32', ], }), ('scipy', '1.5.4', { From 35e0bbf6cdbd1a57064c78c237bb7b9ab6fb5ed9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Mar 2021 15:12:05 +0200 Subject: [PATCH 0608/2365] adding easyconfigs: Seurat-4.0.1-foss-2020b-R-4.0.3.eb --- .../Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..bddbf11b5e --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.0.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} + +exts_list = [ + ('spatstat.utils', '2.1-0', { + 'checksums': ['ed3569fea295b62396c49cdcfe476414b0b0f3e52044175532f316a402d3f8a1'], + }), + ('spatstat.data', '2.1-0', { + 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], + }), + ('spatstat.geom', '2.0-1', { + 'checksums': ['70ebfe115e733b2e6778baf6e2935861472154c0dd21f15a84ec2a61e0a3f6e4'], + }), + ('spatstat.sparse', '2.0-0', { + 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], + }), + ('spatstat.core', '2.0-0', { + 'checksums': ['fde9a91bd32b7a3c8b25e802a16d470dcc919c24da5715149e1d91eeec119ba7'], + }), + (name, version, { + 'checksums': ['77c46e390db8b0aa7c8fec072e39bfe0edca7fb0cda4e32d5ad3ef1a6bba959d'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From efbb703bdfd117efb28d84df95b499e2aa134e57 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 30 Mar 2021 17:01:23 +0200 Subject: [PATCH 0609/2365] adding easyconfigs: RASPA2-2.0.41-foss-2020b.eb --- .../r/RASPA2/RASPA2-2.0.41-foss-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb new file mode 100644 index 0000000000..b1ab0ac609 --- /dev/null +++ b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'RASPA2' +version = '2.0.41' + +homepage = 'https://iraspa.org/raspa/' +description = """RASPA is a software package for simulating adsorption and diffusion of +molecules in flexible nanoporous materials.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/iRASPA/RASPA2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['85d99ad63b83541835f92f09dd41a3c6193a2e4d6ad45baee58ecf3b85713394'] + +dependencies = [ + ('OpenBLAS', '0.3.12'), + ('FFTW', '3.3.8'), + ('ScaLAPACK', '2.1.0'), +] + +preconfigopts = 'rm -rf autom4te.cache && ' +preconfigopts += 'mkdir m4 && ' +preconfigopts += 'aclocal && ' +preconfigopts += 'autoreconf -i && ' +preconfigopts += 'automake --add-missing && ' +preconfigopts += 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/simulate'], + 'dirs': [] +} + +modextrapaths = {'RASPA_DIR': './'} + +moduleclass = 'phys' From b7dd98e8e0626887979a48c419e195c561ea2539 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 30 Mar 2021 18:07:37 +0200 Subject: [PATCH 0610/2365] removing unnecessary dependencies, added sanity check cmd --- .../easyconfigs/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb index b1ab0ac609..8cdf1ce224 100644 --- a/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb @@ -13,10 +13,8 @@ source_urls = ['https://github.com/iRASPA/RASPA2/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['85d99ad63b83541835f92f09dd41a3c6193a2e4d6ad45baee58ecf3b85713394'] -dependencies = [ - ('OpenBLAS', '0.3.12'), - ('FFTW', '3.3.8'), - ('ScaLAPACK', '2.1.0'), +builddependencies = [ + ('Autotools', '20200321') ] preconfigopts = 'rm -rf autom4te.cache && ' @@ -31,6 +29,6 @@ sanity_check_paths = { 'dirs': [] } -modextrapaths = {'RASPA_DIR': './'} +sanity_check_commands = ['simulate -h'] moduleclass = 'phys' From 456408d7d366dd09c8c6d43ade1e67de1adec15f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Mar 2021 19:35:10 +0200 Subject: [PATCH 0611/2365] enable sanity_pip_check for Python bindings for libgpuarray --- .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index c585aaf524..f0a678a0df 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -29,6 +29,7 @@ exts_defaultclass = 'PythonPackage' exts_default_options = { 'download_dep_fail': True, 'use_pip': True, + 'sanity_pip_check': True, } exts_list = [ (name, version, { From 1ebbab00bbb68269fb4f38526ea542d8713841bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Mar 2021 19:35:42 +0200 Subject: [PATCH 0612/2365] remove unneeded source URL from netcdf4-python easyconfig --- .../n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb index 1753ec88f9..b7343ccf1a 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb @@ -11,8 +11,6 @@ description = """Python/numpy interface to netCDF.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), From 8769fa6cdc3ab794418e159f1cd16fcc6146b1ae Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 30 Mar 2021 14:24:47 -0700 Subject: [PATCH 0613/2365] remove Java from RevBayes --- easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb index b055c17afc..cbcc94ca3e 100644 --- a/easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb @@ -23,7 +23,6 @@ builddependencies = [('CMake', '3.18.4')] dependencies = [ ('Boost', '1.74.0'), - ('Java', '11', '', True), ] start_dir = 'projects/cmake' From 069f25bdfa80bf496f7f9b55551b0f465eaa0733 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Mar 2021 12:08:14 +0200 Subject: [PATCH 0614/2365] drop 'v' from cell2location version + fix leidenalg and hyperopt dependency version(suffix) --- ...cell2location-0.05-alpha-fosscuda-2020b.eb | 136 ++++++++++++++++++ 1 file changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb new file mode 100644 index 0000000000..a086e69c6f --- /dev/null +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -0,0 +1,136 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'cell2location' +version = '0.05-alpha' + +homepage = 'https://github.com/BayraktarLab/cell2location/' +description = """Comprehensive mapping of tissue cell architecture via integrated +single cell and spatial transcriptomics (cell2location model)""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Java', '1.8', '', True), + ('SciPy-bundle', '2020.11'), + ('leidenalg', '0.8.3'), + ('hyperopt', '0.2.5'), + ('CMake', '3.18.4'), + ('dill', '0.3.3'), + ('IPython', '7.18.1'), + ('Seaborn', '0.11.1'), + ('matplotlib', '3.3.3'), + ('libgpuarray', '0.7.6'), + ('PyMC3', '3.11.1'), + ('request', '2.88.1', '-nodejs-12.19.0'), + ('PyTables', '3.6.1'), + ('PyTorch', '1.7.1'), + ('statsmodels', '0.12.1'), + ('LLVM', '10.0.1'), + ('Theano', '1.1.2', '-PyMC'), + ('umap-learn', '0.4.6'), + ('pyro-api', '0.1.2'), + ('pyro-ppl', '1.5.2'), +] + +preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " + +use_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +exts_list = [ + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('get_version', '2.1', { + 'use_pip': False, + 'checksums': ['8156b526c2557537b8ca82241fa2b82b3da25939627398f6567dee31ba9725bc'], + }), + ('legacy-api-wrap', '1.2', { + 'use_pip': False, + 'checksums': ['034a44612da7e9943d3964363a98937ab54d55e3301075374abe0d521eb8101b'], + }), + ('descartes', '1.1.0', { + 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], + }), + ('mizani', '0.7.1', { + 'checksums': ['97eea665d17fdc6c827b832925c094839e1ef7bf65b3aa47105e772b6eca9b0a'], + }), + ('anndata', '0.7.5', { + 'checksums': ['2113a7463388013023f153e1a1446add4182883e3320b6e37dda18ee6210e038'], + }), + ('ipykernel', '5.3.4', { + 'checksums': ['9b2652af1607986a1b231c62302d070bc0534f564c393a5d9d130db9abbbe89d'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('natsort', '7.1.0', { + 'checksums': ['33f3f1003e2af4b4df20908fe62aa029999d136b966463746942efbfc821add3'], + }), + ('numba', '0.51.2', { + 'checksums': ['16bd59572114adbf5f600ea383880d7b2071ae45477e84a24994e089ea390768'], + }), + ('llvmlite', '0.34.0', { + 'checksums': ['f03ee0d19bca8f2fe922bb424a909d05c28411983b0c2bc58b020032a0d11f63'], + }), + ('palettable', '3.3.0', { + 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], + }), + ('scanpy', '1.6.0', { + 'checksums': ['542d1f1fc0471e7312d4349142e1c2eee4a465cd514fe4e3337be166f425fa55'], + }), + ('louvain', '0.7.0', { + 'checksums': ['9734fc6bf8c15546d685a8c6d7d7ca0574cad4cb641e9ca91c3334028658f7c6'], + }), + ('loompy', '3.0.6', { + 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], + }), + ('bbknn', '1.3.12', { + 'checksums': ['7dc5257baa278fc92349ac7865674ce70802dc4e3afdafed87a099dff9e91159'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.1', { + 'checksums': ['e1b2358808aded7b2ff00ea0cd4e6a2d978fb2a44ee9b15ac23d64a81bf62706'], + }), + ('plotnine', '0.7.0', { + 'checksums': ['8ee67cbf010ccea32670760e930b7b02177030a89ccdf85e35d156a96ce36cd3'], + }), + ('numpy-groupies', '0.9.13', { + 'modulename': 'numpy_groupies', + 'source_tmpl': 'numpy_groupies-%(version)s.tar.gz', + 'checksums': ['7b17b291322353f07c51598512d077e3731da0a048cfa8f738f3460d1ef0658d'], + }), + ('annoy', '1.17.0', { + 'checksums': ['9891e264041d1dcf3af42f67fbb16cb273c5404bc8c869d0915a3087f71d58dd'], + }), + (name, version, { + 'source_tmpl': 'v0.05-alpha.tar.gz', + 'source_urls': ['https://github.com/BayraktarLab/cell2location/archive'], + 'checksums': ['2df1fe2b2b4ec5fcebc6c1d6146ce0cd79115bd14059b0ae882a41f1029a4efc'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 9c0f014c00fb88f8b49c94df9df5aa8441b9e707 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 31 Mar 2021 19:01:20 +0100 Subject: [PATCH 0615/2365] switch to PyTorch 1.8.1 --- .../p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb new file mode 100644 index 0000000000..f8827697e0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -0,0 +1,78 @@ +name = 'PyTorch' +version = '1.8.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', + 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + # PyTorch-1.7.0_increase-distributed-test-timeout.patch + '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch + # PyTorch-1.8.0_correct-skip-tests-decorators.patch + '4b2fe7616217dd6fd12d667cb1439dde58f84bf234fbf3e6026c4665fc697a2e', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), +] + +excluded_tests = { + '': [ + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! + # https://github.com/pytorch/pytorch/issues/43209 + 'test_quantization', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From 9a548d9da1f8137ec1d4ca096c5ac197fc122b93 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 09:27:24 +0200 Subject: [PATCH 0616/2365] adding easyconfigs: mrcfile-1.3.0-foss-2020b.eb, mrcfile-1.3.0-fosscuda-2020b.eb, voltools-0.4.2-foss-2020b-Python-3.8.6.eb --- .../m/mrcfile/mrcfile-1.3.0-foss-2020b.eb | 30 +++++++++++++++++++ .../m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb new file mode 100644 index 0000000000..a493d51dd8 --- /dev/null +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb @@ -0,0 +1,30 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/03 +easyblock = 'PythonPackage' +name = 'mrcfile' +version = '1.3.0' +homepage = 'https://github.com/ccpem/mrcfile' +description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in +structural biology to store image and volume data. +It allows MRC files to be created and opened easily using a very simple API, +which exposes the file’s header and data as numpy arrays. The code runs in +Python 2 and 3 and is fully unit-tested. +This library aims to allow users and developers to read and write standard- +compliant MRC files in Python as easily as possible, and with no dependencies on +any compiled libraries except numpy. You can use it interactively to inspect +files, correct headers and so on, or in scripts and larger software packages to +provide basic MRC file I/O functions. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +use_pip = True + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..f189f38598 --- /dev/null +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb @@ -0,0 +1,30 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/03 +easyblock = 'PythonPackage' +name = 'mrcfile' +version = '1.3.0' +homepage = 'https://github.com/ccpem/mrcfile' +description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in +structural biology to store image and volume data. +It allows MRC files to be created and opened easily using a very simple API, +which exposes the file’s header and data as numpy arrays. The code runs in +Python 2 and 3 and is fully unit-tested. +This library aims to allow users and developers to read and write standard- +compliant MRC files in Python as easily as possible, and with no dependencies on +any compiled libraries except numpy. You can use it interactively to inspect +files, correct headers and so on, or in scripts and larger software packages to +provide basic MRC file I/O functions. """ + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +use_pip = True + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +moduleclass = 'bio' From 12fe0a204574403363e7c39dedf4082952fae2c8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 10:22:42 +0200 Subject: [PATCH 0617/2365] fix source_url, download_dep_fail, sanity_pip_check --- easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb | 2 +- .../easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb index a493d51dd8..92f47bca91 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb @@ -17,8 +17,8 @@ provide basic MRC file I/O functions. """ toolchain = {'name': 'foss', 'version': '2020b'} use_pip = True +sanity_pip_check = True -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb index f189f38598..fa976cbc9a 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb @@ -17,8 +17,9 @@ provide basic MRC file I/O functions. """ toolchain = {'name': 'fosscuda', 'version': '2020b'} use_pip = True +sanity_pip_check = True +download_dep_fail =True -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] From 47ba73aa7446388cdbf13bd859fcde863294f6ac Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Thu, 1 Apr 2021 09:34:50 +0100 Subject: [PATCH 0618/2365] Removed Theano dependency on mkl-service. Deleted mkl-service-2.3.0-foss-2020b.eb. --- .../easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb | 8 -------- 1 file changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb index bd33ad40df..53824126a7 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb @@ -17,7 +17,6 @@ checksums = ['5da6c2242ea72a991c8446d7fe7d35189ea346ef7d024c890397011114bf10fc'] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('mkl-service', '2.3.0'), ] download_dep_fail = True @@ -31,11 +30,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -local_blas_warning = "Using NumPy C-API based implementation for BLAS functions" -sanity_check_commands = [ - # make sure that warning about falling back to (slow) NumPy C-API for BLAS functions is *not* printed - # mkl-service dependency is required to ensure this doesn't happen - "python -c 'import theano.tensor' 2>&1 | grep '%s'; test $? != 0" % local_blas_warning, -] - moduleclass = 'math' From 96e937932f9f3f8787c832a350c9d5ad3c0ca51d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 10:43:17 +0200 Subject: [PATCH 0619/2365] fix versionsuffix --- .../v/voltools/voltools-0.4.2-foss-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb b/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb new file mode 100644 index 0000000000..612dfe011e --- /dev/null +++ b/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb @@ -0,0 +1,34 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/03 +easyblock = 'PythonBundle' + +name = 'voltools' +version = '0.4.2' + +homepage = 'https://github.com/the-lay/voltools' +description = """CUDA-accelerated numpy 3D affine transformations""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('GPUtil', '1.4.0', { + 'modulename': 'GPUtil', + 'checksums': ['099e52c65e512cdfa8c8763fca67f5a5c2afb63469602d5dcb4d296b3661efb9'], + }), + (name, version, { + 'checksums': ['4a5382e194a2769676e7ec67143055444072d140c19d9b24dbb5ce014ee7a603'], + }), +] + +moduleclass = 'bio' From 3f989a82f73a41ff7692154c2c72d2631b3c8ee9 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 12:05:54 +0200 Subject: [PATCH 0620/2365] remove exts_default_options --- easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb b/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb index 612dfe011e..ee6631361e 100644 --- a/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb +++ b/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb @@ -19,8 +19,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('GPUtil', '1.4.0', { 'modulename': 'GPUtil', From 4962dbef70e9d62f3a87520f4efc47bbf2eb5edc Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 1 Apr 2021 11:21:34 +0100 Subject: [PATCH 0621/2365] Removed PYPI_SOURCE from exts_default_options. --- easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb index 8a7e4f90ee..32ae992ae3 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Keras_Applications', '1.0.8', { 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], From f9b90697faf771d29204fa2f412dac1fa4479d6c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 12:30:07 +0200 Subject: [PATCH 0622/2365] add exts_download_dep_fail --- easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb b/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb index ee6631361e..ee74d601b0 100644 --- a/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb +++ b/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb @@ -17,7 +17,7 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True +exts_download_dep_fail = True exts_list = [ ('GPUtil', '1.4.0', { From cee9cdd7df9cb5e68499574c1ec5d42949a7ad00 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 12:39:39 +0200 Subject: [PATCH 0623/2365] fix download_dep_fail --- easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb | 1 + easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb | 1 - 3 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb index 92f47bca91..7219684d61 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb @@ -18,6 +18,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} use_pip = True sanity_pip_check = True +download_dep_fail = True sources = [SOURCELOWER_TAR_GZ] checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb index fa976cbc9a..0b2fdf52c7 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} use_pip = True sanity_pip_check = True -download_dep_fail =True +download_dep_fail = True sources = [SOURCELOWER_TAR_GZ] checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] diff --git a/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb b/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb index ee74d601b0..0989ba04d1 100644 --- a/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb +++ b/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb @@ -17,7 +17,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_download_dep_fail = True exts_list = [ ('GPUtil', '1.4.0', { From d61d9444b28d3786819585b18b8adb1959773218 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 14:42:49 +0200 Subject: [PATCH 0624/2365] adding easyconfigs: NFFT-3.1.3-foss-2020b.eb, NFFT-3.1.3-fosscuda-2020b.eb --- .../n/NFFT/NFFT-3.1.3-foss-2020b.eb | 22 +++++++++++++++++++ .../n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb | 22 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-foss-2020b.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-foss-2020b.eb new file mode 100644 index 0000000000..600e4ec0ab --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-foss-2020b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' +name = 'NFFT' +version = '3.1.3' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier +transform) is a C subroutine library for computing the nonequispaced +discrete Fourier transform (NDFT) and its generalisations in one or more +dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e4f65f0d1aa81cf76a506f10a9ac68bdcd770a4426671274d372101dca497382'] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3util.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..2d7c67fc27 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' +name = 'NFFT' +version = '3.1.3' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier +transform) is a C subroutine library for computing the nonequispaced +discrete Fourier transform (NDFT) and its generalisations in one or more +dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e4f65f0d1aa81cf76a506f10a9ac68bdcd770a4426671274d372101dca497382'] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3util.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'lib' From 21d25a682bb4ae906d896701a86f599143545197 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 14:54:46 +0200 Subject: [PATCH 0625/2365] removed versionsuffix --- .../PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb | 29 +++++++++++++++++++ .../PyQtGraph-0.11.1-fosscuda-2020b.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb new file mode 100644 index 0000000000..b8ec4d2ff1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' +# TH77EMBL adapted from PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb +name = 'PyQtGraph' +version = '0.11.1' + +homepage = 'http://www.pyqtgraph.org/' +description = """PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +github_account = 'pyqtgraph' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9c103e965fb9398570f07c961030cc20fbb80d516a540011f868600a431c4a0d'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy + ('PyQt5', '5.15.1'), + ('PyOpenGL', '3.1.5'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..2d988f4afb --- /dev/null +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' +# TH77EMBL adapted from PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb +name = 'PyQtGraph' +version = '0.11.1' + +homepage = 'http://www.pyqtgraph.org/' +description = """PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +github_account = 'pyqtgraph' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9c103e965fb9398570f07c961030cc20fbb80d516a540011f868600a431c4a0d'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy + ('PyQt5', '5.15.1'), + ('PyOpenGL', '3.1.5'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'vis' From d8a2112d29d4bac766efb39d9d44efc34d8bb15f Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 1 Apr 2021 15:21:13 +0000 Subject: [PATCH 0626/2365] Removes netCDF since it was added to repo in the meantime. --- .../n/netCDF/netCDF-4.7.4-gompic-2020b.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb deleted file mode 100644 index 7fe6fa75d9..0000000000 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompic-2020b.eb +++ /dev/null @@ -1,41 +0,0 @@ -## -# Author: Robert Mijakovic -## -name = 'netCDF' -version = '4.7.4' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompic', 'version': '2020b'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['netCDF-%(version)s_fix-ocdebug.patch'] -checksums = [ - '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b', # v4.7.4.tar.gz - '94c9883005f189a4551947e04191a68199cf4cdcada4b2d313115720fb4690e9', # netCDF-4.7.4_fix-ocdebug.patch -] - -builddependencies = [ - ('Autotools', '20200321'), - ('CMake', '3.18.4'), - ('Doxygen', '1.8.20'), -] - -dependencies = [ - ('HDF5', '1.10.7'), - ('cURL', '7.72.0'), - ('Szip', '2.1.1'), -] - -# make sure both static and shared libs are built -configopts = [ - "-DBUILD_SHARED_LIBS=OFF ", - "-DBUILD_SHARED_LIBS=ON ", -] - -moduleclass = 'data' From c86acb8125ff87337cd45ac9e477b49a93cb95ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Apr 2021 17:21:19 +0200 Subject: [PATCH 0627/2365] adding easyconfigs: PyOD-0.8.7-intel-2020b.eb, PyOD-0.8.7-foss-2020b.eb --- .../p/PyOD/PyOD-0.8.7-foss-2020b.eb | 29 +++++++++++++++++++ .../p/PyOD/PyOD-0.8.7-intel-2020b.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb diff --git a/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb new file mode 100644 index 0000000000..855ae31318 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyOD' +version = '0.8.7' + +homepage = 'https://pyod.readthedocs.io' +description = "PyOD is a comprehensive and scalable Python toolkit for detecting outlying objects in multivariate data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('statsmodels', '0.12.1'), + ('numba', '0.52.0'), + ('matplotlib', '3.3.3'), +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d891038825869190bb6a8187aadc1957254907b7465c7aab83f07835607e41df'] + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from pyod.models.knn import KNN'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb new file mode 100644 index 0000000000..d02fdae23e --- /dev/null +++ b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyOD' +version = '0.8.7' + +homepage = 'https://pyod.readthedocs.io' +description = "PyOD is a comprehensive and scalable Python toolkit for detecting outlying objects in multivariate data." + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('statsmodels', '0.12.1'), + ('numba', '0.52.0'), + ('matplotlib', '3.3.3'), +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d891038825869190bb6a8187aadc1957254907b7465c7aab83f07835607e41df'] + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from pyod.models.knn import KNN'"] + +moduleclass = 'data' From 4d3192078143c04f69475d8f98de1670008deb4b Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 1 Apr 2021 15:23:48 +0000 Subject: [PATCH 0628/2365] STAR bumped to 2.7.8a --- .../s/STAR/STAR-2.7.8a-GCC-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb new file mode 100644 index 0000000000..987c24ea99 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb @@ -0,0 +1,41 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.8a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e6bf898291a1a350b36d8c031d3f65fc66869e6775a053af57c9cfe275f77305'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/STAR', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' From cd0467d0746f7fa8fcaa4ba8fbe7a76cef206b5a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Apr 2021 17:29:26 +0200 Subject: [PATCH 0629/2365] add missing easyconfigs for PyOD dependencies (statsmodels with foss/2020b, numba with intel/2020b) --- .../n/numba/numba-0.52.0-intel-2020b.eb | 49 +++++++++++++++++++ .../statsmodels-0.12.1-foss-2020b.eb | 29 +++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.52.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.52.0-intel-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.52.0-intel-2020b.eb new file mode 100644 index 0000000000..b5137cf2da --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.52.0-intel-2020b.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.52.0' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('LLVM', '10.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('llvmlite', '0.35.0', { + 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", + 'checksums': [ + '80e51d5aa02ad72da9870e89d21f9b152b0220ca551b4596a6c0614bcde336fc', # llvmlite-0.35.0.tar.gz + # llvmlite-0.31.0_fix-ffi-Makefile.patch + '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', + ], + }), + (name, version, { + 'checksums': ['44661c5bd85e3d3619be0a40eedee34e397e9ccb3d4c458b70e10bf95d1ce933'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb new file mode 100644 index 0000000000..143c22861d --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.12.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + (name, version, { + 'checksums': ['a271b4ccec190148dccda25f0cbdcbf871f408fc1394a10a7dc1af4a62b91c8e'], + }), +] + +moduleclass = 'math' From 845a62aa80f2c2fd97556f55474477c5163371a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Apr 2021 18:04:19 +0200 Subject: [PATCH 0630/2365] enable download_dep_fail for PyOD --- easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb | 1 + easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb index 855ae31318..ea2eaeedee 100644 --- a/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb @@ -20,6 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] checksums = ['d891038825869190bb6a8187aadc1957254907b7465c7aab83f07835607e41df'] +download_dep_fail = True use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb index d02fdae23e..f6d7667e03 100644 --- a/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb @@ -20,6 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] checksums = ['d891038825869190bb6a8187aadc1957254907b7465c7aab83f07835607e41df'] +download_dep_fail = True use_pip = True sanity_pip_check = True From 5c55ed08c119d254365a14a7f1f08f6da880dd2b Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 20:41:40 +0200 Subject: [PATCH 0631/2365] adding easyconfigs: CuPy-8.5.0-fosscuda-2020b.eb, Cython-0.29.22-GCCcore-10.2.0.eb and patches: CuPy-8.5.0_sanitycheck_fix.patch --- .../c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb | 44 +++++++++++++++ .../c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb | 53 +++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..e7d275c6ef --- /dev/null +++ b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'CuPy' +version = '8.5.0' + +homepage = 'https://cupy.dev' +description = "CuPy is an open-source array library accelerated with NVIDIA CUDA." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +# setup.py requirement Cython>=0.29.22. Build fails with 0.29.21 +# after patching setup.py +builddependencies = [('Cython', '0.29.22')] +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), + ('NCCL', '2.8.3', '-CUDA-11.1.1', True), + ('cuTENSOR', '1.2.2.5', '-CUDA-11.1.1', True), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} +postinstallcmds = [ + # req for sanity check on build nodes without libcuda.so. + # will be removed my patched __init__.py at sanity check import. + 'cp $EBROOTCUDA/./targets/x86_64-linux/lib/stubs/libcuda.* %(installdir)s/lib && ls %(installdir)s/lib' +] +exts_list = [ + ('fastrlock', '0.5', { + 'checksums': ['9ae1a31f6e069b5f0f28ba63c594d0c952065de0a375f7b491d21ebaccc5166f'], + }), + ('cupy', version, { + 'patches': ['CuPy-8.5.0_sanitycheck_fix.patch'], + 'checksums': [ + 'fb3f8d3b3454beb249b9880502a45fe493c5a44efacc4c72914cbe1a5dbdf803', # cupy-8.5.0.tar.gz + 'c0acecccec1bfcc0697b9840228fe71813d0ea98cc975f627c106b48c6c02710', # CuPy-8.5.0_sanitycheck_fix.patch + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f10cea5a2c --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , +# Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +# Updated: Pavel Grochal (INUITS) +## +# Thomas Hoffmann, EMBL Heidelberg: Adapted to v0.29.22, GCCcore 10.2.0 +# 2021/03 +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.29.22' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['df6b83c7a6d1d967ea89a2903e4a931377634a297459652e4551734c48195406'] + +builddependencies = [('binutils', '2.35')] + +# Can't use multi_dep because EBPYTHONPREFIXES are not loaded in order. +# This results in not beeing able to choose Cython version in multi_dep. +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True + +use_pip = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cython --version', +] + +moduleclass = 'lang' From e239ebdca96058ff65f6a06b4e41900eca3cbe3d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 2 Apr 2021 09:50:29 +0200 Subject: [PATCH 0632/2365] add extensions OUTRIDER and FRASER + dependencies to R-bundle-Bioconductor-3.12 --- ...le-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index 38eb0cc24c..62fbe0e4ec 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -987,6 +987,33 @@ exts_list = [ ('motifmatchr', '1.12.0', { 'checksums': ['ff98ca2efbe89692deb19156733bf06879ce2c8ed7cde601aa10bc8621b0377f'], }), + ('extraDistr', '1.9.1', { + 'checksums': ['9990348c4dbc611684fcb58ab8db7e856dfde1c9c86ffb7705f4b3dff6b2d7bf'], + }), + ('PRROC', '1.3.1', { + 'checksums': ['479118ce47c527bc97fb58d531a31cabc094d9843d62f16922009dc62e8248d4'], + }), + ('TSP', '1.1-10', { + 'checksums': ['44979f16803806419a94a6b0daeac812f4e7bd52d2fff11561fd4bbc41353b7c'], + }), + ('qap', '0.1-1', { + 'checksums': ['60bd564bb0e6325de44351af33870177d84b1c00ded142a2efb12a16a20d4d34'], + }), + ('seriation', '1.2-9', { + 'checksums': ['8b9279caf60755377ee9023971bff33634f7bb9c055d4ebb493b648512b09dbe'], + }), + ('egg', '0.4.5', { + 'checksums': ['15c8ba7cf2676eb0460de7e5dfbc89fc3175ac22a8869cfd44d66d156fd6c7bb'], + }), + ('heatmaply', '1.2.1', { + 'checksums': ['2dddf6741eaaa49c1354b7092ded5ac6d06df9d6accd879c16c6731bed745743'], + }), + ('OUTRIDER', '1.8.0', { + 'checksums': ['d2476389a30477ea09f5a9cfe4e0e4de756b1f1c952225ec433812fe9a3beb67'], + }), + ('FRASER', '1.2.1', { + 'checksums': ['37562b7e92fd95feb950f160b38427f23a9e31729fa0783b441fc74fc45f7120'], + }), ] modextrapaths = {'R_LIBS': ''} From be51444ca86089060710babb326160e65c8227b0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 2 Apr 2021 12:13:14 +0200 Subject: [PATCH 0633/2365] adding easyconfigs: GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb --- .../GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb new file mode 100644 index 0000000000..2cdd419f4a --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.2.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] + +multi_deps = {'Python': ['3.8.6', '2.7.18']} + +dependencies = [ + ('Java', '1.8', '', True), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' From 9d67340384cf09da8eed789d0dea5980ade52b8b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 2 Apr 2021 14:41:00 +0200 Subject: [PATCH 0634/2365] adding easyconfigs: GTS-0.7.6-GCCcore-10.2.0.eb --- .../g/GTS/GTS-0.7.6-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e38f674aa1 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.35'), +] +dependencies = [ + ('GLib', '2.66.1'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [], +} + +moduleclass = 'vis' From e3541afe3a1db9733b99a5b136b25cb4807b7b77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Apr 2021 13:38:32 +0200 Subject: [PATCH 0635/2365] avoid 0.0.0 install version for various Python apps --- easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb | 2 ++ easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb b/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb index b8301fe060..3193eac6e2 100644 --- a/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb +++ b/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb @@ -27,6 +27,8 @@ dependencies = [ ('Pysam', '0.16.0.1'), ] +preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ + use_pip = True download_dep_fail = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb b/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb index 53530368e6..9ec8b94f25 100644 --- a/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb +++ b/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb @@ -27,6 +27,8 @@ dependencies = [ ('Pysam', '0.16.0.1'), ] +preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ + use_pip = True sanity_pip_check = True download_dep_fail = True From 4636e45b619764ca68195245721de103597084e1 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 5 Apr 2021 20:48:01 +0000 Subject: [PATCH 0636/2365] libxc bumped up to version 5.1.3 --- .../l/libxc/libxc-5.1.3-GCC-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..59a421a6ea --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '5.1.3' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Perl', '5.32.0'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +parallel = 1 + +moduleclass = 'chem' From b08d0d51c83b88aa86843740ad3e754aa03891b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Apr 2021 10:41:56 +0200 Subject: [PATCH 0637/2365] adding easyconfigs: GPyOpt-1.2.6-intel-2020b.eb --- .../g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb diff --git a/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb new file mode 100644 index 0000000000..0ac934a041 --- /dev/null +++ b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'GPyOpt' +version = '1.2.6' + +homepage = 'https://sheffieldml.github.io/GPyOpt' +description = "GPyOpt is a Python open-source library for Bayesian Optimization" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True + +exts_list = [ + ('paramz', '0.9.5', { + 'checksums': ['0917211c0f083f344e7f1bc997e0d713dbc147b6380bc19f606119394f820b9a'], + }), + ('GPy', '1.9.9', { + 'modulename': 'GPy', + 'checksums': ['04faf0c24eacc4dea60727c50a48a07ddf9b5751a3b73c382105e2a31657c7ed'], + }), + (name, version, { + 'modulename': 'GPyOpt', + 'checksums': ['e714daa035bb529a6db23c53665a762a4ab3456b9329c19ad3b03983f94c9b2a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From e1c089c7a17f7117342f45166ccc4ffdfdb6e8fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Apr 2021 11:12:37 +0200 Subject: [PATCH 0638/2365] stick to compiler-only toolchain for Flye 2.8.3 --- .../f/Flye/Flye-2.8.3-GCC-10.2.0.eb | 30 +++++++++++++++++++ .../f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..fbfc9e5978 --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.8.3' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['070f9fbee28eef8e8f87aaecc048053f50a8102a3715e71b16c9c46819a4e07c'] + +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..8a10044a12 --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.8.3' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['070f9fbee28eef8e8f87aaecc048053f50a8102a3715e71b16c9c46819a4e07c'] + +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' From bef27f0c3d90a173dc20ddbeb9d040ae9e6f75ff Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 6 Apr 2021 11:39:41 +0200 Subject: [PATCH 0639/2365] removed source_urls; added sanity_pip_check --- .../easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb index f10cea5a2c..7c9a95c040 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb @@ -27,7 +27,6 @@ docurls = [ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['df6b83c7a6d1d967ea89a2903e4a931377634a297459652e4551734c48195406'] @@ -41,6 +40,8 @@ download_dep_fail = True use_pip = True +sanity_pip_check = True + sanity_check_paths = { 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 6e22dc3dc51310e5c3262b1ca56824e3627120d1 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 6 Apr 2021 15:28:22 +0200 Subject: [PATCH 0640/2365] adding easyconfigs: NewHybrids-1.1_Beta3-GCC-10.2.0.eb --- .../NewHybrids-1.1_Beta3-GCC-10.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb new file mode 100644 index 0000000000..e42cb50b8e --- /dev/null +++ b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb @@ -0,0 +1,45 @@ +# Author: Denis Krišťák (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'NewHybrids' +version = '1.1_Beta3' + +homepage = 'http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm#NewHybs' +description = """This implements a Gibbs sampler to estimate the posterior probability that genetically sampled +individuals fall into each of a set of user-defined hybrid categories.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/eriqande', + 'repo_name': 'newhybrids', + 'commit': '6fc8fd9ca6e64ee0be08af12ec8bfe73a7de00cc', + 'recursive': True, + } +}] + +skipsteps = ['configure'] + +build_cmd = './Compile-with-no-gui-Linux.sh' + +files_to_copy = ['*'] + +postinstallcmds = ['mkdir %(installdir)s/bin/linux', + 'cp %(installdir)s/newhybrids-no-gui-linux.exe %(installdir)s/bin/linux/newhybs'] + +sanity_check_paths = { + 'files': ['newhybrids-no-gui-linux.exe'], + 'dirs': [], +} + +modextrapaths = {'PATH': ['bin/linux']} + +sanity_check_commands = [ + 'newhybs -d %(installdir)s/test_data/TestDat.txt --no-gui | grep Output\ is\ in\ the\ following\ files', +] + +moduleclass = 'bio' From 66253c8e650793b978eea3737e8e93563f174785 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Apr 2021 15:34:16 +0200 Subject: [PATCH 0641/2365] adding easyconfigs: garnett-0.1.20-foss-2020b-R-4.0.3.eb --- .../garnett-0.1.20-foss-2020b-R-4.0.3.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..6e85259214 --- /dev/null +++ b/easybuild/easyconfigs/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'garnett' +local_commit = 'bfca215' +version = '0.1.20' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cole-trapnell-lab.github.io/garnett' +description = """Garnett is a software package that faciliates automated cell type classification from single-cell +expression data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), + ('Monocle3', '0.2.3', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('rly', '1.6.2', { + 'checksums': ['22837a41586b6c7afb3d09b1bf71af9189a8bb846a77c55823a2dc98c72b65ad'], + }), + (name, version, { + 'source_urls': ['https://github.com/cole-trapnell-lab/garnett/archive/'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit, + }], + 'checksums': ['e103de561f5c846ba6ee1ec0f09ca9127d9e392a457bb860929258601485c260'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 996e647744eb53189f9c0ffc510d0f63ec6d3589 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Apr 2021 16:00:52 +0200 Subject: [PATCH 0642/2365] update $R_LIBS_SITE rather than $R_LIBS in easyconfigs installing R packages --- .../easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb | 2 +- .../R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb index b73eacbe67..fdeb49b42a 100644 --- a/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb @@ -81,7 +81,7 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS': ''} +modextrapaths = {'R_LIBS_SITE': ''} sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index 62fbe0e4ec..3c687feedc 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -1016,7 +1016,7 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS': ''} +modextrapaths = {'R_LIBS_SITE': ''} sanity_check_paths = { 'files': [], From ac102d3e09a6c3942e1ef50fe04a8a3f884df419 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Apr 2021 16:03:19 +0200 Subject: [PATCH 0643/2365] add pkg-config build dep for segemehl 0.3.4 with GCC/10.2.0 --- .../easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb index cfa7f2dfd9..f6c29cfd24 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' -name = "segemehl" -version = "0.3.4" +name = 'segemehl' +version = '0.3.4' homepage = 'https://www.bioinf.uni-leipzig.de/Software/segemehl/' description = """segemehl is a software to map short sequencer reads to reference genomes. @@ -18,6 +18,8 @@ source_urls = ['https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] +builddependencies = [('pkg-config', '0.29.2')] + dependencies = [ ('HTSlib', '1.11'), ('ncurses', '6.2'), From 94e6636e398c5b277a26279bbd136d2f15f5ed0e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 6 Apr 2021 16:39:45 +0200 Subject: [PATCH 0644/2365] updating as per review --- .../NewHybrids-1.1_Beta3-GCC-10.2.0.eb | 21 ++++++++----------- 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb index e42cb50b8e..c93b5b6244 100644 --- a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb @@ -1,7 +1,7 @@ # Author: Denis Krišťák (INUITS) # License: GPLv2 -easyblock = 'MakeCp' +easyblock = 'Binary' name = 'NewHybrids' version = '1.1_Beta3' @@ -12,6 +12,8 @@ individuals fall into each of a set of user-defined hybrid categories.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} +extract_sources = True + sources = [{ 'filename': SOURCE_TAR_GZ, 'git_config': { @@ -21,23 +23,18 @@ sources = [{ 'recursive': True, } }] +checksums = ['2cc1d3e95ce167312f3be971a3acd1951bf1cdd49313696a86ee22b7685fc56c'] -skipsteps = ['configure'] - -build_cmd = './Compile-with-no-gui-Linux.sh' - -files_to_copy = ['*'] - -postinstallcmds = ['mkdir %(installdir)s/bin/linux', - 'cp %(installdir)s/newhybrids-no-gui-linux.exe %(installdir)s/bin/linux/newhybs'] +install_cmd = '%(builddir)s/newhybrids/Compile-with-no-gui-Linux.sh && ' +install_cmd += 'mkdir %(installdir)s/bin && ' +install_cmd += 'cp -a %(builddir)s/newhybrids/newhybrids-no-gui-linux.exe %(installdir)s/bin/newhybs && ' +install_cmd += 'cp -ar %(builddir)s/newhybrids/test_data %(installdir)s/' sanity_check_paths = { - 'files': ['newhybrids-no-gui-linux.exe'], + 'files': ['bin/newhybs'], 'dirs': [], } -modextrapaths = {'PATH': ['bin/linux']} - sanity_check_commands = [ 'newhybs -d %(installdir)s/test_data/TestDat.txt --no-gui | grep Output\ is\ in\ the\ following\ files', ] From d66fe6b61ce1b072c0cdf7c0557e230a948ddd2f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 6 Apr 2021 16:56:49 +0200 Subject: [PATCH 0645/2365] tests --- .../easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb index c93b5b6244..0967b36689 100644 --- a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb @@ -6,7 +6,7 @@ easyblock = 'Binary' name = 'NewHybrids' version = '1.1_Beta3' -homepage = 'http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm#NewHybs' +homepage = 'https://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm#NewHybs' description = """This implements a Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories.""" From b6a16c7859a5baaa7f7043944470a6dd82edd6f1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 6 Apr 2021 17:26:14 +0200 Subject: [PATCH 0646/2365] adding easyconfigs: GitPython-3.1.14-GCCcore-10.2.0.eb --- .../GitPython-3.1.14-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..85b9fc305f --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.14' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('git', '2.28.0', '-nodocs'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('smmap', '4.0.0', { + 'checksums': ['7e65386bd122d45405ddf795637b7f7d2b532e7e401d46bbe3fb49b9986d5182'], + }), + ('gitdb', '4.0.7', { + 'checksums': ['96bf5c08b157a666fec41129e6d327235284cca4c81e92109260f353ba138005'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['be27633e7509e58391f10207cd32b2a6cf5b908f92d9cd30da2e514e1137af61'], + }), +] + +moduleclass = 'lib' From 4c03c5153c0889c428d5560e783cd7e148950a04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Apr 2021 18:06:32 +0200 Subject: [PATCH 0647/2365] update to LAPACK 3.9.1 for goblf/2020b --- easybuild/easyconfigs/g/goblf/goblf-2020b.eb | 2 +- .../l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb | 16 ++++++++++++++++ .../ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb | 2 +- 3 files changed, 18 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/g/goblf/goblf-2020b.eb b/easybuild/easyconfigs/g/goblf/goblf-2020b.eb index 9b191e1790..3b85015988 100644 --- a/easybuild/easyconfigs/g/goblf/goblf-2020b.eb +++ b/easybuild/easyconfigs/g/goblf/goblf-2020b.eb @@ -24,7 +24,7 @@ dependencies = [ local_comp, ('OpenMPI', '4.0.5', '', local_comp), # part of gompi toolchain ('BLIS', '0.8.0', '', local_gcccore), - ('LAPACK', '3.9.0', '', local_comp), + ('LAPACK', '3.9.1', '', local_comp), ('ScaLAPACK', '2.1.0', '-bl', local_comp_mpi_tc), ('FFTW', '3.3.8', '', local_comp_mpi_tc), ] diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..3990b2cebe --- /dev/null +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb @@ -0,0 +1,16 @@ +name = 'LAPACK' +version = '3.9.1' + +homepage = 'https://www.netlib.org/lapack/' +description = """LAPACK is written in Fortran90 and provides routines for solving systems of + simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue + problems, and singular value problems.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Reference-LAPACK/lapack/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d0085d2caf997ff39299c05d4bacb6f3d27001d25a4cc613d48c1f352b73e7e0'] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb index b95684c3a0..2fba79399b 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('BLIS', '0.8.0'), - ('LAPACK', '3.9.0'), + ('LAPACK', '3.9.1'), ] # Config Opts based on AOCL User Guide: From 9150138178c7cffe249cf591ec56182006ddc4fd Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 6 Apr 2021 20:33:05 +0200 Subject: [PATCH 0648/2365] updating as per review --- .../n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb index 0967b36689..89ed496184 100644 --- a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb @@ -12,8 +12,6 @@ individuals fall into each of a set of user-defined hybrid categories.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -extract_sources = True - sources = [{ 'filename': SOURCE_TAR_GZ, 'git_config': { @@ -23,7 +21,9 @@ sources = [{ 'recursive': True, } }] -checksums = ['2cc1d3e95ce167312f3be971a3acd1951bf1cdd49313696a86ee22b7685fc56c'] +checksums = [None] + +extract_sources = True install_cmd = '%(builddir)s/newhybrids/Compile-with-no-gui-Linux.sh && ' install_cmd += 'mkdir %(installdir)s/bin && ' @@ -32,7 +32,7 @@ install_cmd += 'cp -ar %(builddir)s/newhybrids/test_data %(installdir)s/' sanity_check_paths = { 'files': ['bin/newhybs'], - 'dirs': [], + 'dirs': ['test_data'], } sanity_check_commands = [ From 6c6b38e9f22730f64c473c07e46f139de659bf73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Apr 2021 21:15:43 +0200 Subject: [PATCH 0649/2365] add Python 3 build dep for HMMER 3.3.x test step --- easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb index 116dc59a97..a39fc442b6 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb @@ -37,6 +37,8 @@ source_urls = [ sources = ['hmmer-%(version)s.tar.gz'] checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] +builddependencies = [('Python', '3.8.6')] + configopts = '--enable-mpi' runtest = 'check' From 37a2dd0030e8a6d5f9f13bf05cec4c2b3cff7258 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 7 Apr 2021 05:38:26 +0000 Subject: [PATCH 0650/2365] adding easyconfigs: R-4.0.5-foss-2020b.eb, R-4.0.5-fosscuda-2020b.eb --- .../easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 2852 +++++++++++++++++ .../easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 2849 ++++++++++++++++ 2 files changed, 5701 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb new file mode 100644 index 0000000000..09000f5679 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -0,0 +1,2852 @@ +## +# Author: Robert Mijakovic +## +name = 'R' +version = '4.0.5' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.9'), +] +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('PCRE2', '10.35'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.5'), # for plottting in R + ('LibTIFF', '4.1.0'), + ('Java', '11', '', True), + ('Tk', '8.6.10'), # for tcltk + ('cURL', '7.72.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.0'), # for igraph + ('NLopt', '2.6.2'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '67.1'), # for rJava & gdsfmt + ('HDF5', '1.10.7'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.10-35'), # for animation + ('GLPK', '4.65'), # for Rglpk + ('nodejs', '12.19.0'), # for V8 (required by rstan) + ('GDAL', '3.2.1') # for sf + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 07 Apr 2021 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9.1', { + 'checksums': ['99e02a955935040bf0834d44d1dc10a3794c8260fd072d3aff3e15ab249e0ac9'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.6', { + 'checksums': ['c9f24756bc000f7a989bd4f9aa93d57f7739dcde77946703f8bb32332a35f012'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '4.0.4', { + 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], + }), + ('bnlearn', '4.6.1', { + 'checksums': ['e4544465af3330e53e4777079c448585a8a97be2d3862a5264169007c20daeaf'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.16', { + 'checksums': ['e7dea648ee018e2c8c8834084051c76f7e8b2b42067772c62035a941c32457a9'], + }), + ('formatR', '1.8', { + 'checksums': ['df7885827149e186b2b902fd01a18d1a514e50f9912f38c308949e2847f10613'], + }), + ('gtools', '3.8.2', { + 'checksums': ['503ba60a41f3c61b8129c25de62c74dab29761d2e661d4addd106e2e02f1dcde'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('highr', '0.8', { + 'checksums': ['4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.10', { + 'checksums': ['783233a15a817a7530d140e9825565a661aa4bdea7c635d11b9c74faa33be3f7'], + }), + ('xfun', '0.22', { + 'checksums': ['3e717b0eb8100f01c84e2d69c2618f9e54b801a44eef5a2ce4c030c123b8a347'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-3', { + 'checksums': ['b1f92be633243185ab86e880a1e1ac5a4dd3c535d01ebd187a4872d0a8c6f194'], + }), + ('NLP', 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['1ab679eb1976d74cd3be5bcad0af7fcc673dbdfd4406bbce32591c8fddfb93b4'], + }), + ('remotes', '2.3.0', { + 'checksums': ['677d676b60288196c4329fcd00747041f0221d241920e918bd1bf6b610316538'], + }), + ('clisymbols', '1.2.0', { + 'checksums': ['0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.1', { + 'checksums': ['b14aaf4e910a9d2d6c65c93e645f0b0159c00898e669f917f83c03dfedb1dfea'], + }), + ('gh', '1.2.1', { + 'checksums': ['00cfbf7a48a0587d651233dd661092fdc52f70ec592e6f98470e891c160eaa9b'], + }), + ('credentials', '1.3.0', { + 'checksums': ['c119ec26fd97b977c3b0cd1eb8fad3c59b84df6262c3adbf5ee9f3d6c9903ff1'], + }), + ('gert', '1.3.0', { + 'checksums': ['071229134517b47ef710fc5586a27458be308daef21cc8c2f603492ed21507ba'], + }), + ('usethis', '2.0.1', { + 'checksums': ['ef269e7a3190791bc77ff1d5cb11f20cb594adedb334805f88db5451f3ffd6c8'], + }), + ('rex', '1.2.0', { + 'checksums': ['06b491f1469078862e40543fd74e1d38b2e0fb61fdf01c8083add4b11ac2eb54'], + }), + ('covr', '3.5.1', { + 'checksums': ['a54cfc3623ea56084158ac5d7fe33f216f45191f6dcddab9c9ed4ec1d9d8ac6c'], + }), + ('devtools', '2.3.2', { + 'checksums': ['e5086106baef6bb925445dfdddb3cd5ff4f8fff96353365b135aba5618d1986d'], + }), + ('Rook', '1.1-1', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.5-12.2', { + 'checksums': ['dd524105c83b82b5c3b3ee2583ef90d4cafa54b0c29817dac48b425b79f90f92'], + }), + ('RMTstat', '0.3', { + 'checksums': ['81eb4c5434d04cb66c749a434c33ceb1c07d92ba79765d4e9233c13a092ec2da'], + }), + ('Lmoments', '1.3-1', { + 'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'], + }), + ('distillery', '1.2', { + 'checksums': ['1eb129b019b5fe9a4599c3e902ecc222c7aa3ff0602b45ee25495c086e82d082'], + }), + ('extRemes', '2.1', { + 'checksums': ['2d760b8d9db81fa70ac20735c10ef612908cea39cc779cc71b171afaebc8c9ac'], + }), + ('tkrplot', '0.0-25', { + 'checksums': ['21ae0e869e024838b9bf42a0c06d55672a2683453dc9218327409086a611ed5c'], + }), + ('misc3d', '0.9-0', { + 'checksums': ['a1e9291d625bd1312bae5b0e26d48b9362f66a8a0fabbf48891ba1d2432e4e82'], + }), + ('multicool', '0.1-11', { + 'checksums': ['1c907e64af2ac39facdf431a5691e69649f64af1f50e198ae39da5bf30026476'], + }), + ('plot3D', '1.3', { + 'checksums': ['b9e4ec2789e34ad249318900e186868650e1a33466b385cb492a45466db3dfc9'], + }), + ('plot3Drgl', '1.0.1', { + 'checksums': ['466d428d25c066c9c96d892f24da930513d42b1bdf76d3b53628c3ba13c3e48a'], + }), + ('OceanView', '1.0.5', { + 'checksums': ['c16e1bed97f4ede46dc017fdd6bd7575d925b57bd2601317bd3ad2357609f885'], + }), + ('ks', '1.12.0', { + 'checksums': ['e6affe52bbfe73e31387462c57dfe56058c5d64f54e5c7b7c794187c6936cee9'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-18.1', { + 'checksums': ['2fa5f78a7603cbae94a5e38e791938596a053d48c609a7c120a19cbb7d93c66f'], + }), + ('penalized', '0.9-51', { + 'checksums': ['eaa80dca99981fb9eb576261f30046cfe492d014cc2bf286c447b03a92e299fd'], + }), + ('clusterRepro', '0.9', { + 'checksums': ['940d84529ff429b315cf4ad25700f93e1156ccacee7b6c38e4bdfbe2d4c6f868'], + }), + ('data.tree', '1.0.0', { + 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('visNetwork', '2.0.9', { + 'checksums': ['5e0b3dc3a91e66e0a359433f03cc856d04b981b0f9ad228d8fa9c96b7fcaa420'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.6.1', { + 'checksums': ['be4e4c520a3692902ce405e8225aef9f3d5f0cd11fcde614f6541e981b63673d'], + }), + ('randomForestSRC', '2.11.0', { + 'checksums': ['6295fa43bb20bd5248e30a3239259185acfb4c2b6219be9c7a9306031a1c3744'], + }), + ('sm', '2.2-5.6', { + 'checksums': ['b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-8', { + 'checksums': ['40e204909100b7338619ae23cd87e0a4058e581c286da2327f36dbb3834b84a2'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.11-2', { + 'checksums': ['8385be32f6b6b6f1b32df15f42073b191d714d870bbb4f95875b64aff6112bbf'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('servr', '0.21', { + 'checksums': ['3fc0da063dd04b796a49ce62bf8e69d5854679520da90cc92ee3fc0a0b2ad389'], + }), + ('rgexf', '0.16.0', { + 'checksums': ['2a671df9ac70cfefd4092754317cb28e32a33df345b80e1975bf838e838245ee'], + }), + ('sem', '3.1-11', { + 'checksums': ['33b1ad7695db13af8cdd214f5d388db494528b433c61c7ad89970cefcc8b430e'], + }), + ('network', '1.16.1', { + 'checksums': ['eb6435794cacc81abe1664391e8dcf1c10112bbb76fff9016dd6dbb8e83efeb1'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('statnet.common', '4.4.1', { + 'checksums': ['4ecf2b84718d7fb60f196215b4cf6f52cd6b26cc9148a6da6981b26e885509fd'], + }), + ('sna', '2.6', { + 'checksums': ['3a016550d9f424a0613c3f5b0b680dbd3a1f20a343173d39a96034340ad9202a'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.4.1', { + 'checksums': ['78ef9eae464d52c5247998b9514a81b178419b857b1a6c00d885e3ae6c03a886'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('BDgraph', '2.63', { + 'checksums': ['cc474e1315a04f67fbf14461d35004c899d031c31f18be7d3db076dbf66a0617'], + }), + ('pbapply', '1.4-3', { + 'checksums': ['8fe6287535be766b5a688810e2cc1ca4e668ac6b42b6e832473fe5701133eb21'], + }), + ('graphlayouts', '0.7.1', { + 'checksums': ['380f8ccb0b08735694e83f661fd56a0d592a78448ae91b89c290ba8582d66717'], + }), + ('tweenr', '1.0.2', { + 'checksums': ['1805f575da6705ca4e5ec1c4605222fc826ba806d9ff9af41770294fe08ff69f'], + }), + ('ggforce', '0.3.3', { + 'checksums': ['2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f'], + }), + ('tidygraph', '1.2.0', { + 'checksums': ['057d6c42fc0144109f3ace7f5058cca7b2fe493c761daa991448b23f86b6129f'], + }), + ('ggraph', '2.0.5', { + 'checksums': ['e36ad49dba92ee8652e18b1fb197be0ceb9f0a2f8faee2194453a62578449654'], + }), + ('qgraph', '1.6.9', { + 'checksums': ['b125a9c1b505632da8b404811c8d6d667736f229d95994ca7913beacabc36b94'], + }), + ('HWxtest', '1.1.9', { + 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], + 'checksums': [ + 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + ], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.19', { + 'checksums': ['4cd2d080628482f4c6ecab593313d7e42516f5ff13fbf9f90e461fcad0580738'], + }), + ('geepack', '1.3-2', { + 'checksums': ['99b53e40f7e5fda7422b143e6fee16513e2f880cb04a97cd403e98c4760670a6'], + }), + ('biom', '0.3.12', { + 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], + }), + ('pim', '2.0.2', { + 'checksums': ['1195dbdbd67348dfef4b6fc34fcec643da685ebe58d34bbe049ab121aca9944f'], + }), + ('minpack.lm', '1.2-1', { + 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], + }), + ('rootSolve', '1.8.2.1', { + 'checksums': ['488451182663197ae4513e46e24f72cadb2297d35a58a3007a0dbf1bf0833031'], + }), + ('diagram', '1.6.5', { + 'checksums': ['e9c03e7712e0282c5d9f2b760bafe2aac9e99a9723578d9e6369d60301f574e4'], + }), + ('FME', '1.3.6.1', { + 'checksums': ['ae0c69f75614e2ef9f2096c205c7f8eb90485c6311213762c1416ece4036be18'], + }), + ('bmp', '0.3', { + 'checksums': ['bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649'], + }), + ('tiff', '0.1-8', { + 'checksums': ['4b7482f70d8ecef9596b766ef1c64102c8b09208cb769c39d9e4db81cb3ba1a2'], + }), + ('readbitmap', '0.1.5', { + 'checksums': ['737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291'], + }), + ('imager', '0.42.8', { + 'checksums': ['8515ed79a03d15a4b68e7d39d02d3cb222615bc78bf9b5902824a669e848f4cf'], + }), + ('signal', '0.7-6', { + 'checksums': ['6b60277b07cf0167f8272059b128cc82f27a9bab1fd33d74c2a9e1f2abca5def'], + }), + ('tuneR', '1.3.3', { + 'checksums': ['bdc3c2017b162d2ba0a249e80361a4f47202e763c21aecfc57380a482a3a692b'], + }), + ('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-7', { + 'checksums': ['52e0397a45325aa9586ec68b94ab9e505bdefaf2a588d634fcb57a6a11659c74'], + }), + ('fftw', '1.0-6', { + 'checksums': ['397ef5ec354b919884f74fba4202bfc13ad11a70b16285c41677aad1d3b170ce'], + }), + ('seewave', '2.1.6', { + 'checksums': ['84a0a0035737574a65f371fa4a20a1a3a66de195efe41975f21be8fb001e7088'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('sf', '0.9-8', { + 'checksums': ['11570a6578701faef0b2a481f6722e8f4e7750eac958c4c7aec65abfa078cf24'], + }), + ('oce', '1.4-0', { + 'checksums': ['3b341448001164dc62b54a26c8f86adf50e68705ddc47615b290b950da734408'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.3', { + 'checksums': ['276164d5eb92c78726c647be16232d2443acbf7061371ddde2672b4fdb7a069a'], + }), + ('memuse', '4.1-0', { + 'checksums': ['58d6d1ca5d6bd481f4ed299eff6a9d5660eb0f8db1abe54c49e144093cba72ad'], + }), + ('pinfsc50', '1.2.0', { + 'checksums': ['ed1fe214b9261feef8abfbf724c2bd9070d68e99a6ea95208aff2c57bbef8794'], + }), + ('vcfR', '1.12.0', { + 'checksums': ['dd87ff010365de363864a44ca49887c0fdad0dd18d0d9c66e44e39c2d4581d52'], + }), + ('glmmML', '1.1.1', { + 'checksums': ['255fe2640933d83ef7ea5813ba8006038c18195147d1f34f47a759210a674dd4'], + }), + ('cowplot', '1.1.1', { + 'checksums': ['c7dce625b456dffc59ba100c816e16226048d12fdd29a7335dc1f6f6e12eed48'], + }), + ('tsne', '0.1-3', { + 'checksums': ['66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69'], + }), + ('sn', '2.0.0', { + 'checksums': ['abd6ccdb3719b482db43ff2d5b12f2efcb8244792ec08e1176c5eb98fcc7886a'], + }), + ('tclust', '1.4-2', { + 'checksums': ['95dcd07dbd16383f07f5cea8561e7f3bf314e4a7483879841103b149fc8c65d9'], + }), + 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['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.5-0', { + 'checksums': ['795ffd3d62bf14d3ecb3f5307bd329cd75798cf4b270ff0e768bc71a35de0ace'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.15', { + 'checksums': ['73d20ff1abd752a9d8267eea9d97be58818554ffe072923810db576c449ecbc2'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.32.0.1', { + 'checksums': ['86161b81e4aecf0243b17cabcd1f887cf4b9104918d91c804810be603d50ab66'], + }), + ('mlegp', '3.1.8', { + 'checksums': ['eac1df085a608451828575028ca05b78dc6b5035da14cabc141bfee5ef986de9'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.6', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.2.0', { + 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.5', { + 'checksums': ['9c41ca817104ab076bfd62cccac7d024658ebf4a11dcd91654f0588868aa8d74'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0-1', { + 'checksums': ['9fc1f7432a40d8911393701ca33e2ad64356c3bd12128f01dd216399b16e3d93'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.17', { + 'checksums': ['792857b2ebd408d6523424d2f6bb7297e241d4b28ab32372f6a9240c8cd554f3'], + }), + ('BMA', '3.18.14', { + 'checksums': ['3bc0fd44001c5817dc6a8eda9fb266967407f8a05ac0a5c05b10c87df462cb23'], + }), + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-58', { + 'checksums': ['2ab6662eaa1103a7b633477e8ebd266b262ed54fac6f9326b160067a2ded9ce7'], + }), + ('bdsmatrix', '1.3-4', { + 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.19.3', { + 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.4', { + 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.9', { + 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '3.0', { + 'checksums': ['ada4e1f8cbb08ba8ff16275ec5f9a453857e0cab63b70d42753989ab4c716b7b'], + }), + ('bbmle', '1.0.23.1', { + 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('terra', '1.1-4', { + 'checksums': ['6f6929d6bc7757281c7e314b43875d79b5bcfd1174d62d3462509b82752950ef'], + }), + ('rasterVis', '0.50.1', { + 'checksums': ['fc40c2a375f3f133d95ca88f53e014ae7b1e5236c8bdca841cb3dae629f575ba'], + }), + ('tictoc', '1.0', { + 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], + }), + ('ISOcodes', '2021.02.24', { + 'checksums': ['152769bcb4ae99d06a767384541c2000c94990a2c6983780837f85e885b539a6'], + }), + ('stopwords', '2.2', { + 'checksums': ['b66bccc786200c6ec600be8340e2801bbc7ee787fa5c5a15bc201306861706b9'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0.1', { + 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + }), + ('topicmodels', '0.2-12', { + 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + }), + ('tidytext', '0.3.0', { + 'checksums': ['7d36be1e504f751c33dc2239751a600bd4ff05af24a0b9cdd549aff909778bc5'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-11', { + 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.4.1', { + 'checksums': ['bc21fb6b4a93a7e95ee1be57e4e787d731895fb8b4743c26b30b43adee475b50'], + }), + ('RcppParallel', '5.0.3', { + 'checksums': ['71121138f25fcc97885b14545b7e7eb92e5f3953aec15e7df3822ae26d8e0c46'], + }), + ('StanHeaders', '2.21.0-7', { + 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], + }), + ('V8', '3.4.0', { + 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + }), + ('rstan', '2.21.2', { + 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.1', { + 'checksums': ['506e684071332dac62005c709833d419f4944a85478e2f4395f218ac314f5e66'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.7.0', { + 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.4.0', { + 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.1.1', { + 'checksums': ['cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481'], + }), + ('leiden', '0.3.7', { + 'checksums': ['770994d2d763c195b53e3e09a987188cbf844fbb3bca2d175e46798663b13892'], + }), + ('future.apply', '1.7.0', { + 'checksums': ['2ffa6adb55f239918ce9679b7eac8dcc4bf2e6bed35c9cbedf4bf90d906345db'], + }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), + ('packrat', '0.6.0', { + 'checksums': ['d99d3474baa264cd255a2e60623a1c2a7b30809d352208015c88d992dc169605'], + }), + ('shinyjs', '2.0.0', { + 'checksums': ['c2cdd9fab41f6b46bb41b288cd9b3fb3a7fe9627b664e3a58a0cb5dd4c19f8ff'], + }), + ('colourpicker', '1.1.0', { + 'checksums': ['2dfbb6262d187d3b17357ff9c22670ced3621feda5b2a2a500558478e4d551e2'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), + ('findpython', '1.0.7', { + 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], + }), + ('argparse', '2.0.3', { + 'checksums': ['d26139c610ea0adf8d6632699cd34c4595ae3e7963bfc7a00cb3b7504f2059b0'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), + ('qqman', '0.1.4', { + 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], + }), + ('rstantools', '2.1.1', { + 'checksums': ['c95b15de8ec577eeb24bb5206e7b685d882f88b5e6902efda924b7217f463d2d'], + }), + ('bayesplot', '1.8.0', { + 'checksums': ['a605f9929e681593a3ef3ca9c836e713314994aaea00f359f71cfc42d151c948'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.16', { + 'checksums': ['3f728c6a5153dca28f69b9355ae9d18c5f7e70d12495c0c047eef673c1053116'], + }), + ('shinystan', '2.5.0', { + 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'], + }), + ('optimx', '2020-4.2', { + 'checksums': ['6381c25c322287fc98ab1b2965d3f68c9a92c587c76aca1d33fd6428b2167101'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('projpred', '2.0.2', { + 'checksums': ['af0a9fb53f706090fe81b6381b27b0b6bd3f7ae1e1e44b0ada6f40972b09a55b'], + }), + ('brms', '2.15.0', { + 'checksums': ['c11701d1d8758590b74bb845b568b736e4455a81b114c7dfde0b27b7bd1bcc2f'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.0', { + 'checksums': ['b423df43e9c4bb8ffafe2de88b93fdcf3a90f964f136580ea1b849a83dba7400'], + }), + ('mcmcse', '1.4-1', { + 'checksums': ['6b181f56d60ddf55c9c08a2468ef9ffe3ec8a1b16cfa9a7742c3872597f85d17'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.6.2', { + 'checksums': ['4264f28e37855188675f6b08530752606dba3d761b36c1e7cca96a75f8208390'], + }), + ('drugCombo', '1.1.1', { + 'checksums': ['9fdc3a7cf63552c32f1c7573258fc4ceacdaf5c475fe79aa4ca8c9226b9f8a38'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.0.1', { + 'checksums': ['a3bb9bdc7a4a79ea38482df3f8cbb6e9082332a0d894eeb4b3dc816344cec0e4'], + }), + ('maxlike', '0.1-8', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-16', { + 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.2', { + 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], + }), + ('ENMeval', '0.3.1', { + 'checksums': ['e7f20c1b4d7ede82a3aca86e3ce3fc4ae46337f812dfc171b499c2558b0183d0'], + }), + ('plotmo', '3.6.0', { + 'checksums': ['c05afcc442f9542868beea5c3c40fb93b049f9b61c42725b2a1e2bc750c241e3'], + }), + ('earth', '5.3.0', { + 'checksums': ['05ace806271a74b3ddf8718a93237fe2a8550a8659ebd87f8079c0bda5e02437'], + }), + ('mda', '0.5-2', { + 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], + }), + ('biomod2', '3.4.6', { + 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], + }), + ('poLCA', '1.4.1', { + 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], + }), + ('PermAlgo', '1.1', { + 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.12', { + 'checksums': ['9acdf912f0e7a68a5b6a7946d5ebb0c2007b3d6cd2e39075eddae2b586354e89'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-1', { + 'checksums': ['e8abadc5614f132edc3fb9cb1c82ce4dacc1315b727fbd49db7399aee24115ba'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-19', { + 'checksums': ['6c7eed2d238ab4d8ebcd624e05a68849fa57bf2929b893bcd1a0990b5fcc304d'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.4.0', { + 'checksums': ['49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + #('gWidgets2tcltk', '1.0-6', { + # 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # # need to run installation via xvfb-run to avoid problems on headless systems: + # # no DISPLAY variable so Tk is not available + # # [tcl] invalid command name "font" + # 'preinstallopts': "xvfb-run ", + # # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + # 'modulename': False, + #}), + ('mgsub', '1.7.2', { + 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], + }), + #('ie2misc', '0.8.6', { + # 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + #}), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '2.1', { + 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], + }), + ('lmom', '2.8', { + 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], + }), + ('gld', '2.6.2', { + 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], + }), + ('DescTools', '0.99.40', { + 'checksums': ['53954f0477eac77328efac562716c8b078e76b5ad5edf0227ba2624aa2b8c7dd'], + }), + ('orthopolynom', '1.0-5', { + 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], + }), + ('gaussquad', '1.0-2', { + 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.0', { + 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], + }), + ('tableone', '0.12.0', { + 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], + }), + ('jstable', '1.0.2', { + 'checksums': ['0d7ffa8ecd1b2df05cf1256406152d211eabfa660bf1cc13bada1d75dfdd6d13'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.2', { + 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], + }), + ('sensemakr', '0.1.3', { + 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.3-15', { + 'checksums': ['f73ead024bc3b65bdb0c5e5cd5458845158914eb579c07be2fd697a3573ebe6f'], + }), + ('metafor', '2.4-0', { + 'checksums': ['b64a678b762e91f1e0a6360b15e79fe19159b243c9f40ad9cc0be833bb4ba9ac'], + }), + ('fmri', '1.9.6', { + 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + }), + ('AnalyzeFMRI', '1.1-23', { + 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.4', { + 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], + }), + ('DEoptim', '2.2-5', { + 'checksums': ['ae12dedcd4a43994e811e7285f8c12bfdb688e7c99d65515cf7e8cb6db13955a'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2013.9-1', { + 'checksums': ['1a1a399682a06a5fea3934985ebb1334005676c6a2a22d06f3c91c3923432908'], + }), + ('Rvmmin', '2018-4.17', { + 'checksums': ['d53ba7ab06596a47990caf101a50935b2b34402f9dd8414f098a873026ff1f56'], + }), + ('Rcgmin', '2013-2.21', { + 'checksums': ['a824a09c32d7565a3e30607c71333506d5b7197478fbe8b43f8a77dad6c12f0a'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '1.3.0', { + 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..37a6c1eba1 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -0,0 +1,2849 @@ +## +# Author: Robert Mijakovic +## +name = 'R' +version = '4.0.5' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.9'), +] +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('PCRE2', '10.35'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.5'), # for plottting in R + ('LibTIFF', '4.1.0'), + ('Java', '11', '', True), + ('Tk', '8.6.10'), # for tcltk + ('cURL', '7.72.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.0'), # for igraph + ('NLopt', '2.6.2'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '67.1'), # for rJava & gdsfmt + ('HDF5', '1.10.7'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.10-35'), # for animation + ('GLPK', '4.65'), # for Rglpk + ('nodejs', '12.19.0'), # for V8 (required by rstan) + ('GDAL', '3.2.1'), # for sf + ('pocl', '1.6'), # for OpenCL support (particularly on POWER) + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +# replace hardcoded CUDA compute capabilitites in liquidSVM +local_cuda_cc = [c.replace('.', '') for c in cuda_compute_capabilities] +local_cuda_arch = "-arch sm_%s" % local_cuda_cc[0] +local_cuda_gencode = ' '.join(['-gencode=arch=compute_%s,code=sm_%s' % (c, c) for c in local_cuda_cc]) +local_liquidSVM_sed = "sed -i 's/-arch sm_30/%s %s/' src/Makevars.in" % (local_cuda_arch, local_cuda_gencode) + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 07 Apr 2021 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9.1', { + 'checksums': ['99e02a955935040bf0834d44d1dc10a3794c8260fd072d3aff3e15ab249e0ac9'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.6', { + 'checksums': ['c9f24756bc000f7a989bd4f9aa93d57f7739dcde77946703f8bb32332a35f012'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '4.0.4', { + 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], + }), + ('bnlearn', '4.6.1', { + 'checksums': ['e4544465af3330e53e4777079c448585a8a97be2d3862a5264169007c20daeaf'], + 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['cc474e1315a04f67fbf14461d35004c899d031c31f18be7d3db076dbf66a0617'], + }), + ('pbapply', '1.4-3', { + 'checksums': ['8fe6287535be766b5a688810e2cc1ca4e668ac6b42b6e832473fe5701133eb21'], + }), + ('graphlayouts', '0.7.1', { + 'checksums': ['380f8ccb0b08735694e83f661fd56a0d592a78448ae91b89c290ba8582d66717'], + }), + ('tweenr', '1.0.2', { + 'checksums': ['1805f575da6705ca4e5ec1c4605222fc826ba806d9ff9af41770294fe08ff69f'], + }), + ('ggforce', '0.3.3', { + 'checksums': ['2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f'], + }), + ('tidygraph', '1.2.0', { + 'checksums': ['057d6c42fc0144109f3ace7f5058cca7b2fe493c761daa991448b23f86b6129f'], + }), + ('ggraph', '2.0.5', { + 'checksums': ['e36ad49dba92ee8652e18b1fb197be0ceb9f0a2f8faee2194453a62578449654'], + }), + ('qgraph', '1.6.9', { + 'checksums': ['b125a9c1b505632da8b404811c8d6d667736f229d95994ca7913beacabc36b94'], + }), + ('HWxtest', '1.1.9', { + 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], + 'checksums': [ + 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + ], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.19', { + 'checksums': ['4cd2d080628482f4c6ecab593313d7e42516f5ff13fbf9f90e461fcad0580738'], + }), + ('geepack', '1.3-2', { + 'checksums': ['99b53e40f7e5fda7422b143e6fee16513e2f880cb04a97cd403e98c4760670a6'], + }), + ('biom', '0.3.12', { + 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], + }), + ('pim', '2.0.2', { + 'checksums': ['1195dbdbd67348dfef4b6fc34fcec643da685ebe58d34bbe049ab121aca9944f'], + }), + ('minpack.lm', '1.2-1', { + 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], + }), + ('rootSolve', '1.8.2.1', { + 'checksums': 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('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-7', { + 'checksums': ['52e0397a45325aa9586ec68b94ab9e505bdefaf2a588d634fcb57a6a11659c74'], + }), + ('fftw', '1.0-6', { + 'checksums': ['397ef5ec354b919884f74fba4202bfc13ad11a70b16285c41677aad1d3b170ce'], + }), + ('seewave', '2.1.6', { + 'checksums': ['84a0a0035737574a65f371fa4a20a1a3a66de195efe41975f21be8fb001e7088'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('sf', '0.9-8', { + 'checksums': ['11570a6578701faef0b2a481f6722e8f4e7750eac958c4c7aec65abfa078cf24'], + }), + ('oce', '1.4-0', { + 'checksums': ['3b341448001164dc62b54a26c8f86adf50e68705ddc47615b290b950da734408'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.3', { + 'checksums': 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('ranger', '0.12.1', { + 'checksums': ['fc308e0ac06718272799928e1a19612de16b05bde481d8f38e11a101df5425ef'], + }), + ('hexbin', '1.28.2', { + 'checksums': ['6241f8d3a6c6be2c1c693c3ddb99554bc103e3c6cf602d0c2787c0ce6fd1702d'], + }), + ('pryr', '0.1.4', { + 'checksums': ['d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b'], + }), + ('moments', '0.14', { + 'checksums': ['2a3b81e60dafdd092d2bdd3513d7038855ca7d113dc71df1229f7518382a3e39'], + }), + ('laeken', '0.5.1', { + 'checksums': ['1aa94a1768969eb999f7a41212af2d8b2943b43a68a92f99c9f77929e19439a5'], + }), + ('VIM', '6.1.0', { + 'checksums': ['1f9eb2ad9b18b7a0435e6074d031b7b5bc7143ff4251514ba20a38a53de00aa9'], + }), + ('smoother', '1.1', { + 'checksums': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], + }), + ('dynamicTreeCut', '1.63-1', { + 'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'], + }), + ('beeswarm', '0.3.1', { + 'checksums': 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['af49389bdeb794da3c39e1d63f59e6219438ecb8613c5ef523b00c6fed5a600c'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.5', { + 'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3.1', { + 'checksums': ['052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.5', { + 'checksums': ['d042d448671355d0664d37fd64dc90932eb780e6494c479d4431d1faae2071a1'], + }), + ('Rssa', '1.0.3', { + 'checksums': ['d3dc8a22c428148b955d84b703ca0bf3993318a86b067edfe4c4de271b3054ea'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.32', { + 'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'], + }), + ('DistributionUtils', '0.6-0', { + 'checksums': ['7443d6cd154760d55b6954142908eae30385672c4f3f838dd49876ec2f297823'], + }), + ('gapfill', '0.9.6-1', { + 'checksums': ['22f04755873e34a9077bb1b1de8d16f5bc56cb8c395c4f797f9ad0b209b1b996'], + }), + ('gee', '4.13-20', { + 'checksums': ['53014cee059bd87dc22f9679dfbf18fe6813b9ab41dfe90361921159edfbf798'], + }), + ('Matching', '4.9-7', { + 'checksums': ['1956ecb5ebe1c88e2112cd277ae5c2ab4b8d8f60743e6e856a2c2e40aa05fc6d'], + }), + ('MatchIt', '4.1.0', { + 'checksums': ['b34767cbb8cfb70c6b781849d5430b11480fac43af0a2d53460a1c57c7997ba1'], + }), + ('RItools', '0.1-17', { + 'checksums': ['75654780e9ca39cb3c43acfaca74080ad74de50f92c5e36e95694aafdfdc0cea'], + }), + ('optmatch', '0.9-13', { + 'checksums': ['f8f327faa95c808773376570793bbabdbc185a6c7fcdce3b96a09c998134d0d8'], + }), + ('SPAtest', '3.1.2', { + 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], + }), + ('SKAT', '2.0.1', { + 'checksums': ['c8637cf5786b926f6bbef3f4ef1d3af5130cc0cfd9094d4835839724b2d0e8c7'], + }), + ('GillespieSSA', '0.6.1', { + 'checksums': ['272e9b6b26001d166fd7ce8d04f32831ba23c676075fbd1e922e27ba2c962052'], + }), + ('startupmsg', '0.9.6', { + 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], + }), + ('distr', '2.8.0', { + 'checksums': ['bb7df05d6b946bcdbbec2e3397c7c7e349b537cabfcbb13a34bcf6312a71ceb7'], + }), + ('distrEx', '2.8.0', { + 'checksums': ['b064cde7d63ce93ec9969c8c4463c1e327758b6f8ea7765217d77f9ba9d590bf'], + }), + ('KODAMA', '1.5', { + 'checksums': ['8ecf53732c1be2bd1e111b3c6de65b66caf28360306e683fe945dc76d4c267dd'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-2', { + 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + }), + ('dtw', '1.22-3', { + 'checksums': ['df7cf9adf613422ddb22a160597eb5f5475ab6c67c0d790092edb7f72ba98f00'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.3', { + 'checksums': ['f5eafab17f2d4a8a2a83821ad3e96ae7c26b62bbce9de414484c657383c7b42e'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-3', { + 'checksums': ['776d5456e14398e44b78b3d7db526559bb7a3537e546a29c88aa192141c756de'], + }), + ('reticulate', '1.18', { + 'checksums': ['b33f855a58f446eefbe38df8a1a4865390f5d4ebd64b2c72266baaee64628513'], + }), + ('hdf5r', '1.3.3', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['a0f83cbf21563e81dbd1a1bd8379623ed0c9c4df4e094c75013abfd7a5271545'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('pulsar', '0.3.7', { + 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], + }), + ('bayesm', '3.1-4', { + 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('gsl', '2.1-6', { + 'checksums': ['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], + }), + ('energy', '1.7-8', { + 'checksums': ['de08e8de037bb30068bbf0c1880b153a586d342304681f4ba103ab808c7f4789'], + }), + ('compositions', '2.0-1', { + 'checksums': ['84a291308faf858e5a9d9570135c2da5e57b0887f407903485fa85d09da61a0f'], + }), + ('clustree', '0.4.3', { + 'checksums': ['5ff3afc3fb3e1d20d033328935084de574250d29545c0a5b69180fe4846fbe53'], + }), + ('plotly', '4.9.3', { + 'checksums': ['d44d1a16d96de28bc2d36f1c897384215eeec44d109546c6e9c2707db0880120'], + }), + ('tweedie', '2.3.3', { + 'checksums': ['a032cad512dac37a8619e6f66cb513eb82a88a5a2ffbe91e92c2d44d1756d0d9'], + }), + ('RcppGSL', '0.3.8', { + 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], + }), + ('mvabund', '4.1.9', { + 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.2.3', { + 'checksums': ['154bf7e65452186841036a2a7f2af89664965a63040ff0bee33f8b3fab8c0e4b'], + }), + ('grpreg', '3.3.1', { + 'checksums': ['f07e202d9da45fe7cb82dd1c6a760c04cc83b4e32aeae2bb40b979fab95305a5'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('ergm', '3.11.0', { + 'checksums': ['4e5506b44badc2343be3657acbf2bca51b47d7c187ff499d5a5e70a9811fe9f2'], + }), + ('networkDynamic', '0.10.1', { + 'checksums': ['22eed8d9dea8d70877c1619eb2bc3f1ac5142ce3db6fd6eb3e0879ca56b76ca0'], + }), + ('tergm', '3.7.0', { + 'checksums': ['afd2b160bda691127f8fc57c4caff61f688cc03e71e622f8e833b2a26dc635df'], + }), + ('ergm.count', '3.4.0', { + 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], + }), + ('tsna', '0.3.1', { + 'checksums': ['bba4b5e04ba647784581a2137f653f60b4c83cfd726c399556054c5a6d2cbd95'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.5-0', { + 'checksums': ['795ffd3d62bf14d3ecb3f5307bd329cd75798cf4b270ff0e768bc71a35de0ace'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.15', { + 'checksums': ['73d20ff1abd752a9d8267eea9d97be58818554ffe072923810db576c449ecbc2'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + # Replace hardcoded CUDA compute capabilities with settings from EB + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': local_liquidSVM_sed + " && LIQUIDSVM_TARGET='empty'", + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.32.0.1', { + 'checksums': ['86161b81e4aecf0243b17cabcd1f887cf4b9104918d91c804810be603d50ab66'], + }), + ('mlegp', '3.1.8', { + 'checksums': ['eac1df085a608451828575028ca05b78dc6b5035da14cabc141bfee5ef986de9'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.6', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.2.0', { + 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.5', { + 'checksums': ['9c41ca817104ab076bfd62cccac7d024658ebf4a11dcd91654f0588868aa8d74'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0-1', { + 'checksums': ['9fc1f7432a40d8911393701ca33e2ad64356c3bd12128f01dd216399b16e3d93'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.17', { + 'checksums': ['792857b2ebd408d6523424d2f6bb7297e241d4b28ab32372f6a9240c8cd554f3'], + }), + ('BMA', '3.18.14', { + 'checksums': ['3bc0fd44001c5817dc6a8eda9fb266967407f8a05ac0a5c05b10c87df462cb23'], + }), + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-58', { + 'checksums': ['2ab6662eaa1103a7b633477e8ebd266b262ed54fac6f9326b160067a2ded9ce7'], + }), + ('bdsmatrix', '1.3-4', { + 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.19.3', { + 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.4', { + 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.9', { + 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '3.0', { + 'checksums': ['ada4e1f8cbb08ba8ff16275ec5f9a453857e0cab63b70d42753989ab4c716b7b'], + }), + ('bbmle', '1.0.23.1', { + 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('terra', '1.1-4', { + 'checksums': ['6f6929d6bc7757281c7e314b43875d79b5bcfd1174d62d3462509b82752950ef'], + }), + ('rasterVis', '0.50.1', { + 'checksums': ['fc40c2a375f3f133d95ca88f53e014ae7b1e5236c8bdca841cb3dae629f575ba'], + }), + ('tictoc', '1.0', { + 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], + }), + ('ISOcodes', '2021.02.24', { + 'checksums': ['152769bcb4ae99d06a767384541c2000c94990a2c6983780837f85e885b539a6'], + }), + ('stopwords', '2.2', { + 'checksums': ['b66bccc786200c6ec600be8340e2801bbc7ee787fa5c5a15bc201306861706b9'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0.1', { + 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + }), + ('topicmodels', '0.2-12', { + 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + }), + ('tidytext', '0.3.0', { + 'checksums': ['7d36be1e504f751c33dc2239751a600bd4ff05af24a0b9cdd549aff909778bc5'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-11', { + 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.4.1', { + 'checksums': ['bc21fb6b4a93a7e95ee1be57e4e787d731895fb8b4743c26b30b43adee475b50'], + }), + ('RcppParallel', '5.0.3', { + 'checksums': ['71121138f25fcc97885b14545b7e7eb92e5f3953aec15e7df3822ae26d8e0c46'], + }), + ('StanHeaders', '2.21.0-7', { + 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], + }), + ('V8', '3.4.0', { + 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + }), + ('rstan', '2.21.2', { + 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.1', { + 'checksums': ['506e684071332dac62005c709833d419f4944a85478e2f4395f218ac314f5e66'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.7.0', { + 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.4.0', { + 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.1.1', { + 'checksums': ['cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481'], + }), + ('leiden', '0.3.7', { + 'checksums': ['770994d2d763c195b53e3e09a987188cbf844fbb3bca2d175e46798663b13892'], + }), + ('future.apply', '1.7.0', { + 'checksums': ['2ffa6adb55f239918ce9679b7eac8dcc4bf2e6bed35c9cbedf4bf90d906345db'], + }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), + ('packrat', '0.6.0', { + 'checksums': ['d99d3474baa264cd255a2e60623a1c2a7b30809d352208015c88d992dc169605'], + }), + ('shinyjs', '2.0.0', { + 'checksums': ['c2cdd9fab41f6b46bb41b288cd9b3fb3a7fe9627b664e3a58a0cb5dd4c19f8ff'], + }), + ('colourpicker', '1.1.0', { + 'checksums': ['2dfbb6262d187d3b17357ff9c22670ced3621feda5b2a2a500558478e4d551e2'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), + ('findpython', '1.0.7', { + 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], + }), + ('argparse', '2.0.3', { + 'checksums': ['d26139c610ea0adf8d6632699cd34c4595ae3e7963bfc7a00cb3b7504f2059b0'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), + ('qqman', '0.1.4', { + 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], + }), + ('rstantools', '2.1.1', { + 'checksums': ['c95b15de8ec577eeb24bb5206e7b685d882f88b5e6902efda924b7217f463d2d'], + }), + ('bayesplot', '1.8.0', { + 'checksums': ['a605f9929e681593a3ef3ca9c836e713314994aaea00f359f71cfc42d151c948'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.16', { + 'checksums': ['3f728c6a5153dca28f69b9355ae9d18c5f7e70d12495c0c047eef673c1053116'], + }), + ('shinystan', '2.5.0', { + 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'], + }), + ('optimx', '2020-4.2', { + 'checksums': ['6381c25c322287fc98ab1b2965d3f68c9a92c587c76aca1d33fd6428b2167101'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('projpred', '2.0.2', { + 'checksums': ['af0a9fb53f706090fe81b6381b27b0b6bd3f7ae1e1e44b0ada6f40972b09a55b'], + }), + ('brms', '2.15.0', { + 'checksums': ['c11701d1d8758590b74bb845b568b736e4455a81b114c7dfde0b27b7bd1bcc2f'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.0', { + 'checksums': ['b423df43e9c4bb8ffafe2de88b93fdcf3a90f964f136580ea1b849a83dba7400'], + }), + ('mcmcse', '1.4-1', { + 'checksums': ['6b181f56d60ddf55c9c08a2468ef9ffe3ec8a1b16cfa9a7742c3872597f85d17'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.6.2', { + 'checksums': ['4264f28e37855188675f6b08530752606dba3d761b36c1e7cca96a75f8208390'], + }), + ('drugCombo', '1.1.1', { + 'checksums': ['9fdc3a7cf63552c32f1c7573258fc4ceacdaf5c475fe79aa4ca8c9226b9f8a38'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.0.1', { + 'checksums': ['a3bb9bdc7a4a79ea38482df3f8cbb6e9082332a0d894eeb4b3dc816344cec0e4'], + }), + ('maxlike', '0.1-8', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-16', { + 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.2', { + 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], + }), + ('ENMeval', '0.3.1', { + 'checksums': ['e7f20c1b4d7ede82a3aca86e3ce3fc4ae46337f812dfc171b499c2558b0183d0'], + }), + ('plotmo', '3.6.0', { + 'checksums': ['c05afcc442f9542868beea5c3c40fb93b049f9b61c42725b2a1e2bc750c241e3'], + }), + ('earth', '5.3.0', { + 'checksums': ['05ace806271a74b3ddf8718a93237fe2a8550a8659ebd87f8079c0bda5e02437'], + }), + ('mda', '0.5-2', { + 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], + }), + ('biomod2', '3.4.6', { + 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], + }), + ('poLCA', '1.4.1', { + 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], + }), + ('PermAlgo', '1.1', { + 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.12', { + 'checksums': ['9acdf912f0e7a68a5b6a7946d5ebb0c2007b3d6cd2e39075eddae2b586354e89'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-1', { + 'checksums': ['e8abadc5614f132edc3fb9cb1c82ce4dacc1315b727fbd49db7399aee24115ba'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-19', { + 'checksums': ['6c7eed2d238ab4d8ebcd624e05a68849fa57bf2929b893bcd1a0990b5fcc304d'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.4.0', { + 'checksums': ['49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + #('gWidgets2tcltk', '1.0-6', { + # 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # # need to run installation via xvfb-run to avoid problems on headless systems: + # # no DISPLAY variable so Tk is not available + # # [tcl] invalid command name "font" + # 'preinstallopts': "xvfb-run ", + # # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + # 'modulename': False, + #}), + ('mgsub', '1.7.2', { + 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], + }), + #('ie2misc', '0.8.6', { + # 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + #}), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '2.1', { + 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], + }), + ('lmom', '2.8', { + 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], + }), + ('gld', '2.6.2', { + 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], + }), + ('DescTools', '0.99.40', { + 'checksums': ['53954f0477eac77328efac562716c8b078e76b5ad5edf0227ba2624aa2b8c7dd'], + }), + ('orthopolynom', '1.0-5', { + 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], + }), + ('gaussquad', '1.0-2', { + 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.0', { + 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], + }), + ('tableone', '0.12.0', { + 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], + }), + ('jstable', '1.0.2', { + 'checksums': ['0d7ffa8ecd1b2df05cf1256406152d211eabfa660bf1cc13bada1d75dfdd6d13'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.2', { + 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], + }), + ('sensemakr', '0.1.3', { + 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.3-15', { + 'checksums': ['f73ead024bc3b65bdb0c5e5cd5458845158914eb579c07be2fd697a3573ebe6f'], + }), + ('metafor', '2.4-0', { + 'checksums': ['b64a678b762e91f1e0a6360b15e79fe19159b243c9f40ad9cc0be833bb4ba9ac'], + }), + ('fmri', '1.9.6', { + 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + }), + ('AnalyzeFMRI', '1.1-23', { + 'checksums': ['4237ca4ffe812e614349cdffa2668de4eda5697d73ea208df0c60808daa29444'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.4', { + 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], + }), + # Specific packages for GPUs + ('OpenCL', '0.2-1', { + 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], + }), + ('RViennaCL', '1.7.1.8', { + 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], + }), +] + +moduleclass = 'lang' From 95d038575fdaccceed20eb12478add523caa6a68 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 7 Apr 2021 12:03:18 +0200 Subject: [PATCH 0651/2365] use GCC instead of foss --- .../c/CLHEP/CLHEP-2.4.4.0-GCC-10.2.0.eb | 27 +++++++++++++++++++ .../g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb | 26 ++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.4.0-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.4.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..190ed762b8 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.4.0-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.4.0' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] +checksums = ['5df78c11733a091da9ae5a24ce31161d44034dd45f20455587db85f1ca1ba539'] + +builddependencies = [('CMake', '3.18.4')] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..1227d2ac3a --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb @@ -0,0 +1,26 @@ +name = 'Geant4' +version = '10.7.1' + +homepage = 'https://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'Geant4' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['a22800227713b46ba0b71bc674f6c937e5cc0cf17a6becf4a10d5ef90693a60b'] + +builddependencies = [('CMake', '3.18.4')] +dependencies = [ + ('expat', '2.2.9'), + # recommended CLHEP version, see https://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.6.html + ('CLHEP', '2.4.4.0'), +] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += " -DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' From fa6d37546233566bfa515f0dee0daa6d9ce10412 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 7 Apr 2021 13:53:34 +0200 Subject: [PATCH 0652/2365] remove Python2 --- .../easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb index 2cdd419f4a..610d9d24aa 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb @@ -33,10 +33,9 @@ source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(versi sources = ['gatk-%(version)s.zip'] checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] -multi_deps = {'Python': ['3.8.6', '2.7.18']} - dependencies = [ ('Java', '1.8', '', True), + ('Python', '3.8.6'), ] modextrapaths = {'PATH': ''} From f3e6a643cf7aa5d598ab0b4f93d341b51124e42e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 7 Apr 2021 14:06:46 +0200 Subject: [PATCH 0653/2365] remove Python versionsuffix --- .../Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb new file mode 100644 index 0000000000..fe7ec68c3f --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb @@ -0,0 +1,91 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '2.47.0' +versionsuffix = '-Java-%(javaver)s' +local_pyver_major = '3' + +homepage = 'https://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Graphviz-2.42.2_skip-install-data-hook.patch'] +checksums = [ + '4b7f61c7c04f39b67b2c87977633d61d9f72ee6f93ff4376acdce140128431d4', # graphviz-2.47.0.tar.gz + '3d06544c435a6255f6a8f3b36df3102060667b50ffd72e4942bbe546b9363859', # Graphviz-2.42.2_skip-install-data-hook.patch +] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), + ('SWIG', '4.0.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.8.6'), + ('FriBidi', '1.0.10'), + ('Gdk-Pixbuf', '2.40.0'), + ('Ghostscript', '9.53.3'), + ('GTS', '0.7.6'), + ('libgd', '2.3.0'), + ('Pango', '1.47.0'), + ('Perl', '5.32.0'), + ('Qt5', '5.14.2'), + ('Tcl', '8.6.10'), + ('zlib', '1.2.11'), +] + +preconfigopts = './autogen.sh NOCONFIG && ' + +configopts = '--enable-python%s=yes ' % local_pyver_major +configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' +# Use ltdl from libtool in EB +configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' +configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' +# Override the hardcoded paths to Java libraries +configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' +configopts += '--with-javalibdir=$JAVA_HOME/lib' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +postinstallcmds = ['%(installdir)s/bin/dot -c'] # Writes plugin configuration + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acyclic', 'bcomps', 'ccomps', 'cluster', 'diffimg', 'dijkstra', 'dot', + 'dot_builtins', 'dotty', 'edgepaint', 'gc', 'gml2gv', 'graphml2gv', 'gv2gml', + 'gvcolor', 'gvedit', 'gvgen', 'gvmap', 'gvmap.sh', 'gvpack', 'gvpr', 'gxl2gv', + 'lefty', 'lneato', 'mm2gv', 'nop', 'prune', 'sccmap', 'tred', 'unflatten', + 'vimdot']] + + ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libcdt', 'libcgraph', 'libgvc', 'libgvpr', 'liblab_gamut', + 'libpathplan', 'libxdot']], + 'dirs': ['include', 'lib/graphviz', 'lib/graphviz/java', 'lib/graphviz/python%s' % local_pyver_major, + 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), + ('python', '-c "import gv"'), +] + +modextrapaths = { + 'CLASSPATH': 'lib/graphviz/java', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'PYTHONPATH': 'lib/graphviz/python%s' % local_pyver_major, + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' From 6e817c44ad5f28db070b9bb7a2cd3aa8bb97a06f Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 7 Apr 2021 12:11:11 +0000 Subject: [PATCH 0654/2365] Uncomments the necessary part --- .../easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 32 +++++++++---------- .../easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 32 +++++++++---------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 09000f5679..7d1c7c7892 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -1592,8 +1592,8 @@ exts_list = [ ('covr', '3.5.1', { 'checksums': ['a54cfc3623ea56084158ac5d7fe33f216f45191f6dcddab9c9ed4ec1d9d8ac6c'], }), - ('devtools', '2.3.2', { - 'checksums': ['e5086106baef6bb925445dfdddb3cd5ff4f8fff96353365b135aba5618d1986d'], + ('devtools', '2.4.0', { + 'checksums': ['728e4f6556efc0af504a44e20cf5dd84819189ade3e0cd5ab075cf031aa19324'], }), ('Rook', '1.1-1', { 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], @@ -1998,8 +1998,8 @@ exts_list = [ ('ROI.plugin.glpk', '1.0-0', { 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], }), - ('spaMM', '3.7.2', { - 'checksums': ['2580a38b2b6165477255bb025913b3d3342c000cc2c6aba10c0748178b04f2d1'], + ('spaMM', '3.7.34', { + 'checksums': ['109b1b12590c30020c0b3fe2ef9f2adf11509e7a81be728d70ce76075d18ef62'], }), ('qgam', '1.3.2', { 'checksums': ['273a40d0bfdc340c049bcb85aea83acd887868d8a69c0062b8399e0b24137a52'], @@ -2694,21 +2694,21 @@ exts_list = [ ('gWidgets2', '1.0-8', { 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), - #('gWidgets2tcltk', '1.0-6', { - # 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], - # # need to run installation via xvfb-run to avoid problems on headless systems: - # # no DISPLAY variable so Tk is not available - # # [tcl] invalid command name "font" - # 'preinstallopts': "xvfb-run ", - # # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... - # 'modulename': False, - #}), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), ('mgsub', '1.7.2', { 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], }), - #('ie2misc', '0.8.6', { - # 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], - #}), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), ('assertive.base', '0.0-9', { 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], }), diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 37a6c1eba1..3616a01a5e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -1602,8 +1602,8 @@ exts_list = [ ('covr', '3.5.1', { 'checksums': ['a54cfc3623ea56084158ac5d7fe33f216f45191f6dcddab9c9ed4ec1d9d8ac6c'], }), - ('devtools', '2.3.2', { - 'checksums': ['e5086106baef6bb925445dfdddb3cd5ff4f8fff96353365b135aba5618d1986d'], + ('devtools', '2.4.0', { + 'checksums': ['728e4f6556efc0af504a44e20cf5dd84819189ade3e0cd5ab075cf031aa19324'], }), ('Rook', '1.1-1', { 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], @@ -2008,8 +2008,8 @@ exts_list = [ ('ROI.plugin.glpk', '1.0-0', { 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], }), - ('spaMM', '3.7.2', { - 'checksums': ['2580a38b2b6165477255bb025913b3d3342c000cc2c6aba10c0748178b04f2d1'], + ('spaMM', '3.7.34', { + 'checksums': ['109b1b12590c30020c0b3fe2ef9f2adf11509e7a81be728d70ce76075d18ef62'], }), ('qgam', '1.3.2', { 'checksums': ['273a40d0bfdc340c049bcb85aea83acd887868d8a69c0062b8399e0b24137a52'], @@ -2705,21 +2705,21 @@ exts_list = [ ('gWidgets2', '1.0-8', { 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), - #('gWidgets2tcltk', '1.0-6', { - # 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], - # # need to run installation via xvfb-run to avoid problems on headless systems: - # # no DISPLAY variable so Tk is not available - # # [tcl] invalid command name "font" - # 'preinstallopts': "xvfb-run ", - # # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... - # 'modulename': False, - #}), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), ('mgsub', '1.7.2', { 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], }), - #('ie2misc', '0.8.6', { - # 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], - #}), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), ('assertive.base', '0.0-9', { 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], }), From 7c1e2bdc2ed28700af7ee25c1f19ea5355563af2 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 7 Apr 2021 17:10:20 +0200 Subject: [PATCH 0655/2365] updating as per review --- .../NewHybrids-1.1_Beta3-GCC-10.2.0.eb | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb index 89ed496184..8f96c2cc11 100644 --- a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb @@ -25,10 +25,18 @@ checksums = [None] extract_sources = True -install_cmd = '%(builddir)s/newhybrids/Compile-with-no-gui-Linux.sh && ' -install_cmd += 'mkdir %(installdir)s/bin && ' -install_cmd += 'cp -a %(builddir)s/newhybrids/newhybrids-no-gui-linux.exe %(installdir)s/bin/newhybs && ' -install_cmd += 'cp -ar %(builddir)s/newhybrids/test_data %(installdir)s/' +# options to be used in compilation +local_compiler_options = "$CC $CFLAGS $CPPFLAGS " + +local_compile_script = "%(builddir)s/newhybrids/Compile-with-no-gui-Linux.sh" +# replacing hardcoded compilation cmd with general options +install_cmd = "sed -i -e 's/gcc -O3/%s/g' %s && " % (local_compiler_options, local_compile_script) +# running compilation script +install_cmd += "%s && " % local_compile_script +# create and copy created binaries & test data +install_cmd += "mkdir %(installdir)s/bin && " +install_cmd += "cp -a %(builddir)s/newhybrids/newhybrids-no-gui-linux.exe %(installdir)s/bin/newhybs && " +install_cmd += "cp -ar %(builddir)s/newhybrids/test_data %(installdir)s/" sanity_check_paths = { 'files': ['bin/newhybs'], @@ -36,7 +44,8 @@ sanity_check_paths = { } sanity_check_commands = [ - 'newhybs -d %(installdir)s/test_data/TestDat.txt --no-gui | grep Output\ is\ in\ the\ following\ files', + # don't run longer than 4 minutes, otherwise it's probably stuck (no test_data found) + 'timeout 240 newhybs -d %(installdir)s/test_data/TestDat.txt --no-gui | grep "Output is in the following files"', ] moduleclass = 'bio' From 211a3a70959536ead6355b762e0623aac1ddde12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Apr 2021 20:51:37 +0200 Subject: [PATCH 0656/2365] stick to Seaborn 0.10.1 + use numba 0.52.0 as dependencies for cell2location --- ...cell2location-0.05-alpha-fosscuda-2020b.eb | 12 +++------ .../Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb | 27 ------------------- 2 files changed, 3 insertions(+), 36 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index a086e69c6f..cb8713dbdb 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -13,14 +13,14 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), - ('Java', '1.8', '', True), + ('Java', '11', '', True), ('SciPy-bundle', '2020.11'), ('leidenalg', '0.8.3'), ('hyperopt', '0.2.5'), ('CMake', '3.18.4'), ('dill', '0.3.3'), ('IPython', '7.18.1'), - ('Seaborn', '0.11.1'), + ('Seaborn', '0.10.1'), ('matplotlib', '3.3.3'), ('libgpuarray', '0.7.6'), ('PyMC3', '3.11.1'), @@ -28,11 +28,11 @@ dependencies = [ ('PyTables', '3.6.1'), ('PyTorch', '1.7.1'), ('statsmodels', '0.12.1'), - ('LLVM', '10.0.1'), ('Theano', '1.1.2', '-PyMC'), ('umap-learn', '0.4.6'), ('pyro-api', '0.1.2'), ('pyro-ppl', '1.5.2'), + ('numba', '0.52.0'), ] preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " @@ -81,12 +81,6 @@ exts_list = [ ('natsort', '7.1.0', { 'checksums': ['33f3f1003e2af4b4df20908fe62aa029999d136b966463746942efbfc821add3'], }), - ('numba', '0.51.2', { - 'checksums': ['16bd59572114adbf5f600ea383880d7b2071ae45477e84a24994e089ea390768'], - }), - ('llvmlite', '0.34.0', { - 'checksums': ['f03ee0d19bca8f2fe922bb424a909d05c28411983b0c2bc58b020032a0d11f63'], - }), ('palettable', '3.3.0', { 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], }), diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb deleted file mode 100644 index e87b55d020..0000000000 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb +++ /dev/null @@ -1,27 +0,0 @@ -# Author: Denis Krišťák (INUITS) - -easyblock = 'PythonPackage' - -name = 'Seaborn' -version = '0.11.1' - -homepage = 'https://seaborn.pydata.org/' -description = """ Seaborn is a Python visualization library based on matplotlib. - It provides a high-level interface for drawing attractive statistical graphics. """ - -toolchain = {'name': 'fosscuda', 'version': '2020b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'] - -dependencies = [ - ('Python', '3.8.6'), - ('matplotlib', '3.3.3'), -] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -moduleclass = 'bio' From 559cb5463178400e2b764262f06b355ae22076e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Apr 2021 20:54:26 +0200 Subject: [PATCH 0657/2365] remove PYPI_SOURCE source URLs, no longer needed --- .../cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 1 - .../s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb | 5 ++--- .../u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb | 1 - 3 files changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index cb8713dbdb..edef61e4bc 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -42,7 +42,6 @@ use_pip = True exts_default_options = { 'download_dep_fail': True, 'sanity_pip_check': True, - 'source_urls': [PYPI_SOURCE], 'use_pip': True, } diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb index b2aa71b3e1..7a62cf629c 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb @@ -17,9 +17,6 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True - -exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ ('patsy', '0.5.1', { @@ -30,4 +27,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'math' diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb index 9850c3ee38..4c3f7db0d3 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb @@ -12,7 +12,6 @@ but also for general non-linear dimension reduction.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3'] From 9c61dfa7c8d056ec3e856b0440b3961d055b1f05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Apr 2021 20:59:18 +0200 Subject: [PATCH 0658/2365] remove default sanity_check_paths from umap-learn easyconfig --- .../u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb index 4c3f7db0d3..5c5bc73b02 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb @@ -24,13 +24,9 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_pip_check = True options = {'modulename': 'umap'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} +sanity_pip_check = True moduleclass = 'tools' From 597baeffe66b9371ab5a1ebd2fd8098db5d3ffa3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Apr 2021 21:03:51 +0200 Subject: [PATCH 0659/2365] stick to GCCcore toolchain for dill + remove netCDF easyconfig using fosscuda/2020b, existing easyconfig with gompic/2020b suffices --- .../d/dill/dill-0.3.3-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/d/dill/dill-0.3.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4f1d3426ae --- /dev/null +++ b/easybuild/easyconfigs/d/dill/dill-0.3.3-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +# Author: Denis Krišťák (INUITS) + +name = 'dill' +version = '0.3.3' + +homepage = 'https://pypi.org/project/dill/' +description = """dill extends python's pickle module for serializing and de-serializing python objects to the majority + of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse + of which is converting a byte stream back to on python object hierarchy.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_ZIP] +checksums = ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From db792a1899cb2fb9af48891c2eab8d083e7fd511 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Apr 2021 22:31:05 +0200 Subject: [PATCH 0660/2365] remove nose extension from cell2location easyconfig + add Bison build dependency --- .../cell2location-0.05-alpha-fosscuda-2020b.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index edef61e4bc..dd0be52167 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -11,6 +11,8 @@ single cell and spatial transcriptomics (cell2location model)""" toolchain = {'name': 'fosscuda', 'version': '2020b'} +builddependencies = [('Bison', '3.7.1')] + dependencies = [ ('Python', '3.8.6'), ('Java', '11', '', True), @@ -73,10 +75,6 @@ exts_list = [ ('ipykernel', '5.3.4', { 'checksums': ['9b2652af1607986a1b231c62302d070bc0534f564c393a5d9d130db9abbbe89d'], }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], - }), ('natsort', '7.1.0', { 'checksums': ['33f3f1003e2af4b4df20908fe62aa029999d136b966463746942efbfc821add3'], }), From 4ed07b611d57737a19008e63c46903a4513eb25c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 8 Apr 2021 15:11:07 +0200 Subject: [PATCH 0661/2365] add ECs for build from source on foss(cuda)/2020b --- .../i/IMOD/IMOD-4.11.5-foss-2020b.eb | 80 ++++++++++++++++ .../i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 92 +++++++++++++++++++ 2 files changed, 172 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb new file mode 100644 index 0000000000..ed59ad6eb9 --- /dev/null +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -0,0 +1,80 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04 +easyblock = 'ConfigureMake' + +name = 'IMOD' +version = '4.11.5' + +homepage = 'https://bio3d.colorado.edu/imod/' +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. IMOD +was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim +Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = [SOURCE_TAR_GZ] +# mercurial repository +# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD +# get lunch +# cd IMOD +# hg update -r IMOD_4-11-5 +# cd .. +# tar czf IMOD-4.11.5.tar.gz IMOD + + +dependencies = [ + ('LibTIFF', '4.1.0'), + ('Qt5', '5.14.2'), + ('Java', '13.0.2', '', True), + ('HDF5', '1.10.7'), + ('Python', '3.8.6'), +] + +# modify all qmake pro files in order to pass CFLAGS +local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&" + +# exports required for configure and build +local_exports = 'export QTDIR=$EBROOTQT5 &&' +local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&' +local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&' +# readw_or_imod.f and others with gfortran10: +# Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2)) +# => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0. +local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&' # required for gfortran10 + +preconfigopts = local_exports +preconfigopts += local_qmake_pass_cflags + +# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. +# CFLAGs are passed with -flags. +configure_cmd = './setup ' +configure_cmd += '-flags "$CFLAGS" ' # inject CFLAGS +configure_cmd += '-i %(installdir)s ' # set installdir +configure_cmd += ' #' # avoid passing unknown arg --prefix + +prebuildopts = local_exports + +# create some missing directories required for installation process: +preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&' + +modextravars = { + 'IMOD_DIR': "%(installdir)s", + 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', + 'IMOD_JAVADIR': '$JAVA_HOME', + 'FOR_DISABLE_STACK_TRACE': '1', +} +modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.' +# Observed problems with alias on a tcl based module system. Use bin/subm python script instead. +# modaliases = { +# 'subm': 'submfg $* &' +# } +sanity_check_paths = { + 'files': ['VERSION', 'bin/subm'], + 'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..d8a23a6cc5 --- /dev/null +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -0,0 +1,92 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04 +easyblock = 'ConfigureMake' + +name = 'IMOD' +version = '4.11.5' + +homepage = 'https://bio3d.colorado.edu/imod/' +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. IMOD +was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim +Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] + +sources = [SOURCE_TAR_GZ] +# mercurial repository +# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD +# get lunch +# cd IMOD +# hg update -r IMOD_4-11-5 +# cd .. +# tar czf IMOD-4.11.5.tar.gz IMOD + + +dependencies = [ + ('LibTIFF', '4.1.0'), + ('Qt5', '5.14.2'), + ('Java', '13.0.2', '', True), + ('HDF5', '1.10.7'), + ('Python', '3.8.6'), +] + +# replace hardcoded CUDA compute capabilitites in machines/rhlinux. +local_cuda_replace = 'echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|' +local_cuda_replace += ' awk \'{' +local_cuda_replace += ' printf "-arch sm_"$1; ' +local_cuda_replace += ' for (i=1;i<=NF; i++){printf(" -gencode=arch=compute_%s,code=sm_%s",$i,$i) } ' +local_cuda_replace += ' }\'' +local_cudaarch_sed = 'sed -i "s/-arch sm_35/`' + local_cuda_replace + '`/g" machines/rhlinux &&' + +# modify all qmake pro files in order to pass CFLAGS +local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&" + +# exports required for configure and build +local_exports = 'export QTDIR=$EBROOTQT5 &&' +local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&' +local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&' +local_exports += 'export CUDA_DIR=$CUDA_HOME &&' +# readw_or_imod.f and others with gfortran10: +# Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2)) +# => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0. +local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&' # required for gfortran10 + +preconfigopts = local_exports +preconfigopts += local_cudaarch_sed +preconfigopts += local_qmake_pass_cflags + +# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. +# CFLAGs are passed with -flags. +configure_cmd = './setup ' +configure_cmd += '-flags "$CFLAGS" ' # inject CFLAGS +configure_cmd += '-i %(installdir)s ' # set installdir +configure_cmd += ' #' # avoid passing unknown arg --prefix + +prebuildopts = local_exports + +# create some missing directories required for installation process: +preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&' + +modextravars = { + 'IMOD_DIR': "%(installdir)s", + 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', + 'IMOD_JAVADIR': '$JAVA_HOME', + 'FOR_DISABLE_STACK_TRACE': '1', +} +modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.' +# Observed problems with alias on a tcl based module system. Use bin/subm python script instead. +# modaliases = { +# 'subm': 'submfg $* &' +# } +sanity_check_paths = { + 'files': ['VERSION', 'bin/subm'], + 'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'], +} + +moduleclass = 'vis' From 37f7ae1a5de4835563ea0a535a0603a5eaf1f8a7 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 8 Apr 2021 16:05:36 +0200 Subject: [PATCH 0662/2365] add checksums. downgrade dependency Java to 11. --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb | 4 +++- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index ed59ad6eb9..1758cf4d8a 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -17,6 +17,8 @@ toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] +checksums = ['5c50f1457134fe5113b95e0939d3181b948d211f25d9a05ad2b4ec0f23251c79'] + # mercurial repository # hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD # get lunch @@ -29,7 +31,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('LibTIFF', '4.1.0'), ('Qt5', '5.14.2'), - ('Java', '13.0.2', '', True), + ('Java', '11', '', True), ('HDF5', '1.10.7'), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index d8a23a6cc5..803e0308fe 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -19,6 +19,8 @@ toolchainopts = {'pic': True, 'openmp': True} cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] sources = [SOURCE_TAR_GZ] +checksums = ['5c50f1457134fe5113b95e0939d3181b948d211f25d9a05ad2b4ec0f23251c79'] + # mercurial repository # hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD # get lunch @@ -31,7 +33,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('LibTIFF', '4.1.0'), ('Qt5', '5.14.2'), - ('Java', '13.0.2', '', True), + ('Java', '11', '', True), ('HDF5', '1.10.7'), ('Python', '3.8.6'), ] From 5c6a15ec5917bfb79478bddd7178e6136df9362b Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 8 Apr 2021 15:26:17 +0100 Subject: [PATCH 0663/2365] Update Theano-1.1.2-foss-2020b-PyMC.eb Added sanity check commands back in. --- .../easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb index 53824126a7..840804ddc2 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb @@ -30,4 +30,9 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +local_blas_warning = "Using NumPy C-API based implementation for BLAS functions" +sanity_check_commands = [ + "python -c 'import theano.tensor' 2>&1 | grep '%s'; test $? != 0" % local_blas_warning, +] + moduleclass = 'math' From 480317f02bf52979adf781212bfa2137b08e2a9b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 9 Apr 2021 13:55:24 +0200 Subject: [PATCH 0664/2365] adding easyconfigs: snakemake-6.1.0-foss-2020b.eb --- .../s/snakemake/snakemake-6.1.0-foss-2020b.eb | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb new file mode 100644 index 0000000000..6fedfae6b7 --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb @@ -0,0 +1,85 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '6.1.0' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('GitPython', '3.1.14'), +] + +use_pip = True +sanity_pip_check = True + +# snakemake-6.1.0_fix_jobs.patch is needed for clusters that do not support copying the full env into the batch job +exts_list = [ + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('ratelimiter', '1.2.0.post0', { + 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], + }), + ('ConfigArgParse', '1.4', { + 'checksums': ['abef9ff44fb0091f0e3bb2ee7e5b26a02b5b62d45408a5272a9bd461f5b59b4b'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('pyrsistent', '0.17.3', { + 'checksums': ['2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e'], + }), + ('traitlets', '5.0.5', { + 'checksums': ['178f4ce988f69189f7e523337a3e11d91c786ded9360174a3d9ca83e79bc5396'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('jupyter-core', '4.7.1', { + 'modulename': 'jupyter_core', + 'source_tmpl': 'jupyter_core-%(version)s.tar.gz', + 'checksums': ['79025cb3225efcd36847d0840f3fc672c0abd7afd0de83ba8a1d3837619122b4'], + }), + ('nbformat', '5.0.8', { + 'checksums': ['f545b22138865bfbcc6b1ffe89ed5a2b8e2dc5d4fe876f2ca60d8e6f702a30f8'], + }), + ('toposort', '1.6', { + 'checksums': ['a7428f56ef844f5055bb9e9e44b343983773ae6dce0fe5b101e08e27ffbd50ac'], + }), + ('amply', '0.1.4', { + 'checksums': ['cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38'], + }), + ('PuLP', '2.4', { + 'checksums': ['b2aff10989b3692e3a59301a0cb0acddeb25dcea378f8804c86007075eae55b5'], + }), + ('smart_open', '4.1.2', { + 'checksums': ['4bbb6233364fc1173cc0af6b7a56ed76fce32509514f1978a995a5835f3177f1'], + }), + (name, version, { + # 'patches': ['snakemake-6.1.0_fix_jobs.patch'], + 'checksums': [ + '6b8dd2018940679438e84d772cce19814bb1c4e68265dc5e0efe6bb07cf71fb4', # snakemake-6.1.0.tar.gz + # '259d95efa252822ffa96b799f24ca930b0934c6d236c0162bf42356d9fe2ac61', # snakemake-6.1.0_fix_jobs.patch + ], + }), +] + +# SNAKEMAKE_LOAD_MODULE is needed for snakemake-6.1.0_fix_jobs.patch to work +# local_snakemake_load is the command for loading this module (here: default EB module naming scheme) +# local_snakemake_load = 'module load %(module_name)s' +# modextravars = {'SNAKEMAKE_LOAD_MODULE': local_snakemake_load} + +sanity_check_paths = { + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], +} + +sanity_check_commands = ['snakemake --help'] + +moduleclass = 'tools' From ac01f18675ea8d5c87c7e61d85b4effcec7d39dc Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 9 Apr 2021 14:20:18 +0200 Subject: [PATCH 0665/2365] add IPython dep, remove duplicate extensions --- .../s/snakemake/snakemake-6.1.0-foss-2020b.eb | 18 +----------------- 1 file changed, 1 insertion(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb index 6fedfae6b7..c821961ac3 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb @@ -13,6 +13,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('PyYAML', '5.3.1'), ('GitPython', '3.1.14'), + ('IPython', '7.18.1'), ] use_pip = True @@ -32,23 +33,6 @@ exts_list = [ ('datrie', '0.8.2', { 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], }), - ('pyrsistent', '0.17.3', { - 'checksums': ['2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e'], - }), - ('traitlets', '5.0.5', { - 'checksums': ['178f4ce988f69189f7e523337a3e11d91c786ded9360174a3d9ca83e79bc5396'], - }), - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('jupyter-core', '4.7.1', { - 'modulename': 'jupyter_core', - 'source_tmpl': 'jupyter_core-%(version)s.tar.gz', - 'checksums': ['79025cb3225efcd36847d0840f3fc672c0abd7afd0de83ba8a1d3837619122b4'], - }), - ('nbformat', '5.0.8', { - 'checksums': ['f545b22138865bfbcc6b1ffe89ed5a2b8e2dc5d4fe876f2ca60d8e6f702a30f8'], - }), ('toposort', '1.6', { 'checksums': ['a7428f56ef844f5055bb9e9e44b343983773ae6dce0fe5b101e08e27ffbd50ac'], }), From 9db1ab91a6e9d3ca53bcc92e5dd6f19ce39f499b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 9 Apr 2021 14:31:37 +0200 Subject: [PATCH 0666/2365] adding easyconfigs: GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb, GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb --- .../GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb | 52 ++++++++++++++++++ .../GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb | 54 +++++++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb new file mode 100644 index 0000000000..610d9d24aa --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb @@ -0,0 +1,52 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.2.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] + +dependencies = [ + ('Java', '1.8', '', True), + ('Python', '3.8.6'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb new file mode 100644 index 0000000000..f11ab54125 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.2.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.8.6'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +modloadmsg = "WARNING: GATK v%(version)s support for Java 11 is in beta state. Use at your own risk.\n" + +moduleclass = 'bio' From b5ea8b1e3bcc4e53960abb78edbca94ca7008bfd Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 9 Apr 2021 15:49:53 +0200 Subject: [PATCH 0667/2365] adding easyconfigs: DROP-1.0.3-foss-2020b-R-4.0.3.eb, tMAE-1.0.0-foss-2020b-R-4.0.3.eb --- .../d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb | 70 +++++++++++++++++++ .../t/tMAE/tMAE-1.0.0-foss-2020b-R-4.0.3.eb | 33 +++++++++ 2 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb create mode 100644 easybuild/easyconfigs/t/tMAE/tMAE-1.0.0-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..232825143d --- /dev/null +++ b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'DROP' +version = '1.0.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://gagneurlab-drop.readthedocs.io' +description = "Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), + ('tMAE', '1.0.0', '-R-%(rver)s'), + ('Java', '11', '', True), + ('GATK', '4.2.0.0', '-Java-%(javaver)s'), + ('Graphviz', '2.47.0', '-Java-%(javaver)s'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('snakemake', '6.1.0'), + ('wget', '1.20.3'), + ('HTSlib', '1.11'), # for tabix + ('SAMtools', '1.11'), + ('BCFtools', '1.11'), +] + +exts_list = [ + ('wbuild', '1.8.0', { + 'checksums': ['3088d3fcbc71106464f20e3546a73df400dc03d17f11e70bdb15d35d7e6c5a7e'], + }), + ('click-log', '0.3.2', { + 'checksums': ['16fd1ca3fc6b16c98cea63acf1ab474ea8e676849dc669d86afafb0ed7003124'], + }), + ('graphviz', '0.16', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['d2d25af1c199cad567ce4806f0449cb74eb30cf451fd7597251e1da099ac6e57'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('about', '5.2', { + 'checksums': ['4a318ad1dcf6e9355b8ae18195c707d26413782b57ac5c740cc696b44350c959'], + }), + ('pandoc', '1.0.2', { + 'ext_postinstallcmds': [ + 'cp -a pandoc/definitions %(installdir)s/lib/python%(pyshortver)s/site-packages/pandoc/', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/boisgera/pandoc/archive'], + 'checksums': ['37134dd3a4c681e988d8570297fcc2b615f80b0604a9b4ffb41c2e6bacd2b64b'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/gagneurlab/drop/archive'], + 'checksums': ['b4f4481bedfec212085646c6f1bebf3d113bc8490e127337d693a01bc95c7e51'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/drop'], + 'dirs': [], +} + +sanity_check_commands = ['drop --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tMAE/tMAE-1.0.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/t/tMAE/tMAE-1.0.0-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..88e2eb6481 --- /dev/null +++ b/easybuild/easyconfigs/t/tMAE/tMAE-1.0.0-foss-2020b-R-4.0.3.eb @@ -0,0 +1,33 @@ +easyblock = 'RPackage' + +name = 'tMAE' +version = '1.0.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/mumichae/tMAE' +description = """ +Package containing functions to: + + perform a negative binomial test on allele-specific counts + add gnomAD minor allele frequencies + MAplot (FC vs total counts) of allele-specific counts and results + allelic counts (ALT vs REF)""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), +] + +github_account = 'mumichae' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['c418876819abcbde3d439d9c6504b32411b412d0242a245437c41465adcc952c'] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From c6af1746f876652cde9fbb450358b1320e48e0d3 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Fri, 9 Apr 2021 15:54:21 +0200 Subject: [PATCH 0668/2365] delete v1.8 duplicate of #12512 --- .../GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb | 52 ------------------- 1 file changed, 52 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb deleted file mode 100644 index 610d9d24aa..0000000000 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb +++ /dev/null @@ -1,52 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , -# Kenneth Hoste (UGent) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -# Modified by: Adam Huffman, Jonas Demeulemeester -# The Francis Crick Institute -# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen -## - -easyblock = 'Tarball' - -name = 'GATK' -version = '4.2.0.0' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://www.broadinstitute.org/gatk/' -description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute - to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, - with a primary focus on variant discovery and genotyping as well as strong emphasis on - data quality assurance. Its robust architecture, powerful processing engine and - high-performance computing features make it capable of taking on projects of any size.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] -sources = ['gatk-%(version)s.zip'] -checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] - -dependencies = [ - ('Java', '1.8', '', True), - ('Python', '3.8.6'), -] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['gatk'], - 'dirs': [], -} -sanity_check_commands = [ - "gatk --help", - "gatk --list", -] - -moduleclass = 'bio' From 2dda3715cac331e37042aaf22c48142586f28ac3 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 9 Apr 2021 09:50:05 -0700 Subject: [PATCH 0669/2365] {math}[fosso/2020b] JAGS 4.3.0 --- .../j/JAGS/JAGS-4.3.0-foss-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2020b.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2020b.eb new file mode 100644 index 0000000000..ceb7e97810 --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2020b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.0' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download') +] +sources = [SOURCE_TAR_GZ] +checksums = ['8ac5dd57982bfd7d5f0ee384499d62f3e0bb35b5f1660feb368545f1186371fc'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' From 2807f81ef675fc7826627f6328129122e6a7e784 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Apr 2021 20:45:50 +0200 Subject: [PATCH 0670/2365] adding easyconfigs: Myokit-1.32.0-fosscuda-2020b.eb, SUNDIALS-5.7.0-fosscuda-2020b.eb --- .../m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb | 47 +++++++++++++++++++ .../SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb | 35 ++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..e991128da6 --- /dev/null +++ b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonPackage' + +name = 'Myokit' +version = '1.32.0' + +homepage = 'http://myokit.org' +description = """Myokit is an open-source Python-based toolkit that facilitates modeling and simulation of cardiac +cellular electrophysiology.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['393ebc85413bd1b573909736caeadd9d7757f41cceb7bd29f3b30f5107237cba'] + +download_dep_fail = True +use_pip = True + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Pillow', '8.0.1'), + ('lxml', '4.6.2'), + ('PyQt5', '5.15.1'), + ('SUNDIALS', '5.7.0'), + ('pocl', '1.6'), +] + +# configparser is part of stdlib in Python 3 +preinstallopts = "sed -i 's/.*configparser.*//g' setup.py && " + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/myokit'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "myokit -h", + "myokit system", + "myokit opencl", # make sure OpenCL features work (requires pocl or other dependency providing OpenCL runtime) + "myokit run example", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..33df49c169 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '5.7.0' + +homepage = 'https://computation.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] + +builddependencies = [('CMake', '3.18.4')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON -DCUDA_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From 4f7fd41781429fcba1228e0e217134273bdff4cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Apr 2021 20:53:39 +0200 Subject: [PATCH 0671/2365] add easyconfig for pocl 1.6 with gcccuda/2020b, as dependency for Myokit with fosscuda/2020b --- .../p/pocl/pocl-1.6-gcccuda-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb new file mode 100644 index 0000000000..d5d54b8902 --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '1.6' + +homepage = 'https://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'gcccuda', 'version': '2020b'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b0a4c0c056371b6f0db726b88fbb76bbee94948fb2abd4dbc8d958f7c42f766c'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Clang', '11.0.1'), + ('hwloc', '2.2.0'), + ('libtool', '2.4.6'), + ('libxml2', '2.9.10'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 8bf0ccfbc43db8449859d88da6bb835d0ae61ea1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 10 Apr 2021 10:00:36 +0200 Subject: [PATCH 0672/2365] remove Python from versionsuffix --- .../CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..33289f4880 --- /dev/null +++ b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'CNVkit' +version = '0.9.8' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/etal/cnvkit' +description = """A command-line toolkit and Python library for detecting copy + number variants and alterations genome-wide from high-throughput sequencing.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-learn', '0.23.2'), + ('Biopython', '1.78'), + ('matplotlib', '3.3.3'), + ('networkx', '2.5'), + ('Pillow', '8.0.1'), + ('Pysam', '0.16.0.1'), + ('PyYAML', '5.3.1'), + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +exts_list = [ + ('reportlab', '3.5.66', { + 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], + }), + ('pyfaidx', '0.5.9.5', { + 'checksums': ['9965644c5bd62bedc0ff7f336cbb2baef6406a36b4ec5c786b199872ce46192b'], + }), + ('pomegranate', '0.13.5', { + 'checksums': ['b1b803fa18c8a8ca4a8fd2824573914bbff7574e3dc6be770ab68efd00503341'], + }), + (name, version, { + 'ext_postinstallcmds': [ + 'cd test/', + 'make ', + ], + 'modulename': 'cnvlib', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/etal/cnvkit/archive/'], + 'checksums': ['57e3081fd12c402abbc448851fda741795f23e68416c2564d9c09930bd56eef8'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["cnvkit.py", "faidx"]], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cnvkit.py --help', +] + +moduleclass = 'bio' From d4456b7edaec38b673fff314052a2a8b467e325e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 12 Apr 2021 10:29:28 +0100 Subject: [PATCH 0673/2365] Rely on automatic creation of bin directory --- .../easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb index 06da9ef94e..191282689e 100644 --- a/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb @@ -33,8 +33,6 @@ configopts = '-DHTSlib_NO_SYSTEM_PATHS=TRUE -DHTSLIB_ROOT=$EBROOTHTSLIB ' separate_build_dir = True -preinstallopts = 'if [ ! -d %(installdir)s/bin ]; then mkdir %(installdir)s/bin; fi' - files_to_copy = [ (['%(builddir)s/easybuild_obj/src/octopus'], 'bin'), 'doc', 'lib', 'LICENSE', 'logo.png', 'README.md', From 3904b5b69d8ba8a86e54fdcf60581643df9d5256 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Mon, 12 Apr 2021 12:44:10 +0100 Subject: [PATCH 0674/2365] adding easyconfigs: Keras-2.4.3-fosscuda-2020b.eb --- .../k/Keras/Keras-2.4.3-fosscuda-2020b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..48fc18c305 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Keras' +version = '2.4.3' + +homepage = 'https://keras.io/' +description = """ +Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Theano', '1.1.2', '-PyMC'), + ('PyYAML', '5.3.1'), + ('h5py', '3.1.0'), + ('TensorFlow', '2.4.1'), +] + +use_pip = True + +exts_list = [ + ('Keras_Applications', '1.0.8', { + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'checksums': ['fedd729b52572fb108a98e3d97e1bac10a81d3917d2103cc20ab2a5f03beb973'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 73ed8c2f103659dd5c83901e3fceea21cc125c87 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 12 Apr 2021 15:27:18 +0200 Subject: [PATCH 0675/2365] Delete cell2location-0.05-alpha-fosscuda-2020b.eb removed obsolete file --- ...cell2location-0.05-alpha-fosscuda-2020b.eb | 127 ------------------ 1 file changed, 127 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb deleted file mode 100644 index dd0be52167..0000000000 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ /dev/null @@ -1,127 +0,0 @@ -# Author: Denis Krišťák (INUITS) - -easyblock = 'PythonBundle' - -name = 'cell2location' -version = '0.05-alpha' - -homepage = 'https://github.com/BayraktarLab/cell2location/' -description = """Comprehensive mapping of tissue cell architecture via integrated -single cell and spatial transcriptomics (cell2location model)""" - -toolchain = {'name': 'fosscuda', 'version': '2020b'} - -builddependencies = [('Bison', '3.7.1')] - -dependencies = [ - ('Python', '3.8.6'), - ('Java', '11', '', True), - ('SciPy-bundle', '2020.11'), - ('leidenalg', '0.8.3'), - ('hyperopt', '0.2.5'), - ('CMake', '3.18.4'), - ('dill', '0.3.3'), - ('IPython', '7.18.1'), - ('Seaborn', '0.10.1'), - ('matplotlib', '3.3.3'), - ('libgpuarray', '0.7.6'), - ('PyMC3', '3.11.1'), - ('request', '2.88.1', '-nodejs-12.19.0'), - ('PyTables', '3.6.1'), - ('PyTorch', '1.7.1'), - ('statsmodels', '0.12.1'), - ('Theano', '1.1.2', '-PyMC'), - ('umap-learn', '0.4.6'), - ('pyro-api', '0.1.2'), - ('pyro-ppl', '1.5.2'), - ('numba', '0.52.0'), -] - -preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " - -use_pip = True - -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} - -exts_list = [ - ('opt-einsum', '3.3.0', { - 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', - 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], - }), - ('pytoml', '0.1.21', { - 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], - }), - ('get_version', '2.1', { - 'use_pip': False, - 'checksums': ['8156b526c2557537b8ca82241fa2b82b3da25939627398f6567dee31ba9725bc'], - }), - ('legacy-api-wrap', '1.2', { - 'use_pip': False, - 'checksums': ['034a44612da7e9943d3964363a98937ab54d55e3301075374abe0d521eb8101b'], - }), - ('descartes', '1.1.0', { - 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], - }), - ('mizani', '0.7.1', { - 'checksums': ['97eea665d17fdc6c827b832925c094839e1ef7bf65b3aa47105e772b6eca9b0a'], - }), - ('anndata', '0.7.5', { - 'checksums': ['2113a7463388013023f153e1a1446add4182883e3320b6e37dda18ee6210e038'], - }), - ('ipykernel', '5.3.4', { - 'checksums': ['9b2652af1607986a1b231c62302d070bc0534f564c393a5d9d130db9abbbe89d'], - }), - ('natsort', '7.1.0', { - 'checksums': ['33f3f1003e2af4b4df20908fe62aa029999d136b966463746942efbfc821add3'], - }), - ('palettable', '3.3.0', { - 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], - }), - ('scanpy', '1.6.0', { - 'checksums': ['542d1f1fc0471e7312d4349142e1c2eee4a465cd514fe4e3337be166f425fa55'], - }), - ('louvain', '0.7.0', { - 'checksums': ['9734fc6bf8c15546d685a8c6d7d7ca0574cad4cb641e9ca91c3334028658f7c6'], - }), - ('loompy', '3.0.6', { - 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], - }), - ('bbknn', '1.3.12', { - 'checksums': ['7dc5257baa278fc92349ac7865674ce70802dc4e3afdafed87a099dff9e91159'], - }), - ('stdlib-list', '0.8.0', { - 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], - }), - ('sinfo', '0.3.1', { - 'checksums': ['e1b2358808aded7b2ff00ea0cd4e6a2d978fb2a44ee9b15ac23d64a81bf62706'], - }), - ('plotnine', '0.7.0', { - 'checksums': ['8ee67cbf010ccea32670760e930b7b02177030a89ccdf85e35d156a96ce36cd3'], - }), - ('numpy-groupies', '0.9.13', { - 'modulename': 'numpy_groupies', - 'source_tmpl': 'numpy_groupies-%(version)s.tar.gz', - 'checksums': ['7b17b291322353f07c51598512d077e3731da0a048cfa8f738f3460d1ef0658d'], - }), - ('annoy', '1.17.0', { - 'checksums': ['9891e264041d1dcf3af42f67fbb16cb273c5404bc8c869d0915a3087f71d58dd'], - }), - (name, version, { - 'source_tmpl': 'v0.05-alpha.tar.gz', - 'source_urls': ['https://github.com/BayraktarLab/cell2location/archive'], - 'checksums': ['2df1fe2b2b4ec5fcebc6c1d6146ce0cd79115bd14059b0ae882a41f1029a4efc'], - }), -] - -sanity_pip_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' From 611a5dc3eed4dca7ee5bb5bbf6addf1cd076b88d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 13 Apr 2021 14:17:43 +0200 Subject: [PATCH 0676/2365] adding easyconfigs: glew-2.1.0-GCCcore-10.2.0.eb --- .../g/glew/glew-2.1.0-GCCcore-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f4f57f0706 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# th77embl updated to GCCcore 10.2.0 +easyblock = 'ConfigureMake' + +name = 'glew' +version = '2.1.0' + +homepage = 'http://glew.sourceforge.net/' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Mesa', '20.2.1')] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all' + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': ['', ] +} + +moduleclass = 'devel' From e5137f5180fcecd6bad6b4cb674cb04716895d65 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 13 Apr 2021 14:24:34 +0200 Subject: [PATCH 0677/2365] adding easyconfigs: freeglut-3.2.1-GCCcore-10.2.0.eb and patches: freeglut-3.2.1_gcc10_fix-1.patch --- .../freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..45d3fbdee6 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.2.1' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['freeglut-3.2.1_gcc10_fix-1.patch'] +checksums = [ + 'd4000e02102acaf259998c870e25214739d1f16f67f99cb35e4f46841399da68', # freeglut-3.2.1.tar.gz + 'f278467e03348b87d9b4ae69f491e503ab80c6d82433cf7468eac89b7f859d37', # freeglut-3.2.1_gcc10_fix-1.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' From 41359d84c9701b0e518fab289bb59fa0b48626d5 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 13 Apr 2021 14:30:03 +0200 Subject: [PATCH 0678/2365] adding easyconfigs: mmtf-cpp-1.0.0-GCCcore-10.2.0.eb, msgpack-c-3.3.0-GCCcore-10.2.0.eb --- .../mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ .../msgpack-c-3.3.0-GCCcore-10.2.0.eb | 30 +++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..914708e254 --- /dev/null +++ b/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04 +easyblock = 'CMakeNinja' + +name = 'mmtf-cpp' +version = '1.0.0' + +homepage = 'http://mmtf.rcsb.org/' +description = """ +The Macromolecular Transmission Format (MMTF) is a new compact binary format to +transmit and store biomolecular structures for fast 3D visualization and +analysis. +""" + + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/rcsb/mmtf-cpp/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['881f69c4bb56605fa63fd5ca50842facc4947f686cbf678ad04930674d714f40'] + +github_account = 'rscb' +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), + ('Ninja', '1.10.1'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('msgpack-c', '3.3.0'), +] +postinstallcmds = ['cd ../%(name)s-%(version)s/docs && doxygen && cd .. && mv docs %(installdir)s/doc'] +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'doc'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..865a94b0f1 --- /dev/null +++ b/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04 +easyblock = 'CMakeMake' + +name = 'msgpack-c' +version = '3.3.0' + +homepage = 'http://msgpack.org/' +description = """MessagePack is an efficient binary serialization format, which lets you exchange +data among multiple languages like JSON, except that it's faster and smaller. +Small integers are encoded into a single byte while typical short strings +require only one extra byte in addition to the strings themselves.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GITHUB_SOURCE] +github_account = 'msgpack' +sources = ['cpp-%(version)s.tar.gz'] +checksums = ['754c3ace499a63e45b77ef4bcab4ee602c2c414f58403bce826b76ffc2f77d0b'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': [('lib/libmsgpackc.%s' % SHLIB_EXT)], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'lib' From 52e5ae1dd695f476e86608309b992540ecac7894 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 13 Apr 2021 14:50:21 +0200 Subject: [PATCH 0679/2365] Fix DMCfun hard-coded num_cores --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 7 ++++++- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 7 ++++++- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 7 ++++++- 3 files changed, 18 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index b27365ac40..295ce520d4 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2801,7 +2801,12 @@ exts_list = [ 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], }), ('DMCfun', '1.3.0', { - 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], + 'patches': ['DMCfun-1.3.0_fix-parallel-detect.patch'], + 'checksums': [ + '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz + # DMCfun-1.3.0_fix-parallel-detect.patch + '555a4746375ec3c27473d6549a785359db91340f5126db5609cf5c6bca97cdff', + ], }), ] diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 4ac9ced88b..96aa1e6bf8 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2811,7 +2811,12 @@ exts_list = [ 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], }), ('DMCfun', '1.3.0', { - 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], + 'patches': ['DMCfun-1.3.0_fix-parallel-detect.patch'], + 'checksums': [ + '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz + # DMCfun-1.3.0_fix-parallel-detect.patch + '555a4746375ec3c27473d6549a785359db91340f5126db5609cf5c6bca97cdff', + ], }), # Specific packages for GPUs ('OpenCL', '0.2-1', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index e3afe51d73..71e33a6505 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2836,7 +2836,12 @@ exts_list = [ 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], }), ('DMCfun', '1.3.0', { - 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], + 'patches': ['DMCfun-1.3.0_fix-parallel-detect.patch'], + 'checksums': [ + '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz + # DMCfun-1.3.0_fix-parallel-detect.patch + '555a4746375ec3c27473d6549a785359db91340f5126db5609cf5c6bca97cdff', + ], }), ] From ceb36f597074dc1bf580a7c094e319c0a93738ee Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 13 Apr 2021 15:00:24 +0200 Subject: [PATCH 0680/2365] mmtf-cpp-1.0.0-GCCcore-10.2.0.eb: https --- .../easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb index 914708e254..d692be29e5 100644 --- a/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb @@ -4,7 +4,7 @@ easyblock = 'CMakeNinja' name = 'mmtf-cpp' version = '1.0.0' -homepage = 'http://mmtf.rcsb.org/' +homepage = 'https://mmtf.rcsb.org/' description = """ The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structures for fast 3D visualization and From 8617f732a1bd5ba71b226f8def0b57075d8cb807 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Apr 2021 16:27:44 +0200 Subject: [PATCH 0681/2365] adding easyconfigs: GST-plugins-base-1.18.4-GCC-10.2.0.eb --- .../GST-plugins-base-1.18.4-GCC-10.2.0.eb | 43 +++++++++++++++++++ .../GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb | 42 ++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..c14fb9e9ef --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.18.4' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['29e53229a84d01d722f6f6db13087231cdf6113dd85c25746b9b58c3d68e8323'] + +builddependencies = [ + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('GObject-Introspection', '1.66.1'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('Bison', '3.7.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('GLib', '2.66.1'), + ('GTK+', '3.24.23'), + ('GStreamer', '1.18.4'), + ('Gdk-Pixbuf', '2.40.0'), + ('X11', '20201008'), + ('Mesa', '20.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..eb6ce3e1ba --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '1.18.4' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] + +builddependencies = [ + ('Bison', '3.7.1'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.66.1'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('GMP', '6.2.0'), + ('GSL', '2.6'), + ('GLib', '2.66.1'), + ('GTK+', '3.24.23'), + ('libunwind', '1.4.0'), +] + +configopts = '--with-dw=no ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' From b7a353693812663664f64ee784f5c4c30e9338b4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Apr 2021 16:31:24 +0200 Subject: [PATCH 0682/2365] adding easyconfigs: wxWidgets-3.1.4-GCC-10.2.0.eb --- .../w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..90a7f361f2 --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb @@ -0,0 +1,70 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.1.4' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f2698297b2d2c6d2372c23144c133e531248a64286c78ae17179155c94971d6f'] + +builddependencies = [ + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.1.0'), + ('expat', '2.2.9'), + ('GTK+', '3.24.23'), + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('SDL2', '2.0.14'), + ('cairo', '1.16.0'), + ('GST-plugins-base', '1.18.4'), + ('GLib', '2.66.1'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webkit --disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From 616d1c7378b3ac9b2384bfe727d2d11b9fda2108 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Apr 2021 16:33:12 +0200 Subject: [PATCH 0683/2365] adding easyconfigs: ctffind-4.1.14-fosscuda-2020b.eb --- .../ctffind/ctffind-4.1.14-fosscuda-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb new file mode 100644 index 0000000000..e011de44ed --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5'), + ('LibTIFF', '4.1.0'), + ('GSL', '2.6'), + ('wxWidgets', '3.1.4'), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From 7f8604722ab889690fa32c5e71152b1db4c9ea1f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Apr 2021 16:48:54 +0200 Subject: [PATCH 0684/2365] GStreamer-1.18.4: Should use MeasonNinja easyblock. --- .../easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb index eb6ce3e1ba..a4c5be9091 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MesonNinja' name = 'GStreamer' version = '1.18.4' @@ -16,6 +16,8 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] builddependencies = [ + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), ('Bison', '3.7.1'), ('flex', '2.6.4'), ('GObject-Introspection', '1.66.1'), @@ -32,7 +34,7 @@ dependencies = [ ('libunwind', '1.4.0'), ] -configopts = '--with-dw=no ' +configopts = '-Dlibdw=disabled ' sanity_check_paths = { 'files': [], From b917503c7fbcd3392e73770d11ff0b547911f554 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Apr 2021 09:02:57 +0200 Subject: [PATCH 0685/2365] adding easyconfigs: tcsh-6.22.03-GCCcore-10.2.0.eb --- .../t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..46a56b3bba --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.22.03' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['be2cfd653d2a0c7f506d2dd14c12324ba749bd484037be6df44a3973f52262b7'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('ncurses', '6.2')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' From 3ded479ecd832138596364aab3246e02470dcec6 Mon Sep 17 00:00:00 2001 From: Loris Bennett Date: Wed, 14 Apr 2021 09:19:52 +0200 Subject: [PATCH 0686/2365] BUSCO v5.1.2 --- .../b/BUSCO/BUSCO-5.1.2-foss-2020b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb new file mode 100644 index 0000000000..07b410d350 --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb @@ -0,0 +1,54 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'BUSCO' +version = '5.1.2' + +homepage = 'https://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['31e3603936c003751a02e9445d41851b85c475136c3e4a61b670cd81297fda06'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for pandas + ('R', '4.0.3'), + ('Biopython', '1.78'), + ('BLAST+', '2.11.0'), + ('HMMER', '3.3.2'), + ('prodigal', '2.6.3'), + ('AUGUSTUS', '3.4.0'), + ('SEPP', '4.4.0'), + ('MetaEuk', '4'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/test_data %(installdir)s', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s', +] + +sanity_check_paths = { + 'files': ['bin/busco', 'bin/generate_plot.py'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages/busco'] +} + +sanity_check_commands = [ + "busco --help", + "busco -i %(installdir)s/test_data/bacteria/genome.fna --mode geno --out test_bacteria.out", + "busco -i %(installdir)s/test_data/eukaryota/genome.fna --mode geno --out test_eukaryota.out", +] + +moduleclass = 'bio' From b04f4978d7b434d04ed29efa09c39659447b187e Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 14 Apr 2021 12:58:56 +0200 Subject: [PATCH 0687/2365] Delete glew-2.1.0-GCCcore-10.2.0.eb rename --- .../g/glew/glew-2.1.0-GCCcore-10.2.0.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb deleted file mode 100644 index f4f57f0706..0000000000 --- a/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-10.2.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# Contribution from the Crick HPC team -# uploaded by J. Sassmannshausen -# th77embl updated to GCCcore 10.2.0 -easyblock = 'ConfigureMake' - -name = 'glew' -version = '2.1.0' - -homepage = 'http://glew.sourceforge.net/' -description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source -C/C++ extension loading library. GLEW provides efficient run-time mechanisms -for determining which OpenGL extensions are supported on the target platform.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s-%(version)s.tgz'] -checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] - -builddependencies = [('binutils', '2.35')] - -dependencies = [('Mesa', '20.2.1')] - -skipsteps = ['configure'] - -preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' -install_cmd = 'make install.all' - -sanity_check_paths = { - 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + - ['bin/glewinfo', 'bin/visualinfo'] + - ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], - 'dirs': ['', ] -} - -moduleclass = 'devel' From cf917b55514eba4ff833008297ead2967cbaf823 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 14 Apr 2021 13:04:43 +0200 Subject: [PATCH 0688/2365] as suggested by @Micket: versionsuffix for glx, egl, and osmesa; update 2.2.0; X11 dependency --- .../g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb | 43 +++++++++++++++++++ .../g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb | 43 +++++++++++++++++++ .../glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb | 43 +++++++++++++++++++ 3 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb create mode 100644 easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb create mode 100644 easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb new file mode 100644 index 0000000000..26665a03de --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb @@ -0,0 +1,43 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# th77embl updated to GCCcore 10.2.0 +easyblock = 'ConfigureMake' +versionsuffix = '-egl' +# available: -glx, -osmesa, -egl acc. to @Micket's suggestion: +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +github_account = 'nigels-com' +sources = ['%(name)s-%(version)s.tgz'] + +builddependencies = [('binutils', '2.35')] +buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +dependencies = [ + ('Mesa', '20.2.1'), + ('X11', '20201008'), +] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all' + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': ['', ] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb new file mode 100644 index 0000000000..7ef0814f8d --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb @@ -0,0 +1,43 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# th77embl updated to GCCcore 10.2.0 +easyblock = 'ConfigureMake' +versionsuffix = '-glx' +# available: -glx, -osmesa, -egl acc. to @Micket's suggestion: +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +github_account = 'nigels-com' +sources = ['%(name)s-%(version)s.tgz'] + +builddependencies = [('binutils', '2.35')] +buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +dependencies = [ + ('Mesa', '20.2.1'), + ('X11', '20201008'), +] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all' + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': ['', ] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb new file mode 100644 index 0000000000..25347ca97f --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb @@ -0,0 +1,43 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# th77embl updated to GCCcore 10.2.0 +easyblock = 'ConfigureMake' +versionsuffix = '-osmesa' +# available: -glx, -osmesa, -egl acc. to @Micket's suggestion: +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +github_account = 'nigels-com' +sources = ['%(name)s-%(version)s.tgz'] + +builddependencies = [('binutils', '2.35')] +buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +dependencies = [ + ('Mesa', '20.2.1'), + ('X11', '20201008'), +] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all' + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': ['', ] +} + +moduleclass = 'devel' From 00a52cf9687b7c26c4c59e092b4db9f958666c8c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 14 Apr 2021 14:38:13 +0200 Subject: [PATCH 0689/2365] checksums --- easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb | 3 ++- easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb | 3 ++- .../easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb index 26665a03de..17e1aad18a 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb @@ -18,9 +18,10 @@ for determining which OpenGL extensions are supported on the target platform.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] -github_account = 'nigels-com' sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] +github_account = 'nigels-com' builddependencies = [('binutils', '2.35')] buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' dependencies = [ diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb index 7ef0814f8d..1add39a7ec 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb @@ -18,9 +18,10 @@ for determining which OpenGL extensions are supported on the target platform.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] -github_account = 'nigels-com' sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] +github_account = 'nigels-com' builddependencies = [('binutils', '2.35')] buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' dependencies = [ diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb index 25347ca97f..ccb30ebc64 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb @@ -18,9 +18,10 @@ for determining which OpenGL extensions are supported on the target platform.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] -github_account = 'nigels-com' sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] +github_account = 'nigels-com' builddependencies = [('binutils', '2.35')] buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' dependencies = [ From 1b78d2918f352d603cf46190f7fe904692d1fa2e Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 14 Apr 2021 15:05:40 +0200 Subject: [PATCH 0690/2365] removed useless stuff --- easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb | 3 +-- easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb | 3 +-- .../easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb | 3 +-- 3 files changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb index 17e1aad18a..61dd4c138a 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb @@ -21,7 +21,6 @@ source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%( sources = ['%(name)s-%(version)s.tgz'] checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] -github_account = 'nigels-com' builddependencies = [('binutils', '2.35')] buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' dependencies = [ @@ -38,7 +37,7 @@ sanity_check_paths = { 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + ['bin/glewinfo', 'bin/visualinfo'] + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], - 'dirs': ['', ] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb index 1add39a7ec..b995d85444 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb @@ -21,7 +21,6 @@ source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%( sources = ['%(name)s-%(version)s.tgz'] checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] -github_account = 'nigels-com' builddependencies = [('binutils', '2.35')] buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' dependencies = [ @@ -38,7 +37,7 @@ sanity_check_paths = { 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + ['bin/glewinfo', 'bin/visualinfo'] + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], - 'dirs': ['', ] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb index ccb30ebc64..77964f2f35 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb @@ -21,7 +21,6 @@ source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%( sources = ['%(name)s-%(version)s.tgz'] checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] -github_account = 'nigels-com' builddependencies = [('binutils', '2.35')] buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' dependencies = [ @@ -38,7 +37,7 @@ sanity_check_paths = { 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + ['bin/glewinfo', 'bin/visualinfo'] + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], - 'dirs': ['', ] + 'dirs': [] } moduleclass = 'devel' From affe08ee11c4fa19ef835e2f8e58e865c655fb38 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 14 Apr 2021 16:14:25 +0100 Subject: [PATCH 0691/2365] adding easyconfigs: Octopus-vcf-0.7.2-foss-2020b.eb --- .../Octopus-vcf-0.7.2-foss-2020b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.2-foss-2020b.eb b/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.2-foss-2020b.eb new file mode 100644 index 0000000000..4ee59d1df1 --- /dev/null +++ b/easybuild/easyconfigs/o/Octopus-vcf/Octopus-vcf-0.7.2-foss-2020b.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMakeCp' + +# To avoid a naming clash +name = 'Octopus-vcf' +version = '0.7.2' + +homepage = 'https://github.com/luntergroup/octopus' +description = """Octopus is a mapping-based variant caller that implements several calling models within + a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a + tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities + in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in + reasonable time.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/luntergroup/octopus/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['887096c7357b1ba7f0653f9ad34fa32f56f80ba618fe4daaf6837d4737e7838d'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('git', '2.28.0', '-nodocs'), +] + +dependencies = [ + ('Boost', '1.74.0'), + ('HTSlib', '1.11'), + ('GMP', '6.2.0'), + ('Python', '3.8.6'), +] + +configopts = '-DHTSlib_NO_SYSTEM_PATHS=TRUE -DHTSLIB_ROOT=$EBROOTHTSLIB ' + +separate_build_dir = True + +files_to_copy = [ + (['%(builddir)s/easybuild_obj/src/octopus'], 'bin'), + 'doc', 'lib', 'LICENSE', 'logo.png', 'README.md', + 'resources', 'scripts', 'test' +] + +sanity_check_commands = ['octopus -h'] + +sanity_check_paths = { + 'files': ['bin/octopus'], + 'dirs': ['doc', 'lib', 'resources'] +} + +moduleclass = 'bio' From db68035c9e7aee75f47955837381d782eae6ea54 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Apr 2021 19:50:07 +0200 Subject: [PATCH 0692/2365] adding easyconfigs: WPS-4.2-foss-2020b-dmpar.eb, WRF-4.2.2-foss-2020b-dmpar.eb and patches: WPS-4.2_netCDF-Fortran_seperate_path.patch, WPS-4.2_GCC-10-allow-argument-mismatch.patch, WRF-4.2.2_netCDF-Fortran_separate_path.patch --- .../w/WPS/WPS-4.2-foss-2020b-dmpar.eb | 40 +++++++++++++++++ .../w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb | 43 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.2-foss-2020b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.2-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.2-foss-2020b-dmpar.eb new file mode 100644 index 0000000000..7161c17020 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.2-foss-2020b-dmpar.eb @@ -0,0 +1,40 @@ +name = 'WPS' +version = '4.2' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', + 'WPS-%(version)s_GCC-10-allow-argument-mismatch.patch', +] +checksums = [ + '3e175d033355d3e7638be75bc7c0bc0de6da299ebd175a9bbc1b7a121acd0168', # v4.2.tar.gz + '25359a9abfc6a4afc2f7b9624727eeea47d1a6421b99dbc8dd9b54a37d378ae5', # WPS-4.2_netCDF-Fortran_seperate_path.patch + 'c195d82e189780631b8c31110199b09a52e447b47fe2dd31d86dc86846a61148', # WPS-4.2_GCC-10-allow-argument-mismatch.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +builddependencies = [ + ('Perl', '5.32.0'), +] + +dependencies = [ + ('WRF', '4.2.2', versionsuffix), + ('JasPer', '2.0.24'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb new file mode 100644 index 0000000000..20b645cfdb --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb @@ -0,0 +1,43 @@ +name = 'WRF' +version = '4.2.2' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', +] +checksums = [ + '7be2968c67c2175cd40b57118d9732eda5fdb0828edaa25baf57cc289da1a9b8', # v4.2.2.tar.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + 'fcc0d0c9604a1aba83b665594e945fb8f3b79ecb9f69df3f2874e273a40ce3d9', # WRF-4.2.2_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20200321'), + ('tcsh', '6.22.03'), + ('time', '1.9'), + ('Perl', '5.32.0'), +] + +dependencies = [ + ('JasPer', '2.0.24'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' From 74104fdd7d5c516e4b35c46c12fbc90a5c334c93 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Apr 2021 20:03:32 +0200 Subject: [PATCH 0693/2365] bump dependencies for WRF 39.1.1 with 2020b toolchain --- easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb | 6 +++--- .../easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb index 54909c4e81..9fea5e7036 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb @@ -34,13 +34,13 @@ checksums = [ # csh is used by WRF install scripts builddependencies = [ - ('tcsh', '6.22.02'), + ('tcsh', '6.22.03'), ('time', '1.9'), ] dependencies = [ - ('libtirpc', '1.2.6'), - ('JasPer', '2.0.14'), + ('libtirpc', '1.3.1'), + ('JasPer', '2.0.24'), ('netCDF', '4.7.4'), ('netCDF-Fortran', '4.5.3'), ] diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb index 9f9491846b..44a0736663 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb @@ -34,13 +34,13 @@ checksums = [ # csh is used by WRF install scripts builddependencies = [ - ('tcsh', '6.22.02'), + ('tcsh', '6.22.03'), ('time', '1.9'), ] dependencies = [ - ('libtirpc', '1.2.6'), - ('JasPer', '2.0.14'), + ('libtirpc', '1.3.1'), + ('JasPer', '2.0.24'), ('netCDF', '4.7.4'), ('netCDF-Fortran', '4.5.3'), ] From 3c30ac1cfcf1b9dc564ea7f691d0db7e0a6d0890 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 15 Apr 2021 09:21:22 +0200 Subject: [PATCH 0694/2365] source_urls and sanity_check_paths --- .../m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb index 865a94b0f1..73c851471f 100644 --- a/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb @@ -12,10 +12,9 @@ require only one extra byte in addition to the strings themselves.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [GITHUB_SOURCE] -github_account = 'msgpack' -sources = ['cpp-%(version)s.tar.gz'] -checksums = ['754c3ace499a63e45b77ef4bcab4ee602c2c414f58403bce826b76ffc2f77d0b'] +source_urls = ['https://github.com/msgpack/msgpack-c/releases/download/cpp-%(version)s'] +sources = ['msgpack-%(version)s.tar.gz'] +checksums = ['6e114d12a5ddb8cb11f669f83f32246e484a8addd0ce93f274996f1941c1f07b'] builddependencies = [ ('CMake', '3.18.4'), @@ -23,8 +22,11 @@ builddependencies = [ ] sanity_check_paths = { - 'files': [('lib/libmsgpackc.%s' % SHLIB_EXT)], - 'dirs': ['include', 'lib'], + 'files': [ + ['lib/libmsgpackc.%s' % x for x in ['a', '%s' % SHLIB_EXT]], + ['include/msgpack.%s' % x for x in ['h', 'hpp']] # check for both, C and C++ headers + ], + 'dirs': ['lib/pkgconfig', 'include/msgpack'], } moduleclass = 'lib' From 0f4ddf72e6915002f961d42cd840ccaf35385fee Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 15 Apr 2021 10:43:52 +0200 Subject: [PATCH 0695/2365] add Archive::Zip and Compress::Raw::Zlib to Perl v5.32.0 --- .../easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 76d0b56cf8..f1f6b4e61f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -22,6 +22,7 @@ dependencies = [ ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.0'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File + ('UnZip', '6.0'), # for Archive::Zip ] # OpenSSL is required for Net::SSLeay @@ -1796,6 +1797,16 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY/'], 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], }), + ('Archive::Zip', '1.68', { + 'source_tmpl': 'Archive-Zip-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'], + 'checksums': ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'], + }), + ('Compress::Raw::Zlib', '2.101', { + 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['9d1b9515e8277c1b007e33fad1fd0f18717d56bf647e3794d61289c45b1aabb2'], + }), ] moduleclass = 'lang' From 843819bea68028d00b45a76328c2d9c29af90970 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 15 Apr 2021 10:47:59 +0200 Subject: [PATCH 0696/2365] add Zip as dependency of Perl v5.32.0 --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index f1f6b4e61f..11927cd353 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -23,6 +23,7 @@ dependencies = [ ('libreadline', '8.0'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File ('UnZip', '6.0'), # for Archive::Zip + ('Zip', '3.0'), # for Archive::Zip ] # OpenSSL is required for Net::SSLeay From 228d3c7d6573f088b3e062824e670373bd93dc47 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 15 Apr 2021 10:58:06 +0200 Subject: [PATCH 0697/2365] adding easyconfigs: netCDF-Fortran-4.5.3-gompic-2020b.eb --- .../netCDF-Fortran-4.5.3-gompic-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb new file mode 100644 index 0000000000..ca40c6a2e2 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb @@ -0,0 +1,25 @@ +name = 'netCDF-Fortran' +version = '4.5.3' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompic', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c6da30c2fe7e4e614c1dff4124e857afbd45355c6798353eccfa60c0702b495a'] + +builddependencies = [ + ('M4', '1.4.18'), +] + +dependencies = [('netCDF', '4.7.4')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' From acb7c4c254e5f61a11f680ccad30b80664c2edc0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 15 Apr 2021 11:10:49 +0200 Subject: [PATCH 0698/2365] move VEP v103.1 from foss/2020b to GCC/10.2.0 --- .../easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..cbfacd066a --- /dev/null +++ b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +name = 'VEP' +version = '103.1' + +homepage = 'https://www.ensembl.org/info/docs/tools/vep' +description = """Variant Effect Predictor (VEP) determines the effect of your + variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, + transcripts, and protein sequence, as well as regulatory regions. + Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently + used routines in VEP.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3512a2c3514f7c10b0348b45bf9fe621dc691100e43f14bec48842b1e11bbf8b'] + +dependencies = [ + ('Perl', '5.32.0'), + ('DBD-mysql', '4.050'), + ('BioPerl', '1.7.8'), + ('Bio-DB-HTS', '3.01'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('Bio::EnsEMBL::XS', '2.3.2', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], + 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], + }), +] + +moduleclass = 'bio' From 5f3fde3cf463d75090c2b7a5bd1486c3d7487d53 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 15 Apr 2021 11:49:17 +0200 Subject: [PATCH 0699/2365] {tools}[foss/2020{a,b}] mongolite w/ R-4.0.{0,3,4} --- .../mongolite-2.3.0-foss-2020b-R-4.0.3.eb | 31 +++++++++++++++++++ .../mongolite-2.3.0-foss-2020b-R-4.0.4.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/m/mongolite/mongolite-2.3.0-foss-2020b-R-4.0.3.eb create mode 100644 easybuild/easyconfigs/m/mongolite/mongolite-2.3.0-foss-2020b-R-4.0.4.eb diff --git a/easybuild/easyconfigs/m/mongolite/mongolite-2.3.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/m/mongolite/mongolite-2.3.0-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..c5ed32c3dc --- /dev/null +++ b/easybuild/easyconfigs/m/mongolite/mongolite-2.3.0-foss-2020b-R-4.0.3.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'mongolite' +version = '2.3.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/%(name)s' +description = """High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. + Includes support for aggregation, indexing, map-reduce, streaming, encryption, + enterprise authentication, and GridFS. The online user manual provides an overview + of the available methods in the package: .""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/jeroen/mongolite/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ea691b3f74571152212f3ab96e1f0413240534d1ca4659f12b653bffac97bf66'] + +dependencies = [('R', '4.0.3')] + +osdependencies = [ + OS_PKG_OPENSSL_DEV, + ('cyrus-sasl-devel', 'libsasl2-dev'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['mongolite'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mongolite/mongolite-2.3.0-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/mongolite/mongolite-2.3.0-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..551c52c4f5 --- /dev/null +++ b/easybuild/easyconfigs/m/mongolite/mongolite-2.3.0-foss-2020b-R-4.0.4.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'mongolite' +version = '2.3.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/%(name)s' +description = """High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. + Includes support for aggregation, indexing, map-reduce, streaming, encryption, + enterprise authentication, and GridFS. The online user manual provides an overview + of the available methods in the package: .""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/jeroen/mongolite/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ea691b3f74571152212f3ab96e1f0413240534d1ca4659f12b653bffac97bf66'] + +dependencies = [('R', '4.0.4')] + +osdependencies = [ + OS_PKG_OPENSSL_DEV, + ('cyrus-sasl-devel', 'libsasl2-dev'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['mongolite'], +} + +moduleclass = 'tools' From d3258d64a45ec49abcedc5aeba2f0a53040aa168 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 15 Apr 2021 12:03:04 +0200 Subject: [PATCH 0700/2365] Fix typo in Delly config, make it actually OMP parallel --- easybuild/easyconfigs/d/Delly/Delly-0.8.7-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Delly/Delly-0.8.7-gompi-2020b.eb b/easybuild/easyconfigs/d/Delly/Delly-0.8.7-gompi-2020b.eb index f3283826a1..a91dbfee3e 100644 --- a/easybuild/easyconfigs/d/Delly/Delly-0.8.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/d/Delly/Delly-0.8.7-gompi-2020b.eb @@ -28,7 +28,7 @@ dependencies = [ ('Boost', '1.74.0'), ] -build_cmd = 'make PARELLEL=1 -B src/delly' +build_cmd = 'make PARALLEL=1 -B src/delly' files_to_copy = [ (['src/delly'], 'bin'), From 9856aa2413578500340319b56738e25086990730 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Thu, 15 Apr 2021 11:37:48 +0100 Subject: [PATCH 0701/2365] Create tmux-3.2-GCCcore-10.2.0.eb New easyconfig for tmux 3.2. --- .../t/tmux/tmux-3.2-GCCcore-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/t/tmux/tmux-3.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tmux/tmux-3.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..df0fc99300 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.2-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.2' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['664d345338c11cbe429d7ff939b92a5191e231a7c1ef42f381cebacb1e08a399'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('make', '4.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.2'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' From c757973c33dcde7d45fc4240319859412507dab1 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 15 Apr 2021 14:49:05 +0200 Subject: [PATCH 0702/2365] renamed; switch toolchain SYSTEM -> GCCcore/10.2.0 --- .../g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1031e4d395 --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '0.9.9.8' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'GLM-0.9.9.8_fix_missing_install.patch', +] +checksums = [ + '7d508ab72cb5d43227a3711420f06ff99b0a0cb63ee2f93631b162bfe1fe9592', # 0.9.9.8.tar.gz + '1cc199f9d66679b0b5e9a9fbe20bca0d9b15760fa172ca8759dd15bab35802ca', # GLM-0.9.9.8_fix_missing_install.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' From a5eee1b094053c736e028ac8901ba7c57f7858ac Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 15 Apr 2021 15:49:07 +0200 Subject: [PATCH 0703/2365] Fix potential memory leak in OpenBLAS 0.3.12 --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index 8d522bf013..6f432e2a0d 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -15,11 +15,14 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', ] checksums = [ '65a7d3a4010a4e3bd5c0baa41a234797cd3a1735449a4a5902129152601dc57b', # v0.3.12.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch + '4b3ab7260975ea2cfd7460731c0201b2c1e374cd83ae90d55b8da3e670633ba0', ] # extensive testing can be enabled by uncommenting the line below From 21dafe370ef295969c8c2add5baed63d6a272744 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 15 Apr 2021 15:54:31 +0200 Subject: [PATCH 0704/2365] Consistently use pip to install Python packages in Python ECs --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 23 ++++++++++--------- .../p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 18 ++++++++------- 2 files changed, 22 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index ac42a9c106..2e903efcf8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -38,14 +38,15 @@ exts_default_options = { # order is important! # package versions updated 13 October 2020, to the most recent versions still supporting Python 2.x exts_list = [ + ('pip', '20.3.4', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], + 'pip_ignore_installed': False, + }), ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'use_pip': False, 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], - }), - ('pip', '20.3.4', { - 'use_pip': False, - 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], + 'pip_ignore_installed': False, }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], @@ -334,15 +335,15 @@ exts_list = [ 'checksums': ['063910098161199b81e453025653ec53556c1be7165a9b7c50be2f4d57eae1c3'], }), ('pastel', '0.2.1', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d'], }), ('clikit', '0.6.2', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59'], }), ('entrypoints', '0.3', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), ('SecretStorage', '2.3.1', { @@ -358,7 +359,7 @@ exts_list = [ 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], }), ('tomlkit', '0.7.0', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618'], }), ('shellingham', '1.3.2', { @@ -389,7 +390,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '0.8.1', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['3d0e22d30117851b45970b6c14aca4ab0b18b1b53c8af57bed13208147e4069f'], }), ('cachy', '0.3.0', { @@ -402,7 +403,7 @@ exts_list = [ 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], }), ('ptyprocess', '0.6.0', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], }), ('lockfile', '0.12.2', { diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 4371dc3f09..daca0fe096 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -50,12 +50,14 @@ exts_default_options = { # package versions updated 13 October 2020 exts_list = [ ('pip', '20.2.3', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + 'pip_ignore_installed': False, }), ('setuptools', '50.3.0', { 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['39060a59d91cf5cf403fa3bacbb52df4205a8c3585e0b9ba4b30e0e19d4c4b18'], + 'pip_ignore_installed': False, }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], @@ -332,22 +334,22 @@ exts_list = [ 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], }), ('crashtest', '0.3.1', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['42ca7b6ce88b6c7433e2ce47ea884e91ec93104a4b754998be498a8e6c3d37dd'], }), ('pylev', '1.3.0', { 'checksums': ['063910098161199b81e453025653ec53556c1be7165a9b7c50be2f4d57eae1c3'], }), ('pastel', '0.2.1', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d'], }), ('clikit', '0.6.2', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59'], }), ('jeepney', '0.4.3', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], }), ('SecretStorage', '3.1.2', { @@ -362,7 +364,7 @@ exts_list = [ 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], }), ('tomlkit', '0.7.0', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618'], }), ('shellingham', '1.3.2', { @@ -393,7 +395,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '0.8.1', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['3d0e22d30117851b45970b6c14aca4ab0b18b1b53c8af57bed13208147e4069f'], }), ('cachy', '0.3.0', { @@ -406,7 +408,7 @@ exts_list = [ 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], }), ('ptyprocess', '0.6.0', { - 'use_pip': False, + 'source_tmpl': SOURCE_WHL, 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], }), ('lockfile', '0.12.2', { From 807e44609bafcec3937eb36ad6891bf27c71f0d7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 15 Apr 2021 18:16:57 +0200 Subject: [PATCH 0705/2365] adding easyconfigs: Archive-Zip-1.68-GCCcore-10.2.0.eb --- .../Archive-Zip-1.68-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..703e64d643 --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +dependencies = [ + ('Perl', '5.32.0'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' From 7bcb5814fa763da01e571fd7dc8344d6401cb2bb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 15 Apr 2021 18:18:23 +0200 Subject: [PATCH 0706/2365] remove Archive::Zip from Perl v5.32.0 --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 11927cd353..1ed7727cea 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -22,8 +22,6 @@ dependencies = [ ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.0'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('UnZip', '6.0'), # for Archive::Zip - ('Zip', '3.0'), # for Archive::Zip ] # OpenSSL is required for Net::SSLeay @@ -1798,11 +1796,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY/'], 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], }), - ('Archive::Zip', '1.68', { - 'source_tmpl': 'Archive-Zip-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'], - 'checksums': ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'], - }), ('Compress::Raw::Zlib', '2.101', { 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], From 4ac125882d4055c16966a6eb88566201cbb209c9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 15 Apr 2021 18:21:55 +0200 Subject: [PATCH 0707/2365] add dependency on Archive-Zip to VEP v103.1 --- easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb index cbfacd066a..b53ccb6277 100644 --- a/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb @@ -16,6 +16,7 @@ checksums = ['3512a2c3514f7c10b0348b45bf9fe621dc691100e43f14bec48842b1e11bbf8b'] dependencies = [ ('Perl', '5.32.0'), + ('Archive-Zip', '1.68'), ('DBD-mysql', '4.050'), ('BioPerl', '1.7.8'), ('Bio-DB-HTS', '3.01'), From 09ca9047a381547c2dc9e994bcbf777ec522bd99 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 15 Apr 2021 19:03:54 +0200 Subject: [PATCH 0708/2365] Fix sources and checksums --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 16 +++++++------- .../p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 22 +++++++++---------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index 2e903efcf8..c343b9d7ea 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -39,9 +39,9 @@ exts_default_options = { # package versions updated 13 October 2020, to the most recent versions still supporting Python 2.x exts_list = [ ('pip', '20.3.4', { - 'source_tmpl': SOURCE_WHL, - 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], 'pip_ignore_installed': False, + 'source_tmpl': SOURCE_WHL, + 'checksums': ['217ae5161a0e08c0fb873858806e3478c9775caffce5168b50ec885e358c199d'], }), ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', @@ -336,15 +336,15 @@ exts_list = [ }), ('pastel', '0.2.1', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d'], + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('clikit', '0.6.2', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59'], + 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], }), ('entrypoints', '0.3', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + 'checksums': ['589f874b313739ad35be6e0cd7efde2a4e9b6fea91edcc34e58ecbb8dbe56d19'], }), ('SecretStorage', '2.3.1', { 'modulename': False, # Doesn't work properly under Python2, but is required for keyring @@ -360,7 +360,7 @@ exts_list = [ }), ('tomlkit', '0.7.0', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618'], + 'checksums': ['6babbd33b17d5c9691896b0e68159215a9387ebfa938aa3ac42f4a4beeb2b831'], }), ('shellingham', '1.3.2', { 'checksums': ['576c1982bea0ba82fb46c36feb951319d7f42214a82634233f58b40d858a751e'], @@ -391,7 +391,7 @@ exts_list = [ }), ('cleo', '0.8.1', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['3d0e22d30117851b45970b6c14aca4ab0b18b1b53c8af57bed13208147e4069f'], + 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], }), ('cachy', '0.3.0', { 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], @@ -404,7 +404,7 @@ exts_list = [ }), ('ptyprocess', '0.6.0', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + 'checksums': ['d7cc528d76e76342423ca640335bd3633420dc1366f258cb31d05e865ef5ca1f'], }), ('lockfile', '0.12.2', { 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index daca0fe096..ed6f449a50 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -50,9 +50,9 @@ exts_default_options = { # package versions updated 13 October 2020 exts_list = [ ('pip', '20.2.3', { - 'source_tmpl': SOURCE_WHL, - 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], 'pip_ignore_installed': False, + 'source_tmpl': SOURCE_WHL, + 'checksums': ['0f35d63b7245205f4060efe1982f5ea2196aa6e5b26c07669adcf800e2542026'], }), ('setuptools', '50.3.0', { 'source_tmpl': '%(name)s-%(version)s.zip', @@ -334,23 +334,23 @@ exts_list = [ 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], }), ('crashtest', '0.3.1', { - 'source_tmpl': SOURCE_WHL, - 'checksums': ['42ca7b6ce88b6c7433e2ce47ea884e91ec93104a4b754998be498a8e6c3d37dd'], + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], }), ('pylev', '1.3.0', { 'checksums': ['063910098161199b81e453025653ec53556c1be7165a9b7c50be2f4d57eae1c3'], }), ('pastel', '0.2.1', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d'], + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('clikit', '0.6.2', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59'], + 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], }), ('jeepney', '0.4.3', { - 'source_tmpl': SOURCE_WHL, - 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d6c6b49683446d2407d2fe3acb7a368a77ff063f9182fe427da15d622adc24cf'], }), ('SecretStorage', '3.1.2', { 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], @@ -365,7 +365,7 @@ exts_list = [ }), ('tomlkit', '0.7.0', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618'], + 'checksums': ['6babbd33b17d5c9691896b0e68159215a9387ebfa938aa3ac42f4a4beeb2b831'], }), ('shellingham', '1.3.2', { 'checksums': ['576c1982bea0ba82fb46c36feb951319d7f42214a82634233f58b40d858a751e'], @@ -396,7 +396,7 @@ exts_list = [ }), ('cleo', '0.8.1', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['3d0e22d30117851b45970b6c14aca4ab0b18b1b53c8af57bed13208147e4069f'], + 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], }), ('cachy', '0.3.0', { 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], @@ -409,7 +409,7 @@ exts_list = [ }), ('ptyprocess', '0.6.0', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + 'checksums': ['d7cc528d76e76342423ca640335bd3633420dc1366f258cb31d05e865ef5ca1f'], }), ('lockfile', '0.12.2', { 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], From 2aad2d24e042e4d3a5b70ec59829f27220fbfbb1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 15 Apr 2021 20:11:01 +0200 Subject: [PATCH 0709/2365] add comment for ext_postinstallcmds --- easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb index 232825143d..6361cbff22 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -25,6 +25,7 @@ dependencies = [ ('BCFtools', '1.11'), ] +# added ext_postinstallcmds to pandoc: import fails if pandoc/definitions dir is not installed exts_list = [ ('wbuild', '1.8.0', { 'checksums': ['3088d3fcbc71106464f20e3546a73df400dc03d17f11e70bdb15d35d7e6c5a7e'], From 949a1dcd672a6c34439f63eb83c4f54bd0ae83f7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Apr 2021 10:24:41 +0200 Subject: [PATCH 0710/2365] add build dependency on binutils to Archive-Zip v1.68 --- .../a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb index 703e64d643..09c556f1fb 100644 --- a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb @@ -12,6 +12,10 @@ source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] +builddependencies = [ + ('binutils', '2.35'), +] + dependencies = [ ('Perl', '5.32.0'), ('UnZip', '6.0'), From bab9d3d71e0652ef36c1f850a8151be4753d6671 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Fri, 16 Apr 2021 11:42:06 +0200 Subject: [PATCH 0711/2365] Add ARM fix to fosscuda easyconfig --- .../easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 5f6def8751..5ab6551adb 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -13,7 +13,13 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -checksums = ['cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2'] +patches = [ + 'Arrow-0.17.1_fix-arm.patch', +] +checksums = [ + 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz + 'd1076d35966056c39e0c88b8fadaaa7660ee4d8c07fc2c5bdf1d5d6e683ff44a', # Arrow-0.17.1_fix-arm.patch +] builddependencies = [ ('CMake', '3.18.4'), From 56d2c0dac14713035c0701e8a5f13f20c75795d2 Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Fri, 16 Apr 2021 10:14:57 -0400 Subject: [PATCH 0712/2365] add Python dependency to AUGUSTUS-3.4.0-foss-2020b.eb --- easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb index 0377e4b9b7..b165abec20 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb @@ -32,6 +32,7 @@ dependencies = [ ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), ('BamTools', '2.5.1'), ('SQLite', '3.33.0'), + ('Python', '3.8.6'), ] skipsteps = ['configure'] From 751ab82dad4f46afc6d257060ee48166aa922e89 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Apr 2021 16:44:50 +0200 Subject: [PATCH 0713/2365] adding easyconfigs: Nektar++-5.0.1-foss-2020b.eb --- .../n/Nektar++/Nektar++-5.0.1-foss-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb new file mode 100644 index 0000000000..9c7790dada --- /dev/null +++ b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Nektar++' +version = '5.0.1' + +homepage = 'https://www.nektar.info' +description = """Nektar++ is a tensor product based finite element package +designed to allow one to construct efficient classical low polynomial order +h-type solvers (where h is the size of the finite element) as well as higher +p-order piecewise polynomial order solvers.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['http://www.nektar.info/downloads/file'] +sources = [{'download_filename': 'nektar-5-0-1-tar-xz', 'filename': '%(namelower)s-%(version)s.tar.xz'}] +checksums = ['d38401321250e21a29a73dd491e05ca077dd177a32c222c961693b3189542d06'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.74.0'), + ('HDF5', '1.10.7'), + ('METIS', '5.1.0'), + ('PETSc', '3.14.4'), + ('VTK', '9.0.1'), +] + +preconfigopts = 'export OPENBLAS_HOME=$EBROOTOPENBLAS LAPACK_DIR=$EBROOTOPENBLAS BLAS_DIR=$EBROOTOPENBLAS && ' + +configopts = '-DNEKTAR_USE_OPENBLAS=True ' + +moduleclass = 'cae' From 06e3c20ae96ba7be5e76d02347baae4ac1e28bf5 Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Fri, 16 Apr 2021 13:41:52 -0400 Subject: [PATCH 0714/2365] initial commit for OpenMM-7.5.0-fosscuda-2020b --- .../o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..77b1921e02 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb @@ -0,0 +1,65 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.0' +#versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = [ + '516748b4f1ae936c4d70cc6401174fc9384244c65cd3aef27bc2c53eac6d6de5', # 7.5.0.tar.gz +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SWIG', '4.0.2'), +] + +#Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON -DCUDA_CUDA_LIBRARY=$EBROOTCUDACORE/lib64/stubs/libcuda.so" + +pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} +modextravars = { + 'OPENMM_CUDA_COMPILER': 'nvcc', +} + +moduleclass = 'bio' From 64a1903c18cc42db6b1f4640bfbbf318e3600d36 Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Fri, 16 Apr 2021 14:00:42 -0400 Subject: [PATCH 0715/2365] fix style issues --- easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb index 77b1921e02..420b7a7e03 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb @@ -7,7 +7,6 @@ easyblock = 'CMakeMake' name = 'OpenMM' version = '7.5.0' -#versionsuffix = '-Python-%(pyver)s' homepage = 'http://openmm.org' description = "OpenMM is a toolkit for molecular simulation." @@ -34,7 +33,7 @@ dependencies = [ ('SWIG', '4.0.2'), ] -#Flags for CUDA-enabled build +# Flags for CUDA-enabled build configopts = "-DOPENMM_BUILD_CUDA_LIB=ON -DCUDA_CUDA_LIBRARY=$EBROOTCUDACORE/lib64/stubs/libcuda.so" pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" From 8912779d36d128727cc0677cd18191ca73a18b24 Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Fri, 16 Apr 2021 14:53:09 -0400 Subject: [PATCH 0716/2365] add Perl to list of dependencies (to support scripts) --- easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb index b165abec20..b88bf94194 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb @@ -33,6 +33,7 @@ dependencies = [ ('BamTools', '2.5.1'), ('SQLite', '3.33.0'), ('Python', '3.8.6'), + ('Perl','5.32.0'), ] skipsteps = ['configure'] From 8a550185e33878fb31e60ac96a74f0b698793506 Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Fri, 16 Apr 2021 14:56:47 -0400 Subject: [PATCH 0717/2365] Update easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb index b88bf94194..aef949181c 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb @@ -33,7 +33,7 @@ dependencies = [ ('BamTools', '2.5.1'), ('SQLite', '3.33.0'), ('Python', '3.8.6'), - ('Perl','5.32.0'), + ('Perl', '5.32.0'), ] skipsteps = ['configure'] From 4a503478794167df59c0e9212ea63d4de89bb66f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 17 Apr 2021 07:38:12 +0200 Subject: [PATCH 0718/2365] Add missing sanity_check_paths --- .../n/Nektar++/Nektar++-5.0.1-foss-2020b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb index 9c7790dada..4cef23c8dd 100644 --- a/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb @@ -33,4 +33,25 @@ preconfigopts = 'export OPENBLAS_HOME=$EBROOTOPENBLAS LAPACK_DIR=$EBROOTOPENBLAS configopts = '-DNEKTAR_USE_OPENBLAS=True ' +sanity_check_paths = { + 'files': ['bin/%s' % x + for x in ['AcousticSolver', 'AddModeTo2DFld', 'ADRSolver', 'Aliasing', 'APESolver', 'CardiacEPSolver', + 'CFLStep', 'CollectionsUnitTests', 'CollectionTiming', 'CompressibleBL', + 'CompressibleFlowSolver', 'Deriv3DHomo1D', 'Deriv3DHomo1D_SingleMode', 'Deriv3DHomo2D', + 'DiffusionSolver', 'DiffusionSolverTimeInt', 'DummySolver', 'ErrorStream', + 'ExtractMeanModeFromHomo1DFld', 'ExtractSurface2DCFS', 'ExtractSurface3DCFS', 'FieldConvert', + 'Fld2DTo2D5', 'Fld2Tecplot', 'FldAddFalknerSkanBL', 'FoundationDemo', 'HDGHelmholtz1D', + 'HDGHelmholtz2D', 'HDGHelmholtz3D', 'HDGHelmholtz3DHomo1D', 'Helmholtz1D', 'Helmholtz2D', + 'Helmholtz3D', 'Helmholtz3DHomo1D', 'Helmholtz3DHomo2D', 'IncNavierStokesSolver', + 'LibUtilitiesUnitTests', 'LinearAlgebraUnitTests', 'LinearElasticSolver', + 'LocalRegionsUnitTests', 'LocProject', 'MMFDiffusion', 'MMFSolver', 'NekMesh', 'NodalDemo', + 'NonLinearEnergy', 'PartitionAnalyse', 'PostProcHDG2D', 'PostProcHDG3D', 'PrePacing', + 'PulseWaveSolver', 'ShallowWaterSolver', 'StdEquiToCoeff2D', 'StdProject', + 'SteadyAdvectionDiffusionReaction2D', 'Tester', 'TimeIntegrationDemo', 'UnitTests']] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) + for x in ['bCollections', 'libFieldUtils', 'libGlobalMapping', 'libLibUtilities', 'libLocalRegions', + 'libMultiRegions', 'libNekMeshUtils', 'libSolverUtils', 'libSpatialDomains', 'libStdRegions']], + 'dirs': ['include/nektar++', 'lib/nektar++/cmake'], +} + moduleclass = 'cae' From bb73febaeae270d64f75d46fbda4a0c14882ecc3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 17 Apr 2021 08:35:50 +0200 Subject: [PATCH 0719/2365] Add missing https --- easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb index 4cef23c8dd..e2f035b590 100644 --- a/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb @@ -12,7 +12,7 @@ p-order piecewise polynomial order solvers.""" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} -source_urls = ['http://www.nektar.info/downloads/file'] +source_urls = ['https://www.nektar.info/downloads/file'] sources = [{'download_filename': 'nektar-5-0-1-tar-xz', 'filename': '%(namelower)s-%(version)s.tar.xz'}] checksums = ['d38401321250e21a29a73dd491e05ca077dd177a32c222c961693b3189542d06'] From fc629a0954f0ef2add7553f066ffb8ffee9d9c74 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 18 Apr 2021 17:50:37 +0200 Subject: [PATCH 0720/2365] Fix stupid typo in library sanity check. --- easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb index e2f035b590..52d6a1fc99 100644 --- a/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb @@ -49,8 +49,8 @@ sanity_check_paths = { 'PulseWaveSolver', 'ShallowWaterSolver', 'StdEquiToCoeff2D', 'StdProject', 'SteadyAdvectionDiffusionReaction2D', 'Tester', 'TimeIntegrationDemo', 'UnitTests']] + ['lib/lib%s.%s' % (x, SHLIB_EXT) - for x in ['bCollections', 'libFieldUtils', 'libGlobalMapping', 'libLibUtilities', 'libLocalRegions', - 'libMultiRegions', 'libNekMeshUtils', 'libSolverUtils', 'libSpatialDomains', 'libStdRegions']], + for x in ['bCollections', 'FieldUtils', 'GlobalMapping', 'LibUtilities', 'LocalRegions', + 'MultiRegions', 'NekMeshUtils', 'SolverUtils', 'SpatialDomains', 'StdRegions']], 'dirs': ['include/nektar++', 'lib/nektar++/cmake'], } From ba7e8c3f26b5d837462dda0fd13b060062f07990 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 19 Apr 2021 08:33:35 +0200 Subject: [PATCH 0721/2365] Fix one more stupid typo in library sanity check. --- easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb index 52d6a1fc99..daf63dd2f9 100644 --- a/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb @@ -49,7 +49,7 @@ sanity_check_paths = { 'PulseWaveSolver', 'ShallowWaterSolver', 'StdEquiToCoeff2D', 'StdProject', 'SteadyAdvectionDiffusionReaction2D', 'Tester', 'TimeIntegrationDemo', 'UnitTests']] + ['lib/lib%s.%s' % (x, SHLIB_EXT) - for x in ['bCollections', 'FieldUtils', 'GlobalMapping', 'LibUtilities', 'LocalRegions', + for x in ['Collections', 'FieldUtils', 'GlobalMapping', 'LibUtilities', 'LocalRegions', 'MultiRegions', 'NekMeshUtils', 'SolverUtils', 'SpatialDomains', 'StdRegions']], 'dirs': ['include/nektar++', 'lib/nektar++/cmake'], } From e7bd2e5eacf26fe3d68008a33167da99c3aec1d4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 19 Apr 2021 10:56:42 +0200 Subject: [PATCH 0722/2365] adding easyconfigs: MotionCor2-1.4.2-GCCcore-10.2.0.eb --- .../MotionCor2-1.4.2-GCCcore-10.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4f2bf4aeab --- /dev/null +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ake Sandgren +# HPC2N +# Umea University + +name = 'MotionCor2' +version = '1.4.2' + +homepage = 'https://msg.ucsf.edu/' +description = """MotionCor2 correct anisotropic image motion at the +single pixel level across the whole frame, suitable for both single +particle and tomographic images. Iterative, patch-based motion detection +is combined with spatial and temporal constraints and dose weighting. + +Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, +Yifan Cheng and David A. Agard (2016) Anisotropic Correction of +Beam-induced Motion for Improved Single-particle Electron +Cryo-microscopy, Nature Methods, submitted. +BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# No longer directly downloadable, available from https://msg.ucsf.edu/software +sources = [ + '%(name)s_%(version)s.zip', +] +checksums = ['5a1b952f46816e396b918b92fcb118376c02be3636371bd6fcef00f315685b8d'] + +# CUDA is a build dependency to make sure it gets installed. +# It's actually a runtime dependency, but that's handled in the wrapper to +# make sure it doesn't conflict with whatever toolchain happens to be loaded. +# Change CUDA version to match the latest one used in this version +# of MotionCor2 +builddependencies = [ + ('binutils', '2.35'), + ('CUDAcore', '11.1.1', '', True), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5'), + ('XZ', '5.2.5'), + ('LibTIFF', '4.1.0'), + ('jbigkit', '2.1'), +] + +moduleclass = 'bio' From 9cb5221194282b823689692f651d37e613c49285 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 19 Apr 2021 09:49:37 +0000 Subject: [PATCH 0723/2365] wget: dependency fix --- .../l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb | 22 +++++++++++++++++++ .../w/wget/wget-1.20.3-GCCcore-10.2.0.eb | 2 +- 2 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..761a876107 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libidn2' +version = '2.3.0' + +homepage = 'http://www.gnu.org/software/libidn' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/libidn'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e1cb1db3d2e249a6a3eb6f0946777c2e892d5c5dc7bd91c74394fc3a01cab8b5'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/idn2', 'lib/libidn2.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb index 16e7bb29ad..c878ea314f 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ ('PCRE', '8.44'), - ('libidn', '1.36'), + ('libidn2', '2.3.0'), ('zlib', '1.2.11'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons From 1fc429ec4d91ed7b536ae13580b61c256034df23 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 19 Apr 2021 10:41:45 +0000 Subject: [PATCH 0724/2365] Replaces homepage http link with https. --- easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb index 761a876107..d99084fe53 100644 --- a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libidn2' version = '2.3.0' -homepage = 'http://www.gnu.org/software/libidn' +homepage = 'https://www.gnu.org/software/libidn' description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names.""" From d762d354a8e89d505c15b264afd2f772367a5164 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 19 Apr 2021 12:20:37 +0000 Subject: [PATCH 0725/2365] Adds the headers to other newly added files --- .../easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb index d99084fe53..684e717287 100644 --- a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb @@ -1,3 +1,6 @@ +## +# Author: Robert Mijakovic +## easyblock = 'ConfigureMake' name = 'libidn2' From b1a40e4ea1dde8c35b02e2dc3d3340c22a514d98 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Apr 2021 15:28:52 +0200 Subject: [PATCH 0726/2365] adding easyconfigs: onedrive-2.4.11-GCCcore-10.2.0.eb, LDC-1.25.1-GCCcore-10.2.0-linux-x86_64.eb --- .../onedrive-2.4.11-GCCcore-10.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b61736bb0c --- /dev/null +++ b/easybuild/easyconfigs/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'onedrive' +version = '2.4.11' + +homepage = 'https://abraunegg.github.io/' +description = """ +A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for Business, +OneDrive for Office365 and SharePoint.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/abraunegg/onedrive/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['839ec89c0b2a2c71db19668f7d333f9ef5d6910451b49fba1c2dc8e53885aa2f'] + +builddependencies = [ + ('binutils', '2.35'), + ('LDC', '1.25.1', '-linux-x86_64'), +] + +dependencies = [ + ('cURL', '7.72.0'), + ('SQLite', '3.33.0'), +] + +_compldir = '%(installdir)s/share/tab_completion' +configopts = 'DC="$EBROOTLDC"/bin/ldc2 --with-systemdsystemunitdir=no ' +configopts += '--enable-completions --with-bash-completion-dir=%s ' % _compldir +configopts += '--with-zsh-completion-dir=%s --with-fish-completion-dir=%s ' % (_compldir, _compldir) + +sanity_check_paths = { + 'files': ['bin/onedrive'], + 'dirs': ['etc', 'share'], +} + +sanity_check_commands = ['onedrive -h'] + +# optionally enable tab completion for bash (zsh: '_onedrive', fish: 'onedrive.fish') +modluafooter = 'execute {cmd="source $EBROOTONEDRIVE/share/tab_completion/onedrive",modeA={"load"}}' + +moduleclass = 'tools' From 85273d24c533815614e0f8a12294063a12dc94bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 19 Apr 2021 15:54:31 +0200 Subject: [PATCH 0727/2365] adding easyconfigs: PyFoam-2020.5-foss-2020b.eb --- .../p/PyFoam/PyFoam-2020.5-foss-2020b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb b/easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb new file mode 100644 index 0000000000..2104001428 --- /dev/null +++ b/easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'PyFoam' +version = '2020.5' + +homepage = 'http://openfoamwiki.net/index.php/Contrib/PyFoam' +description = "A Python library to control OpenFOAM-runs and manipulate OpenFOAM-data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1965041e96349719b77371961e569d179ca19c1386a8dedc6d9f774ac5353ada'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': name} + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ["bin/pyFoam%s.py" % x for x in ('Execute', 'Runner', 'Version')], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyFoam%s.py --help" % x for x in ('Execute', 'Runner', 'Version')] + +sanity_pip_check = True + +moduleclass = 'lib' From 7afb886594e1cd324fe53725afdc2812902d16fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 19 Apr 2021 17:45:21 +0200 Subject: [PATCH 0728/2365] drop Java versionsuffix for canu 2.1.1 --- .../c/canu/canu-2.1.1-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7a7d3c59ec --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'canu' +version = '2.1.1' + +homepage = 'https://canu.readthedocs.io' +description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/marbl/canu/releases/download/v%(version)s/'] +sources = ['canu-%(version)s.tar.xz'] +checksums = ['18c030ada93286be90c364387879025c17001c8e445e64719c866bc6c7609b98'] + +builddependencies = [ + ('binutils', '2.35'), + # Makefile checks git version, before making (futile) attempt to update git submodules + ('git', '2.28.0', '-nodocs'), +] + +dependencies = [ + ('Java', '11', '', True), + ('Perl', '5.32.0'), + ('gnuplot', '5.4.1'), +] + +start_dir = 'src' + +files_to_copy = ['build/bin', 'build/lib', 'build/share', 'README*'] + +sanity_check_paths = { + 'files': ['bin/bogus', 'bin/canu', 'bin/meryl', 'bin/overlapPair', 'lib/libcanu.a'], + 'dirs': ['lib/site_perl', 'share'], +} +sanity_check_commands = [ + "canu -version", + "canu -options", +] + +moduleclass = 'bio' From 60d311c6908e5583b084850b56487c873900ae97 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 19 Apr 2021 19:11:14 +0200 Subject: [PATCH 0729/2365] adding easyconfigs: CIRCexplorer2-2.3.8-foss-2020b.eb, Cufflinks-20190706-GCC-10.2.0.eb, TopHat-2.1.2-GCC-10.2.0.eb --- .../Cufflinks-20190706-GCC-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-10.2.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-10.2.0.eb new file mode 100644 index 0000000000..af9650a7fd --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-10.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'Cufflinks' +version = '20190706' +local_commit = 'dc3b0cb' + +homepage = 'http://cole-trapnell-lab.github.io/%(namelower)s/' +description = "Transcript assembly, differential expression, and differential regulation for RNA-Seq" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'cole-trapnell-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['444c632083a473fe4fd99ff189cef5bbd95daee0912e8eefe79534bf225fbcb6'] + +builddependencies = [ + ('Eigen', '3.3.8'), + ('Autotools', '20200321'), + ('SAMtools', '1.11'), +] + +dependencies = [ + ('Boost', '1.74.0'), + ('zlib', '1.2.11'), + ('HTSlib', '1.11'), +] + +preconfigopts = 'autoreconf -i && export LIBS="${LIBS} -lhts" && export CFLAGS="$CFLAGS -fcommon" && ' +configopts = '--with-boost=${EBROOTBOOST} --with-bam=${EBROOTSAMTOOLS}' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' From ca208f97e641edfacff30643263466cc57f3d4fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 19 Apr 2021 21:46:08 +0200 Subject: [PATCH 0730/2365] adding easyconfigs: pygmo-2.16.1-foss-2020b.eb, pagmo-2.17.0-foss-2020b.eb --- .../p/pagmo/pagmo-2.17.0-foss-2020b.eb | 36 +++++++++++++ .../p/pygmo/pygmo-2.16.1-foss-2020b.eb | 52 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/p/pagmo/pagmo-2.17.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pagmo/pagmo-2.17.0-foss-2020b.eb b/easybuild/easyconfigs/p/pagmo/pagmo-2.17.0-foss-2020b.eb new file mode 100644 index 0000000000..7458df08fd --- /dev/null +++ b/easybuild/easyconfigs/p/pagmo/pagmo-2.17.0-foss-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'pagmo' +version = '2.17.0' + +homepage = 'https://esa.github.io/pagmo2' +description = "pagmo is a C++ scientific library for massively parallel optimization." + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/esa/pagmo2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1b95b036f75e6fa0b21082ab228dbd63cd18ca10d9622ac53629245e0f95c35c'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Boost', '1.74.0'), + ('tbb', '2020.3'), + ('Eigen', '3.3.8'), + ('NLopt', '2.6.2'), +] + +configopts = "-DPAGMO_WITH_EIGEN3=ON -DPAGMO_WITH_NLOPT=ON -DPAGMO_BUILD_TESTS=ON" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libpagmo.%s' % SHLIB_EXT], + 'dirs': ['include/pagmo', 'lib/cmake/pagmo'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb new file mode 100644 index 0000000000..fff50e2e31 --- /dev/null +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakePythonPackage' + +name = 'pygmo' +version = '2.16.1' + +homepage = 'https://esa.github.io/pygmo2' +description = "pygmo is a scientific Python library for massively parallel optimization." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/esa/pygmo2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['54d4fa99e4bff539fca67dfcdc909499fd3f1a3186f7c7fc8200f19512954166'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('pybind11', '2.6.0'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), + ('pagmo', '2.17.0'), + ('matplotlib', '3.3.3'), + ('networkx', '2.5'), +] + +runtest = False + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('dill', '0.3.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 0cfce037ab2c35adb24b72918312c86fb62b8f96 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Apr 2021 10:17:38 +0200 Subject: [PATCH 0731/2365] switch to Python 2.7.18 as dependency for TopHat (and CIRCexplorer2) --- ...xplorer2-2.3.8-foss-2020b-Python-2.7.18.eb | 45 +++++++++++++++++ .../TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb | 49 +++++++++++++++++++ 2 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..818300dd5c --- /dev/null +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonPackage' + +name = 'CIRCexplorer2' +version = '2.3.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://circexplorer2.readthedocs.io/' +description = "CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8261ee884f6d895131ce681d5eda6554376e973851a9de4dc50e2b3e242ccc80'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11'), + # sticking to v2.1.0, since using v2.1.1 has problems, cfr. https://www.biostars.org/p/186979/ + ('TopHat', '2.1.2', versionsuffix), + ('Cufflinks', '20190706'), + ('BEDTools', '2.30.0'), + ('Kent_tools', '411'), + ('STAR', '2.7.6a'), + ('BWA', '0.7.17'), + ('segemehl', '0.3.4'), + ('Pysam', '0.16.0.1'), + ('pybedtools', '0.8.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'circ2'} + +sanity_check_paths = { + 'files': ['bin/CIRCexplorer2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["CIRCexplorer2 denovo --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..5e3929fa84 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' +description = "TopHat is a fast splice junction mapper for RNA-Seq reads." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'cstd': 'gnu++98', 'pic': True} + +github_account = 'infphilo' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(namelower)s-2.0.13-zlib.patch'] +checksums = [ + '15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1', # v2.1.2.tar.gz + 'a33075c2affda995ddbd250933dbcaf94f68768b1eebead58a69705fc40306ef', # tophat-2.0.13-zlib.patch +] + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('Boost', '1.74.0'), + ('zlib', '1.2.11'), + ('Python', '2.7.18'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['tophat --version'] + +moduleclass = 'bio' From 4f08e3fbe73bcc45ddfe18ecfdbceb4f83b22c51 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 20 Apr 2021 12:43:36 +0200 Subject: [PATCH 0732/2365] Revert "add Compress::Raw::Zlib to Perl v5.32.0" --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 1ed7727cea..76d0b56cf8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -1796,11 +1796,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY/'], 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], }), - ('Compress::Raw::Zlib', '2.101', { - 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], - 'checksums': ['9d1b9515e8277c1b007e33fad1fd0f18717d56bf647e3794d61289c45b1aabb2'], - }), ] moduleclass = 'lang' From 459dafe4707dd2c9f04e26d0107a9205b854fa09 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Apr 2021 14:24:20 +0200 Subject: [PATCH 0733/2365] adding easyconfigs: SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb --- ...bundle-2020.11-foss-2020b-Python-2.7.18.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..bcceac76a1 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2020.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', '2.7.18'), +] + +use_pip = True +sanity_pip_check = True + +# order is important! +exts_list = [ + ('numpy', '1.16.6', { + 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': [ + 'e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff', # numpy-1.16.6.zip + # numpy-1.16.2_relax-long-complex-test.patch + '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb', + ], + }), + ('scipy', '1.2.3', { + 'patches': ['scipy-1.2.3_fix_nan_problem_in_vi.patch'], + 'checksums': [ + 'ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57', # scipy-1.2.3.tar.gz + # scipy-1.2.3_fix_nan_problem_in_vi.patch + '0513c5d0491a3f062ed024b6aa7b382706e8c42b3a3fdd26ff7a4d305ac9a30d', + ], + 'prebuildopts': 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ', + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('numexpr', '2.7.3', { + 'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '0.24.2', { + 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], + }), + ('mpmath', '1.1.0', { + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +moduleclass = 'lang' From 38a48ec1fff275aab33e790e8def5656ef100a20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Apr 2021 14:50:29 +0200 Subject: [PATCH 0734/2365] also use Python 2 for dependencies of CIRCexplorer2 --- ...xplorer2-2.3.8-foss-2020b-Python-2.7.18.eb | 6 +-- ...Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb | 39 +++++++++++++++++++ ...bedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb | 26 +++++++++++++ 3 files changed, 68 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb index 818300dd5c..17ee6efaae 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb @@ -15,7 +15,7 @@ checksums = ['8261ee884f6d895131ce681d5eda6554376e973851a9de4dc50e2b3e242ccc80'] dependencies = [ ('Python', '2.7.18'), - ('SciPy-bundle', '2020.11'), + ('SciPy-bundle', '2020.11', versionsuffix), # sticking to v2.1.0, since using v2.1.1 has problems, cfr. https://www.biostars.org/p/186979/ ('TopHat', '2.1.2', versionsuffix), ('Cufflinks', '20190706'), @@ -24,8 +24,8 @@ dependencies = [ ('STAR', '2.7.6a'), ('BWA', '0.7.17'), ('segemehl', '0.3.4'), - ('Pysam', '0.16.0.1'), - ('pybedtools', '0.8.2'), + ('Pysam', '0.16.0.1', versionsuffix), + ('pybedtools', '0.8.2', versionsuffix), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..7496740a8f --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.16.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a61e98e299fa93ba121aab521081282b61bc978bb9052d33b26b38f8fe15573e'] + +dependencies = [ + ('Python', '2.7.18'), + ('ncurses', '6.2'), + ('cURL', '7.72.0'), + ('XZ', '5.2.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..37d55f3c11 --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pybedtools' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a184a36099458627e7ef52ea88218f7c00dc9c505b4256ece9ede58b1efa8771'] + +dependencies = [ + ('Python', '2.7.18'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.16.0.1', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' From b8dc800428292efdc3e9aec64d125764f420262a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Apr 2021 14:52:04 +0200 Subject: [PATCH 0735/2365] remove PYPI_SOURCE source URL in CIRCexplorer2 easyconfig --- .../CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb index 17ee6efaae..aaec5e3760 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb @@ -9,7 +9,6 @@ description = "CIRCexplorer2 is a comprehensive and integrative circular RNA ana toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['8261ee884f6d895131ce681d5eda6554376e973851a9de4dc50e2b3e242ccc80'] From 3259041e6835d1d4d37a1773a9d2d7f65115331a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 09:30:38 +0200 Subject: [PATCH 0736/2365] adding easyconfigs: SCons-4.1.0.post1-GCCcore-10.2.0.eb --- .../SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6d851b6b51 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '4.1.0.post1' + +homepage = 'https://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ecb062482b9d80319b56758c0341eb717735437f86a575bac3552804428bd73e'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/sconsign'], + 'dirs': [], +} + +sanity_check_commands = ["scons --help"] + +sanity_pip_check = True + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' From 6d2cc195b08ddc485cd6e50c47a0a454d84236a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 11:20:45 +0200 Subject: [PATCH 0737/2365] {chem}[intel/2020b] WIEN2k v19.2, DFT-D3 v3.2.0 --- .../DFT-D3-3.2.0-iccifort-2020.4.304.eb | 34 ++++++++++++++ .../w/WIEN2k/WIEN2k-19.2-intel-2020b.eb | 45 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..113163554c --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.2.0' + +homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical + quantum chemical methods.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3'] +sources = [{'download_filename': 'dftd3.tgz', 'filename': SOURCELOWER_TGZ}] +checksums = ['d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59'] + +# Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version +# numbering. Also, the authors are prone (alas) to stealth upgrades, so that two +# tarballs with the same version number can have different checksums. For this +# reason, it is suggested to manually download and rename the tarball. The +# checksum may also need updating from time to time. +# Checksum last updated: 20 September 2018 +# Date tarball was reported to have been modified: 14 June 2016 +prebuildopts = "sed -i 's/OSTYPE=LINUXL/OSTYPE=LINUXI/' Makefile && " + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +sanity_check_commands = ["dftd3"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb new file mode 100644 index 0000000000..5e5f66e861 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb @@ -0,0 +1,45 @@ +name = 'WIEN2k' +version = '19.2' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['f28c0bc94f813b805f8204a43b487cc4f8cf0e7f1595206eb8c0dbd423a436de'] + +dependencies = [ + ('DFT-D3', '3.2.0'), + ('ELPA', '2020.11.001'), + ('FFTW', '3.3.8'), + ('libxc', '4.3.4'), +] + +osdependencies = [('glibc-static', 'libc6-dev')] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1', r'^:ENE.*-1248.14']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.*total forces', + ]), +] + +moduleclass = 'chem' From 784ca72a68ece90bec72b3b2b47d342e8e54f159 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 21 Apr 2021 12:36:47 +0200 Subject: [PATCH 0738/2365] Fix slurm and pbs variables --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 295ce520d4..651058535c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2805,7 +2805,7 @@ exts_list = [ 'checksums': [ '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz # DMCfun-1.3.0_fix-parallel-detect.patch - '555a4746375ec3c27473d6549a785359db91340f5126db5609cf5c6bca97cdff', + '96cccbe650dfab5619e3b6e782062ab72e9f1038ddf05b439dd097e1d8a59a79', ], }), ] diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 96aa1e6bf8..ca8da8466b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2815,7 +2815,7 @@ exts_list = [ 'checksums': [ '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz # DMCfun-1.3.0_fix-parallel-detect.patch - '555a4746375ec3c27473d6549a785359db91340f5126db5609cf5c6bca97cdff', + '96cccbe650dfab5619e3b6e782062ab72e9f1038ddf05b439dd097e1d8a59a79', ], }), # Specific packages for GPUs diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 71e33a6505..2f41f2816e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2840,7 +2840,7 @@ exts_list = [ 'checksums': [ '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz # DMCfun-1.3.0_fix-parallel-detect.patch - '555a4746375ec3c27473d6549a785359db91340f5126db5609cf5c6bca97cdff', + '96cccbe650dfab5619e3b6e782062ab72e9f1038ddf05b439dd097e1d8a59a79', ], }), ] From 9e83dc9a10088b9153e74d510bd84c6411364acb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 14:06:34 +0200 Subject: [PATCH 0739/2365] {lang}[GCCcore/10.2.0] LDC v1.25.1 --- .../l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f509313572 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeNinja' + +name = 'LDC' +version = '1.25.1' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s'] +sources = ['ldc-%(version)s-src.tar.gz'] +checksums = ['0e3716fe9927be91264d1fde5c41071026f6c44262735e9ebda538089b612d40'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Ninja', '1.10.1'), + # building LDC from source required LDC 0.17.x + ('LDC', '0.17.6', '-%(arch)s', True), +] + +dependencies = [ + ('LLVM', '11.0.0'), +] + +configopts = "-DLLVM_ROOT_DIR=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/ldc2', 'bin/ldmd2'], + 'dirs': ['include/d', 'lib'], +} + +sanity_check_commands = [ + "ldc2 --help", + "ldmd2 --help", +] + +moduleclass = 'lang' From 6123c3e0af56913fe93a56cdc1e937f95383afaa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 14:08:40 +0200 Subject: [PATCH 0740/2365] adding easyconfigs: Sambamba-0.8.0-GCC-10.2.0.eb --- .../s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..6198ea51bd --- /dev/null +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'Sambamba' +version = '0.8.0' + +homepage = 'https://lomereiter.github.io/sambamba/' +description = """Sambamba is a high performance modern robust and fast tool + (and library), written in the D programming language, for working with SAM + and BAM files. Current functionality is an important subset of samtools + functionality, including view, index, sort, markdup, and depth.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/biod/sambamba/archive/'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/biod', + 'repo_name': 'sambamba', + 'commit': 'cdc5f84', + 'recursive': True, + } +}] +checksums = [None] + +builddependencies = [ + ('LDC', '1.25.1'), + ('Python', '3.8.6'), +] + +files_to_copy = [(['bin/sambamba-%(version)s'], 'bin')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s sambamba-%(version)s sambamba"] + +sanity_check_paths = { + 'files': ['bin/sambamba'], + 'dirs': [], +} + +sanity_check_commands = ["sambamba 2>&1 | grep '^sambamba %(version)s'"] + +moduleclass = 'bio' From 5812e6527fbaff4ab12005b674675ae6f4ac632b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 14:09:16 +0200 Subject: [PATCH 0741/2365] adding easyconfigs: samblaster-0.1.26-GCC-10.2.0.eb --- .../samblaster-0.1.26-GCC-10.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb new file mode 100644 index 0000000000..cc04b3f897 --- /dev/null +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb @@ -0,0 +1,37 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org fizwit@github.com +easyblock = 'MakeCp' + +name = 'samblaster' +version = '0.1.26' + +description = """samblaster is a fast and flexible program for marking + duplicates in read-id grouped1 paired-end SAM files.""" + +homepage = 'https://github.com/GregoryFaust/samblaster' + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/GregoryFaust/samblaster/archive/'] +sources = [{ + 'download_filename': 'v.%(version)s.zip', + 'filename': SOURCE_ZIP +}] +checksums = ['79ff6f8306482e73e04678424bf14b840d80561660bb59deac1b75ada2f330cf'] + +files_to_copy = [ + (["samblaster"], "bin/"), + 'README.md', + 'SAMBLASTER_Supplemental.pdf', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/samblaster', 'README.md'], + 'dirs': [] +} + +sanity_check_commands = ["samblaster --help"] + +moduleclass = 'bio' From 89b410c3e64e0f45a08049f409b4ed767f6802f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 14:09:44 +0200 Subject: [PATCH 0742/2365] adding easyconfigs: gawk-5.1.0-GCC-10.2.0.eb --- .../g/gawk/gawk-5.1.0-GCC-10.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/gawk/gawk-5.1.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.1.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..03d927882b --- /dev/null +++ b/easybuild/easyconfigs/g/gawk/gawk-5.1.0-GCC-10.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gawk' +version = '5.1.0' + +homepage = 'https://www.gnu.org/software/gawk' +description = """The awk utility interprets a special-purpose programming language that makes it possible to handle +simple data-reformatting jobs with just a few lines of code.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['03a0360edcd84bec156fe211bbc4fc8c78790973ce4e8b990a11d778d40b1a26'] + +sanity_check_paths = { + 'files': ['bin/gawk'], + 'dirs': [], +} + +sanity_check_commands = ["gawk --help"] + +moduleclass = 'tools' From daf9970eb9a7f22c5e0f20e87f03c781cf260667 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 14:12:34 +0200 Subject: [PATCH 0743/2365] adding easyconfigs: LUMPY-0.3.1-foss-2020b.eb --- .../l/LUMPY/LUMPY-0.3.1-foss-2020b.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/l/LUMPY/LUMPY-0.3.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/LUMPY/LUMPY-0.3.1-foss-2020b.eb b/easybuild/easyconfigs/l/LUMPY/LUMPY-0.3.1-foss-2020b.eb new file mode 100644 index 0000000000..6b1e20f8df --- /dev/null +++ b/easybuild/easyconfigs/l/LUMPY/LUMPY-0.3.1-foss-2020b.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'LUMPY' +version = '0.3.1' + +homepage = 'https://github.com/arq5x/lumpy-sv' +description = """A probabilistic framework for structural variant discovery. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/arq5x/lumpy-sv/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6a75dffafd238417011416c62d4351f64ea71bd018b5a7660383566f2cbb7c5d'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.11'), + ('samblaster', '0.1.26'), + ('Sambamba', '0.8.0'), + ('gawk', '5.1.0'), + ('bzip2', '1.0.8'), + ('cURL', '7.72.0'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), +] + +prebuildopts = "export ZLIB_PATH=$EBROOTZLIB/lib && " + +# prevent building of included HTSlib for lumpy_filter +prebuildopts += "mkdir bin && ln -s $EBROOTSAMTOOLS/lib/libhts.a lib/htslib/libhts.a && " +prebuildopts += "sed -i 's/-lz/-lz -llzma -lbz2/g' src/filter/Makefile && " +prebuildopts += "make -C src/filter && cp src/filter/lumpy_filter bin/ && " + +buildopts = "lumpyexpress lumpy" + +files_to_copy = [(['bin/*'], 'bin'), 'data', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/lumpy', 'bin/lumpy_filter', 'bin/lumpyexpress'], + 'dirs': [], +} + +sanity_check_commands = ["lumpyexpress -h"] + +moduleclass = 'bio' From 65764ea7e4b66b8debbec06d3a18389353c0e41e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 21 Apr 2021 14:44:10 +0200 Subject: [PATCH 0744/2365] remove LDC binary in favor of from source version --- .../easyconfigs/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb index b61736bb0c..dab738f167 100644 --- a/easybuild/easyconfigs/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ checksums = ['839ec89c0b2a2c71db19668f7d333f9ef5d6910451b49fba1c2dc8e53885aa2f'] builddependencies = [ ('binutils', '2.35'), - ('LDC', '1.25.1', '-linux-x86_64'), + ('LDC', '1.25.1'), ] dependencies = [ From 1eb38cbe03fd9ed26e08c88a54aebcb06e0d1ced Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 15:30:52 +0200 Subject: [PATCH 0745/2365] adding easyconfigs: OpenMM-7.5.0-foss-2020b.eb --- .../o/OpenMM/OpenMM-7.5.0-foss-2020b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb new file mode 100644 index 0000000000..04383ac6bc --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb @@ -0,0 +1,56 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.0' + +homepage = 'http://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['516748b4f1ae936c4d70cc6401174fc9384244c65cd3aef27bc2c53eac6d6de5'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +separate_build_dir = True + +dependencies = [ + ('FFTW', '3.3.8'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SWIG', '4.0.2'), +] + +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From deae88db7385cd8be8f8ec2f251353af56afac65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 15:52:07 +0200 Subject: [PATCH 0746/2365] fix source URLs for recent ELPA versions --- easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb index ae57cde8dc..312d380e03 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb @@ -15,7 +15,7 @@ description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['15591f142eeaa98ab3201d27ca9ac328e21beabf0803b011a04183fcaf6efdde'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb index 43fe81a27f..209492c7de 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb @@ -15,7 +15,7 @@ description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['15591f142eeaa98ab3201d27ca9ac328e21beabf0803b011a04183fcaf6efdde'] From f2c3e3c067d62c01b2b7cdb987331e0d717599ad Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 21 Apr 2021 16:19:06 +0200 Subject: [PATCH 0747/2365] adding easyconfigs: ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb, ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb --- .../ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb | 37 +++++++++++++++++ .../ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb | 40 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb create mode 100644 easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..53c3b5c829 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'ASAP3' +version = '3.12.7' +_aseversion = '3.21.1' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/asap/' +description = """ASAP is a calculator for doing large-scale classical molecular +dynamics within the Campos Atomic Simulation Environment (ASE).""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': False} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d0903650389d3c162e016fe8162c7a920be9fa7e88cdcf41b953163584ae9348'] + +builddependencies = [ + ('pkgconfig', '1.5.1', '-python'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('ASE', _aseversion), + ('kim-api', '2.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..76029e0a09 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb @@ -0,0 +1,40 @@ +easyblock = "PythonPackage" + +name = 'ASAP3' +version = '3.12.7' +_aseversion = '3.21.1' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/asap/' +description = """ASAP is a calculator for doing large-scale classical molecular +dynamics within the Campos Atomic Simulation Environment (ASE).""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': False} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d0903650389d3c162e016fe8162c7a920be9fa7e88cdcf41b953163584ae9348'] + +builddependencies = [ + ('pkgconfig', '1.5.1', '-python'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('ASE', _aseversion), + ('kim-api', '2.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'phys' From 1c3ba47d4152ffe0f044bd6e36a40cbffab6e72b Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 21 Apr 2021 15:19:16 +0100 Subject: [PATCH 0748/2365] adding easyconfigs: cryoDRGN-0.3.2-fosscuda-2020b.eb --- .../cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..8a4b7e8a02 --- /dev/null +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'cryoDRGN' +version = '0.3.2' + +homepage = 'http://cb.csail.mit.edu/cb/cryodrgn/' +description = """cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous + reconstruction. + CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In + particular, the method models a continuous distribution over 3D structures by using a neural + network based representation for the volume. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), + ('JupyterLab', '2.2.8'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('numba', '0.52.0'), + ('scikit-learn', '0.23.2'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('colorlover', '0.3.0', { + 'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'], + }), + ('retrying', '1.3.3', { + 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], + }), + ('plotly', '4.14.3', { + 'checksums': ['7d8aaeed392e82fb8e0e48899f2d3d957b12327f9d38cdd5802bc574a8a39d91'], + }), + ('cufflinks', '0.17.3', { + 'checksums': ['48c1b3406dc030004121966489eebc5518cea70fd4e3f16379b491328501a644'], + }), + ('pynndescent', '0.5.2', { + 'checksums': ['d9fd22210b8d64368376ff392e876fb72fe3cda282396cfa6a59440ab6600771'], + }), + ('umap-learn', '0.5.1', { + 'checksums': ['3e3e5e526109866012a9da79f423c922edc379c6cac9bf65ea08fbb9dd93ff3a'], + 'modulename': 'umap', + }), + ('seaborn', '0.11.1', { + 'checksums': ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'], + }), + (name.lower(), version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/zhonge/cryodrgn/archive'], + 'checksums': ['1efecc2a0add2392411076082c122039a490f5ddf3e01f1da38aea1a81592077'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' From b82734218a8f5fb5308fe2d652c30774ac608ef5 Mon Sep 17 00:00:00 2001 From: jfgrimm <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 21 Apr 2021 15:51:51 +0100 Subject: [PATCH 0749/2365] Use https instead of http in homepage URL --- .../easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index 8a4b7e8a02..e848444349 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'cryoDRGN' version = '0.3.2' -homepage = 'http://cb.csail.mit.edu/cb/cryodrgn/' +homepage = 'https://cb.csail.mit.edu/cb/cryodrgn/' description = """cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction. CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In From 8433446bc79a90c6d7d9e08c9fec173fc4cbf116 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 21 Apr 2021 17:11:40 +0200 Subject: [PATCH 0750/2365] adding easyconfigs: PySAT-0.1.7.dev1-GCC-10.2.0.eb, DFA-2.1.2-GCCcore-10.2.0.eb, pydot-1.4.2-GCCcore-10.2.0.eb, py-aiger-6.1.14-GCCcore-10.2.0.eb --- .../d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb | 37 +++++++++ .../p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb | 45 +++++++++++ .../py-aiger-6.1.14-GCCcore-10.2.0.eb | 77 +++++++++++++++++++ .../p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb | 25 ++++++ 4 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a510be9b2b --- /dev/null +++ b/easybuild/easyconfigs/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'DFA' +version = '2.1.2' + +homepage = 'https://github.com/mvcisback/dfa' +description = "Python library for modeling DFAs, Moore Machines, and Transition Systems." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('pydot', '1.4.2'), + ('pytest-xdist', '2.1.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('funcy', '1.15', { + 'checksums': ['65b746fed572b392d886810a98d56939c6e0d545abb750527a717c21ced21008'], + }), + ('lazytree', '0.3.2', { + 'checksums': ['7a035efb5fb61d9209375e594780c1039af1feda02118f7fcbd74fdf6e4321da'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['3dd082944293997ed0af9bc565271b3296664673aa71877e65de60579c811cf5'], + }), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb b/easybuild/easyconfigs/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb new file mode 100644 index 0000000000..6e7c393204 --- /dev/null +++ b/easybuild/easyconfigs/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'PySAT' +version = '0.1.7.dev1' + +homepage = 'https://pysathq.github.io/' +description = """ +PySAT is a Python toolkit, which aims at providing a simple and unified +interface to a number of state-of-art Boolean satisfiability (SAT) solvers as +well as to a variety of cardinality and pseudo-Boolean encodings.""" + +# PySAT includes solvers in C and C++ +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), + ('py-aiger', '6.1.14'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pypblib', '0.0.4', { + 'checksums': ['71dd930bf177ca38d6eeb473702d05df07e11f20382db0c766465297eaf49062'], + }), + ('python-sat', version, { + 'modulename': 'pysat', + 'checksums': ['7c0ee769f6e3969f6f3b40d575a6629f1760a94033b933004ce527f3d1639089'], + }), +] + +# check provided examples and solvers +local_examples = ['fm', 'genhard', 'lbx', 'lsu', 'mcsls', 'models', 'musx', 'rc2'] +local_solvers = ['Cadical', 'CNFPlus', 'Gluecard3', 'Gluecard4', 'Glucose3', 'Glucose4', 'Lingeling', 'MapleChrono', + 'MapleCM', 'Maplesat', 'Minicard', 'Minisat22', 'MinisatGH', 'Mergesat3'] + +sanity_check_paths = { + 'files': ['bin/%s.py' % x for x in local_examples], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'from pysat.solvers import %s'" % s for s in local_solvers] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f292e1aa4b --- /dev/null +++ b/easybuild/easyconfigs/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb @@ -0,0 +1,77 @@ +easyblock = 'PythonBundle' + +name = 'py-aiger' +version = '6.1.14' + +homepage = 'https://github.com/mvcisback/py-aiger' +description = """ +A python library for manipulating sequential and combinatorial circuits. +This module provides the py-aiger extensions: aiger_bv, aiger_cnf, aiger_ptltl, +aiger_coins, aiger_gridworld, aiger_dfa""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('DFA', '2.1.2'), # needed by py-aiger-dfa +] + +use_pip = True +sanity_pip_check = True + +# sortedcontainers<3.0.0,>=2.3.0 required, Python/3.8.6 contains sortedcontainers 2.2.2 +exts_list = [ + ('sortedcontainers', '2.3.0', { + 'checksums': ['59cc937650cf60d677c16775597c89a960658a09cf7c1a668f86e1e4464b10a1'], + }), + ('bidict', '0.21.2', { + 'checksums': ['4fa46f7ff96dc244abfc437383d987404ae861df797e2fd5b190e233c302be09'], + }), + ('funcy', '1.15', { + 'checksums': ['65b746fed572b392d886810a98d56939c6e0d545abb750527a717c21ced21008'], + }), + ('parsimonious', '0.8.1', { + 'checksums': ['3add338892d580e0cb3b1a39e4a1b427ff9f687858fdd61097053742391a9f6b'], + }), + ('toposort', '1.6', { + 'checksums': ['a7428f56ef844f5055bb9e9e44b343983773ae6dce0fe5b101e08e27ffbd50ac'], + }), + (name, version, { + 'modulename': 'aiger', + 'checksums': ['74b1bc428d0ff7b273bc929d761ce7e55ccc42083350c41a0f8e59d53836e667'], + }), + ('py-aiger-bv', '4.6.1', { + 'modulename': 'aiger_bv', + 'checksums': ['eae1757b2a12bada8d6fe1c35ef83688aba3f28aa951e5436e5947319a5a3521'], + }), + ('py-aiger-cnf', '5.0.1', { + 'modulename': 'aiger_cnf', + 'checksums': ['85c1446e6cad0353716df7eb1a902eb4487ce27691c4a1e16a3c9699ed733276'], + }), + ('py-aiger-ptltl', '3.1.0', { + 'modulename': 'aiger_ptltl', + 'checksums': ['f1bbd5b7259e6e83020e07676ed22ccf71bb3b04ad9d5cb7bf231b76ef8bf1b8'], + }), + ('py-aiger-coins', '3.3.0', { + 'modulename': 'aiger_coins', + 'checksums': ['f596b05640c376ee7abf50b3127eff45aaa38765892584428893bbd142058136'], + }), + ('py-aiger-discrete', '0.1.8', { + 'modulename': 'aiger_gridworld', + 'checksums': ['70ad69a06368651a8ff57ea176b7bb7509aca70218b39a3d416339b8b1541a67'], + }), + ('py-aiger-gridworld', '0.4.0', { + 'modulename': 'aiger_gridworld', + 'checksums': ['1ddf31909a2330eeca1834d60321ad59f7942543ed81ba10a66a0328430bbc0f'], + }), + ('py-aiger-dfa', '0.3.1', { + 'modulename': 'aiger_dfa', + 'checksums': ['05f31bf5ad42781fed6a2ca228059a35467cda3b4f1de0f4d98b0482be90fa00'], + }), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8476b86031 --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pydot' +version = '1.4.2' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('Graphviz', '2.47.0', '-Java-11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From e99aa0b64ffe33d73960a4622ac4cddcb96dcc7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 17:18:10 +0200 Subject: [PATCH 0751/2365] adding easyconfigs: OpenMM-7.5.0-intel-2020b.eb and patches: OpenMM-7.5.0_fix-stdint-include.patch --- .../o/OpenMM/OpenMM-7.5.0-intel-2020b.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb new file mode 100644 index 0000000000..07e2f42038 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.0' + +homepage = 'http://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMM-%(version)s_fix-stdint-include.patch'] +checksums = [ + '516748b4f1ae936c4d70cc6401174fc9384244c65cd3aef27bc2c53eac6d6de5', # 7.5.0.tar.gz + 'c55e0866f02fb904e2ebba98687e3a74f256fd56c2cf32a0871aa2f427b969d9', # OpenMM-7.5.0_fix-stdint-include.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +separate_build_dir = True + +dependencies = [ + ('FFTW', '3.3.8'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SWIG', '4.0.2'), +] + +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 395886af0c7ff37bfce4cd683b4855dabc5050c1 Mon Sep 17 00:00:00 2001 From: jfgrimm <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 21 Apr 2021 16:46:41 +0100 Subject: [PATCH 0752/2365] Add explicit dep on LLVM 10.0.1 --- .../easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index e848444349..e0c6b26a8a 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -22,6 +22,7 @@ dependencies = [ ('numba', '0.52.0'), ('scikit-learn', '0.23.2'), ('matplotlib', '3.3.3'), + ('LLVM', '10.0.1'), ] use_pip = True From b7f1548cdccdfc5c7fa8908d0651820d28fdd838 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 21 Apr 2021 15:50:29 -0700 Subject: [PATCH 0753/2365] {devel}[foss/2020b] Spark 3.1.1 --- .../s/Spark/Spark-3.1.1-foss-2020b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb new file mode 100644 index 0000000000..ba34f767b6 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -0,0 +1,53 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'Tarball' + +name = 'Spark' +version = '3.1.1' + +homepage = 'https://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' +] +sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] +checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] + +dependencies = [ + ('Python', '3.8.6'), + ('Java', '11', '', True), + # ('Hadoop', '2.10.0', '-native'), + ('Arrow', '0.17.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py4j', '0.10.9.2', { + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], + 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyspark', 'bin/spark-shell'], + 'dirs': ['python'] +} + +sanity_check_commands = [ + "pyspark -h", + "python -c 'import pyspark'", +] + +modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} + +modextravars = {'SPARK_HOME': '%(installdir)s'} + +moduleclass = 'devel' From e0ea659dff9ff93c6dc8568c562ebfed858f5e30 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 21 Apr 2021 17:53:07 -0700 Subject: [PATCH 0754/2365] non Cuda foss Arrow --- .../a/Arrow/Arrow-0.17.1-foss-2020b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb new file mode 100644 index 0000000000..e4c0d64a27 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '0.17.1' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'http://apache.belnet.be/arrow/arrow-%(version)s/', + 'https://www-eu.apache.org/dist/arrow/arrow-%(version)s/', +] +sources = ['apache-arrow-%(version)s.tar.gz'] +patches = ['Arrow-0.16.0_fix-intel.patch'] +checksums = [ + 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz + '7c1569087f93959a0dfc163d80e5f542edb4d7ed0b9d71a2a05b4081211ad2b9', # Arrow-0.16.0_fix-intel.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Autotools', '20200321'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('pkg-config', '0.29.2'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11',), # for numpy + ('Boost', '1.74.0'), +] + +separate_build_dir = True +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/python/development.html +configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' From ec7915907a9d6a64fe6f4c8f3fcc8fd609b7fea8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 08:16:04 +0200 Subject: [PATCH 0755/2365] add -Java versionsuffix for Hadoop easyconfig using GCCcore/10.2.0 toolchain, since it depends on Java 1.8 --- ...p-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb new file mode 100644 index 0000000000..cb15f9404e --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb @@ -0,0 +1,55 @@ +name = 'Hadoop' +version = '2.10.0' +versionsuffix = '-native-Java-%(javaver)s' + +homepage = 'https://archive.cloudera.com/cdh5/cdh/5/' +description = """Hadoop MapReduce by Cloudera""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'http://www.eu.apache.org/dist/%(namelower)s/common/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/common/%(namelower)s-%(version)s/', + 'https://archive.apache.org/dist/%(namelower)s/common/%(namelower)s-%(version)s/', +] +sources = ['hadoop-%(version)s-src.tar.gz'] +patches = [ + 'Hadoop-TeraSort-on-local-filesystem.patch', + 'Hadoop-2.9.2_fix-zlib.patch', + 'HADOOP-14597.04.patch', + 'Hadoop-2.10.0_tirpc.patch', +] +checksums = [ + 'baa9b125359a30eb209fbaa953e1b324eb61fa65ceb9a7cf19b0967188d8b1c0', # hadoop-2.10.0-src.tar.gz + 'd0a69a6936b4a01505ba2a20911d0cec4f79440dbc8da52b9ddbd7f3a205468b', # Hadoop-TeraSort-on-local-filesystem.patch + '1a1d084c7961078bdbaa84716e9639e37587e1d8c0b1f89ce6f12dde8bbbbc5c', # Hadoop-2.9.2_fix-zlib.patch + 'ea93c7c2b03d36f1434c2f2921c031cdc385a98f337ed8f4b3103b45b0ad0da3', # HADOOP-14597.04.patch + '9d66f604e6e03923d8fcb290382936fb93511001bb593025b8d63ababdca3a96', # Hadoop-2.10.0_tirpc.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Maven', '3.6.3', '', True), + ('protobuf', '2.5.0'), # *must* be this version - https://issues.apache.org/jira/browse/HADOOP-13363 + ('CMake', '3.18.4'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +# https://cwiki.apache.org/confluence/display/HADOOP/Hadoop+Java+Versions +dependencies = [ + ('Java', '1.8', '', True), + ('libtirpc', '1.3.1'), +] + +build_native_libs = True + +extra_native_libs = [ + ('snappy', 'lib*/libsnappy.%s*' % SHLIB_EXT), + ('zlib', 'lib*/libz.%s*' % SHLIB_EXT), +] + +parallel = 1 + +moduleclass = 'tools' From 65729c8758ef1083f2de5eb806f5ebe658178cc5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Apr 2021 10:40:26 +0100 Subject: [PATCH 0756/2365] Allow cryoDRGN to use older LLVM for numba --- .../easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index e0c6b26a8a..e848444349 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -22,7 +22,6 @@ dependencies = [ ('numba', '0.52.0'), ('scikit-learn', '0.23.2'), ('matplotlib', '3.3.3'), - ('LLVM', '10.0.1'), ] use_pip = True From ebeec90f982171c19046f24f68d96d2e6b76051e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 22 Apr 2021 13:22:51 +0200 Subject: [PATCH 0757/2365] {vis}[GCCcore/10.2.0] Molden 6.8 --- .../m/Molden/Molden-6.8-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molden/Molden-6.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/Molden/Molden-6.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Molden/Molden-6.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4245f9b4d6 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-6.8-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'Molden' +version = '6.8' + +homepage = 'https://www3.cmbi.umcn.nl/molden/' +description = """Molden is a package for displaying Molecular Density from the + Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical + packages Mopac/Ampac""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden'] +sources = ['%(namelower)s%(version)s.tar.gz'] +checksums = ['4dfbf6524b60112afb5720cba3c200a07a0f57b5d190e05ec14cceae1edf5782'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('X11', '20201008')] + +buildopts = 'CC="$CC" FC="$F90 -std=legacy" molden' + +files_to_copy = [(['bin/molden'], 'bin'), 'CopyRight', 'README', 'REGISTER'] + +sanity_check_paths = { + 'files': ['bin/molden', 'README', 'REGISTER'], + 'dirs': [], +} + +moduleclass = 'chem' From f62f7e65423d1c1ef63e1883862590045a380ad9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:13:08 +0200 Subject: [PATCH 0758/2365] {vis}[foss/2020b] matplotlib v2.2.5, Tkinter v2.7.18 w/ Python 2.7.18 --- ...tplotlib-2.2.5-foss-2020b-Python-2.7.18.eb | 64 +++++++++++++++++++ .../Tkinter/Tkinter-2.7.18-GCCcore-10.2.0.eb | 22 +++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..39d7dd5cf4 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '2.2.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', versionsuffix), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('subprocess32', '3.5.4', { + 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], + }), + ('backports.functools_lru_cache', '1.6.1', { + 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], + }), + ('kiwisolver', '1.1.0', { + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': ['a3037a840cd9dfdc2df9fee8af8f76ca82bfab173c0f9468193ca7a89a2b60ea'], + }), +] + +postinstallcmds = [ + 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b75688dff4 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +name = 'Tkinter' +version = '2.7.18' + +homepage = 'https://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.10'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' From 7159856a4258961d842ab166fdcefa4d50a0311a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:15:28 +0200 Subject: [PATCH 0759/2365] adding easyconfigs: DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb --- ...roPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..8dd1572be9 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.5.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '2.7.18')] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["sumtrees.py --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 1cca7bd83a938f95c8428fdbe7a2ffa324ae0646 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:16:59 +0200 Subject: [PATCH 0760/2365] adding easyconfigs: CheckM-1.0.18-foss-2020b-Python-2.7.18.eb --- .../CheckM-1.0.18-foss-2020b-Python-2.7.18.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..889126fb59 --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonPackage' + +name = 'CheckM' +version = '1.0.18' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of +genomes recovered from isolates, single cells, or metagenomes.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://pypi.python.org/packages/source/c/checkm-genome', + 'https://data.ace.uq.edu.au/public/CheckM_databases/', +] +sources = [ + 'checkm-genome-%(version)s.tar.gz', + { + 'filename': 'checkm_data_2015_01_16.tar.gz', + 'extract_cmd': "mkdir -p %(builddir)s/data && cd %(builddir)s/data && tar xfvz %s", + }, +] +checksums = [ + '0dcf31eab5e340a0fff37d7a5091d46d9269b0708db8f789adcd7cbd2a09a2b7', # checkm-genome-1.0.18.tar.gz + '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c', # checkm_data_2015_01_16.tar.gz +] + +dependencies = [ + ('Python', '2.7.18'), + ('pplacer', '1.1.alpha19', '', True), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('SciPy-bundle', '2020.11', versionsuffix), + ('matplotlib', '2.2.5', versionsuffix), + ('Pysam', '0.16.0.1', versionsuffix), + ('DendroPy', '4.5.2', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +# also install CheckM databases, see https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm +postinstallcmds = [ + "cp -a %(builddir)s/data %(installdir)s", + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "%(installdir)s/bin/checkm data setRoot %(installdir)s/data", +] + +sanity_check_paths = { + 'files': ['bin/checkm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["checkm test %(builddir)s/checkm_test_results"] + +sanity_pip_check = True + +moduleclass = 'bio' From d68c3719ecfa317a4c5a46c292988bf825bf01f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:19:22 +0200 Subject: [PATCH 0761/2365] adding easyconfigs: Biopython-1.76-foss-2020b-Python-2.7.18.eb --- ...Biopython-1.76-foss-2020b-Python-2.7.18.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..a593b6c844 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.76' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3873cb98dad5e28d5e3f2215a012565345a398d3d2c4eebf7cd701757b828c72'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From eadc38e8f4ac841d095fcae142c46007d6c7781c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:19:52 +0200 Subject: [PATCH 0762/2365] adding easyconfigs: parallel-20210322-GCCcore-10.2.0.eb --- .../parallel-20210322-GCCcore-10.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20210322-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20210322-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20210322-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..198953d8b4 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20210322-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20210322' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Perl', '5.32.0')] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = ["parallel --help"] + +moduleclass = 'tools' From e1098742a2d2dc4df98b4124e585bc03afbe513d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:20:27 +0200 Subject: [PATCH 0763/2365] adding easyconfigs: scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb --- ...t-learn-0.20.4-foss-2020b-Python-2.7.18.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..77f71dfdbf --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.20.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dfa8a3f33907614030cdfbc8b6f553dacbecaf09f922244f128af3060a137cfc'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', versionsuffix) +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'sklearn'} + +moduleclass = 'data' From cc664694f02d2fe9de23d9c5c9ec8464e9d074db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:21:02 +0200 Subject: [PATCH 0764/2365] adding easyconfigs: MEGAHIT-1.2.9-GCCcore-10.2.0-Python-2.7.18.eb --- ...AHIT-1.2.9-GCCcore-10.2.0-Python-2.7.18.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..3a5d31987a --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.2.0-Python-2.7.18.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'MEGAHIT' +version = '1.2.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex +metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('bzip2', '1.0.8'), + ('gzip', '1.10'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s', + 'bin/%(namelower)s_core', + 'bin/%(namelower)s_core_no_hw_accel', + 'bin/%(namelower)s_core_popcnt', + 'bin/%(namelower)s_toolkit', + ], + 'dirs': [], +} + +moduleclass = 'bio' From 4d8a4e7f37c284c7d7a22b4d17dfcf4e599250cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:23:59 +0200 Subject: [PATCH 0765/2365] adding easyconfigs: CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb --- .../CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..d1d4b72dc2 --- /dev/null +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonPackage' + +name = 'CONCOCT' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://concoct.readthedocs.io' +description = """Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a +program for unsupervised binning of metagenomic contigs by using nucleotide +composition, coverage data in multiple samples and linkage data from paired end +reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/BinPro/CONCOCT/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['00aecacb4b720ac123a63e65072c61e0b5a8690d844c869aaee4dbf287c82888'] + +dependencies = [ + ('Python', '2.7.18'), + ('BEDTools', '2.30.0'), + ('Biopython', '1.76', versionsuffix), + ('Bowtie2', '2.4.2'), + ('CheckM', '1.0.18', versionsuffix), + ('GSL', '2.6'), + ('MEGAHIT', '1.2.9', versionsuffix), + ('parallel', '20210322'), + ('picard', '2.25.0', '-Java-11', True), + ('Pysam', '0.16.0.1', versionsuffix), + ('SAMtools', '1.11'), + ('scikit-learn', '0.20.4', versionsuffix), +] + +download_dep_fail = True + +use_pip = True + +sanity_check_paths = { + 'files': ['bin/concoct'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["concoct --help"] + +moduleclass = 'bio' From 5e8f73afd04930c9682cc14433adc8c5882f52d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:26:03 +0200 Subject: [PATCH 0766/2365] {bio}[gompi/2020b] bmtagger v3.101 --- .../b/bmtagger/bmtagger-3.101-gompi-2020b.eb | 41 +++++++++++++++++++ .../s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb | 34 +++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/b/bmtagger/bmtagger-3.101-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/bmtagger/bmtagger-3.101-gompi-2020b.eb b/easybuild/easyconfigs/b/bmtagger/bmtagger-3.101-gompi-2020b.eb new file mode 100644 index 0000000000..afe9d05064 --- /dev/null +++ b/easybuild/easyconfigs/b/bmtagger/bmtagger-3.101-gompi-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'bmtagger' +version = '3.101' + +homepage = 'ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/' +description = "Best Match Tagger for removing human reads from metagenomics datasets" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'cstd': 'c++98'} + +source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/'] +sources = [{'download_filename': 'bmtools.tar.gz', 'filename': 'bmtools-%(version)s.tar.gz'}] +patches = [ + 'bmtagger-%(version)s_fix-hardcoding.patch', + 'bmtagger-%(version)s_fix-templates.patch', +] +checksums = [ + '81ac6d47aa478c2e0ef760f15b9c71e1c52430c96a2c8d064667ebbef148e873', # bmtools-3.101.tar.gz + '8779edd4dab6c0a3bc1bbcc5f265d61ccfd685972a0570bc3a84f5a131972195', # bmtagger-3.101_fix-hardcoding.patch + '3832e4b4573e0fd8cb567069614f25a9ac51cb31135dd9c97329bf4eb15b1feb', # bmtagger-3.101_fix-templates.patch +] + +dependencies = [ + ('BLAST+', '2.11.0'), + ('SRPRISM', '3.1.2'), +] + +files_to_copy = [(['bmtagger/bmfilter', 'bmtagger/bmtagger.sh', 'bmtagger/bmtool', 'bmtagger/extract_fullseq'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bmfilter', 'bin/bmtagger.sh', 'bin/bmtool', 'bin/extract_fullseq'], + 'dirs': [], +} + +sanity_check_commands = [ + "bmtool -h", + "bmfilter -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d8ec072f09 --- /dev/null +++ b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'SRPRISM' +version = '3.1.2' + +homepage = 'https://github.com/ncbi/SRPRISM' +description = "Single Read Paired Read Indel Substitution Minimizer" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/ncbi/SRPRISM/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Java', '11', '', True), + ('NGS', '2.10.9'), + ('bzip2', '1.0.8'), +] + +prebuildopts = "cd srprism/lib && " +buildopts = " && cd ../app && make" + +files_to_copy = [(['srprism/app/srprism'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/srprism'], + 'dirs': [], +} + +sanity_check_commands = ["srprism help"] + +moduleclass = 'bio' From 9011eb680aef7fb8a8595fe05c5326b9a0a9fae7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:29:42 +0200 Subject: [PATCH 0767/2365] {bio}[gompi/2020b] MaxBin v2.2.7 --- .../FragGeneScan-1.31-GCCcore-10.2.0.eb | 37 ++++++++++++++ .../i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.2.0.eb | 49 +++++++++++++++++++ .../m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb | 38 ++++++++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4f843adbc4 --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [("Perl", "5.32.0")] + +fix_perl_shebang_for = ['*.pl'] + +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +sanity_check_commands = [ + './run_FragGeneScan.pl help', + './run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..554db4afcb --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Updated: Pavel Grochal (INUITS) +# License: GPLv2 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in prebuildopts + +# modified by Tom Strempel +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.3' + +homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads +Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. +IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth +contigs are removed iteratively with cutoff threshold from low to high to reduce the errors +in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled +locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD +can iterate k value of de Bruijn graph to a very large value with less gaps and less branches +to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] +sources = ['idba-%(version)s.tar.gz'] +checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] + +prebuildopts = './configure && ' + +# we delete every .o and Makefile file which is left in bin folder +buildopts = ' && rm -fr bin/*.o bin/Makefile*' + +files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] + +pretestopts = "cd test && " +runtest = "check" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb new file mode 100644 index 0000000000..cec4e9e46b --- /dev/null +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'MaxBin' +version = '2.2.7' + +# https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html doesn't work +homepage = 'https://sourceforge.net/projects/maxbin/' +description = """MaxBin is software for binning assembled metagenomic sequences +based on an Expectation-Maximization algorithm.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e40c8db96efe3d132a179e740208099105f231a8e10f95ef286631423472fda7'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Perl', '5.32.0'), + ('Bowtie2', '2.4.2'), + ('FragGeneScan', '1.31'), + ('HMMER', '3.3.2'), + ('IDBA-UD', '1.1.3'), +] + +prebuildopts = "cd src && " + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['run_MaxBin.pl', 'src/MaxBin'], + 'dirs': [], +} + +modextrapaths = {'PATH': ['', 'src']} + +moduleclass = 'bio' From f34c6a635106b372533062bca168d740a07db0e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 17:32:14 +0200 Subject: [PATCH 0768/2365] adding easyconfigs: QUAST-5.0.2-foss-2020b-Python-2.7.18.eb --- .../QUAST-5.0.2-foss-2020b-Python-2.7.18.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..e7f2fc926b --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'QUAST' +version = '5.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ablab/%(namelower)s' +description = """QUAST evaluates genome assemblies by computing various metrics. +It works both with and without reference genomes. The tool accepts multiple +assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '2.7.18'), + ('Perl', '5.32.0'), + ('matplotlib', '2.2.5', versionsuffix), + ('Java', '11', '', True), + ('Boost', '1.74.0'), +] + +use_pip = True + +exts_list = [ + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + (name, version, { + 'install_target': 'install_full', + 'modulename': 'quast_libs', + 'source_tmpl': 'quast_%(version)s.tar.gz', + 'source_urls': ['https://github.com/ablab/quast/archive/'], + 'checksums': ['9f30c03e0bfd261492fe6b72fb07645bdee5b29d741f75fc75857b6fa095d91d'], + }), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s quast.py quast"] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "wget quast.sf.net/test_data.tar.gz && " + "tar xzf test_data.tar.gz && " + "%(namelower)s.py --test && " + "rm ./test_data.tar.gz ./test_data -rf", + "%(namelower)s -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 6c7c8524d40cbc1251a1e503017710d75d54216d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 18:01:08 +0200 Subject: [PATCH 0769/2365] adding easyconfigs: Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb, pigz-2.6-GCCcore-10.2.0.eb, cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb --- .../cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb | 56 +++++++++++++++++++ .../p/pigz/pigz-2.6-GCCcore-10.2.0.eb | 49 ++++++++++++++++ ...m_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb | 50 +++++++++++++++++ 3 files changed, 155 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..26af108903 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,56 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modufied by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '1.18' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A +tails and other types of unwanted sequence from your high-throughput sequencing +reads.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), + ('NASM', '2.15.05'), +] + +dependencies = [('Python', '2.7.18')] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('xopen', '0.8.4', { + 'checksums': ['dcd8f5ef5da5564f514a990573a48a0c347ee1fdbb9b6374d31592819868f7ba'], + }), + (name, version, { + 'checksums': ['17aabf9b19d09a426d96030a83ad003c97b26dba9d45bf5570d33088fcd533f9'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cutadapt --help", + "python -c 'import cutadapt.seqio'", # requires xopen +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..226510c6db --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# +# 2.4.0: +# Jonas Demeulemeester +# The Francis Crick Institute +## +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.6' + +homepage = 'https://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://zlib.net/pigz/', + 'https://zlib.net/pigz/fossils/', +] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..add7564676 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,50 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# +# Updated to version 0.6.2: Pavel Grochal (INUITS) +# Updated to version 0.6.5: Alex Domingo (VUB) +# +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.6.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore is a wrapper around Cutadapt and FastQC to +consistently apply adapter and quality trimming to FastQ files, with extra +functionality for RRBS data.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b8db8ffd131d9d9e7c8532a5a1f1caee656c0c58d3eafd460fee3c39b9fcab5e'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '2.7.18'), + ('Java', '11', '', True), + ('pigz', '2.6'), + ('Perl', '5.32.0'), + ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('cutadapt', '1.18', versionsuffix), +] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s", + "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", +] + +sanity_check_paths = { + 'files': ["bin/trim_galore"], + 'dirs': [], +} + +sanity_check_commands = [ + "trim_galore --help" +] + +moduleclass = 'bio' From a09d2715212b1982e4a4924937063024325b2c47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 18:03:32 +0200 Subject: [PATCH 0770/2365] adding easyconfigs: Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb --- .../Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..94387013b4 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['da33aa8c20a9a342ce73831d02831a10413f54a05471c7f31edf34f225d456ae'] + +dependencies = [ + ('Python', '2.7.18'), + ('matplotlib', '2.2.5', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From a9384bc69461d5dbeb6a5ded7c98a5acced65f2f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Apr 2021 17:05:44 +0100 Subject: [PATCH 0771/2365] adding easyconfigs: scanpy-1.7.2-foss-2020b.eb, pandas-1.2.4-foss-2020b.eb, numexpr-2.7.3-foss-2020b.eb, Bottleneck-1.3.2-foss-2020b.eb --- .../s/scanpy/scanpy-1.7.2-foss-2020b.eb | 105 ++++++++++++++++++ 1 file changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb new file mode 100644 index 0000000000..e4e665c5d1 --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb @@ -0,0 +1,105 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.7.2' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Autotools', '20200321'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('matplotlib', '3.3.3'), + ('networkx', '2.5'), + ('numba', '0.52.0'), + ('pandas', '1.2.4'), + ('PyTables', '3.6.1'), + ('statsmodels', '0.12.1'), + ('scikit-learn', '0.23.2'), +] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('tqdm', '4.60.0', { + 'checksums': ['ebdebdb95e3477ceea267decfc0784859aa3df3e27e22d23b83e9b272bf157ae'], + }), + ('seaborn', '0.11.1', { + 'checksums': ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'], + }), + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('anndata', '0.7.6', { + 'checksums': ['a3cc67bba9a4cd4b5984aec64c4f577c2d5a4695f4064027f8e6a9dac1f508b2'], + }), + ('six', '1.15.0', { + 'checksums': ['30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259'], + }), + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + ('pynndescent', '0.5.2', { + 'checksums': ['d9fd22210b8d64368376ff392e876fb72fe3cda282396cfa6a59440ab6600771'], + }), + ('umap-learn', '0.3.10', { + 'modulename': 'umap', + 'checksums': ['21ce6b6d7486905318ba6458b5a9ba2cfb935878d30c24e6fba64ee3bd504d09'], + }), + ('get_version', '2.1', { + 'use_pip': False, + 'checksums': ['8156b526c2557537b8ca82241fa2b82b3da25939627398f6567dee31ba9725bc'], + }), + ('legacy-api-wrap', '1.2', { + 'modulename': 'legacy_api_wrap', + 'use_pip': False, + 'checksums': ['034a44612da7e9943d3964363a98937ab54d55e3301075374abe0d521eb8101b'], + }), + ('stdlib-list', '0.8.0', { + 'modulename': 'stdlib_list', + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.1', { + 'checksums': ['e1b2358808aded7b2ff00ea0cd4e6a2d978fb2a44ee9b15ac23d64a81bf62706'], + }), + ('texttable', '1.6.3', { + 'checksums': ['ce0faf21aa77d806bbff22b107cc22cce68dc9438f97a2df32c93e9afa4ce436'], + }), + ('python-igraph', '0.9.1', { + 'modulename': 'igraph', + 'checksums': ['f1895a83c57180f03c50fb77334a4d5029327aefee14f03381e10d34a1794410'], + }), + ('leidenalg', '0.8.4', { + 'build_cmd': "build --no-pkg-config", + 'checksums': ['45764e0fc8829d23dee7698bd91d07c2027423d6309bd66b9711cdfecbcf8459'], + }), + (name, version, { + 'checksums': ['ad5e7afdf1948753cd27f6f27ee904df1ce455855eec8520985effe86c53c630'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['igraph', 'natsort', 'scanpy', 'tqdm']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'bio' From d633679b3152e0eaaa4ea23a77ac281219f81d6a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 18:37:03 +0200 Subject: [PATCH 0772/2365] {bio}[gompi/2020b] taxator-tk v1.3.3, SeqAn v2.4.0 --- .../s/SeqAn/SeqAn-2.4.0-GCCcore-10.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cb9f064fb0 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'SeqAn' +version = '2.4.0' + +homepage = 'https://github.com/seqan/seqan' + +description = """ + SeqAn is an open source C++ library of efficient algorithms and data structures + for the analysis of sequences with the focus on biological data. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/seqan/seqan/archive/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +postinstallcmds = [ + "mkdir -p %(installdir)s/util/cmake", + "cp -a %(builddir)s/seqan-*/util/cmake/seqan-config.cmake %(installdir)s/util/cmake/", + "cp -a %(builddir)s/seqan-*/include %(installdir)s", +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["gustaf_mate_joining", "mason_materializer", "mason_variator", + "rabema_prepare_sam", "razers3", "seqan_tcoffee", "s4_join", "samcat", "splazers", + "yara_mapper"]] + ['util/cmake/seqan-config.cmake'], + 'dirs': ['include/seqan'], +} + +moduleclass = 'bio' From 77223a06c2b1146d200458a11fdc2df152cfc734 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 19:16:58 +0200 Subject: [PATCH 0773/2365] {bio}[foss/2020b] metaWRAP v1.3 (+ deps) w/ Python 2.7.18 --- .../k/Kraken/Kraken-1.1.1-GCCcore-10.2.0.eb | 50 +++++++++++++++++ .../KronaTools-2.8-GCCcore-10.2.0.eb | 40 +++++++++++++ .../MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 40 +++++++++++++ .../metaWRAP-1.3-foss-2020b-Python-2.7.18.eb | 56 +++++++++++++++++++ .../p/prokka/prokka-1.14.5-gompi-2020b.eb | 47 ++++++++++++++++ .../SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb | 47 ++++++++++++++++ 6 files changed, 280 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..de1ed07683 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PackedBinary' + +name = 'Kraken' +version = '1.1.1' + +homepage = 'https://ccb.jhu.edu/software/%(namelower)s/' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# Part is compiled with CXX, the rest is in Perl +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1_CXX-CXXFLAGS.patch'] +checksums = [ + '73e48f40418f92b8cf036ca1da727ca3941da9b78d4c285b81ba3267326ac4ee', # v1.1.1.tar.gz + '84c017d6a80ccaac1e23561c83cac90bcc3d62baa8d31657a7dafbc2c3f29726', # Kraken-1.1.1_CXX-CXXFLAGS.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Perl', '5.32.0'), + ('wget', '1.20.3'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_%(namelower)s.sh %(installdir)s' + +sanity_check_paths = { + 'files': ['add_to_library.sh', 'build_kraken_db.sh', 'check_for_jellyfish.sh', 'classify', 'clean_db.sh', + 'cp_into_tempfile.pl', 'db_shrink', 'db_sort', 'download_genomic_library.sh', + 'download_taxonomy.sh', 'kraken', 'kraken-build', 'kraken-filter', 'krakenlib.pm', + 'kraken-mpa-report', 'kraken-report', 'kraken-translate', 'make_seqid_to_taxid_map', + 'read_merger.pl', 'report_gi_numbers.pl', 'set_lcas', 'shrink_db.sh', + 'standard_installation.sh', 'upgrade_db.sh', 'verify_gi_numbers.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f1ccf12fc5 --- /dev/null +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# this is a bug fix to make sure the symlinks in bin are not getting destroyed +# by Easybuild when it is tidying up +# This build also links updateTaxonomy.sh and updateAccessions.sh in the bin folder +# so users can install their own Taxonomy database + +easyblock = 'Binary' + +name = 'KronaTools' +version = '2.8' + +homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' +description = """Krona Tools is a set of scripts to create Krona charts from +several Bioinformatics tools as well as from text and XML files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] +sources = [{ + 'filename': '%(name)s-%(version)s.tar', + 'extract_cmd': 'tar xvf %s -C %(installdir)s/../', +}] + +extract_sources = True + +builddependencies = [('binutils', '2.35')] +dependencies = [('Perl', '5.32.0')] + +install_cmd = 'cd %(installdir)s/../%(name)s-%(version)s; ./install.pl --prefix=%(installdir)s; ' +install_cmd += 'cd %(installdir)s/bin; ' +install_cmd += 'ln -s ../../%(name)s-%(version)s/updateTaxonomy.sh . ;' +install_cmd += 'ln -s ../../%(name)s-%(version)s/updateAccessions.sh . ' + +sanity_check_paths = { + 'files': ['bin/ktClassifyBLAST', 'bin/ktImportBLAST', 'bin/ktImportTaxonomy'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..e98f41bec9 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'MetaBAT' +version = '2.15' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/berkeleylab/metabat' +description = "An efficient tool for accurately reconstructing single genomes from complex microbial communities" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('Perl', '5.32.0'), + ('Boost', '1.74.0'), + ('zlib', '1.2.11'), + ('SAMtools', '1.11'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), +] + +fix_perl_shebang_for = ['bin/*.pl'] + +prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " + +sanity_check_paths = { + 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..5b92735029 --- /dev/null +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,56 @@ +easyblock = 'Tarball' + +name = 'metaWRAP' +version = '1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/bxlab/metaWRAP' +description = """MetaWRAP aims to be an easy-to-use metagenomic wrapper suite +that accomplishes the core tasks of metagenomic analysis from start to finish: +read quality control, assembly, visualization, taxonomic profiling, extracting +draft genomes (binning), and functional annotation.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/bxlab/metaWRAP/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('Java', '11', '', True), +] + +# see https://github.com/bxlab/metaWRAP/blob/master/installation/dependancies.md +dependencies = [ + ('Python', '2.7.18'), + ('Perl', '5.32.0'), + ('R', '4.0.3'), + ('BLAST+', '2.11.0'), + ('bmtagger', '3.101'), + ('Bowtie2', '2.4.2'), + ('BWA', '0.7.17'), + ('CheckM', '1.0.18', versionsuffix), + ('FastQC', '0.11.9', '-Java-11', True), + ('Kraken', '1.1.1'), + ('KronaTools', '2.8'), + ('MEGAHIT', '1.2.9', versionsuffix), + ('MetaBAT', '2.15', versionsuffix), + ('CONCOCT', '1.1.0', versionsuffix), + ('MaxBin', '2.2.7'), + ('QUAST', '5.0.2', versionsuffix), + ('SAMtools', '1.11'), + ('SPAdes', '3.15.2', versionsuffix), + ('Trim_Galore', '0.6.6', versionsuffix), + ('Seaborn', '0.9.1', versionsuffix), + ('Salmon', '1.4.0'), + ('taxator-tk', '1.3.3'), + ('prokka', '1.14.5'), +] + +sanity_check_paths = { + 'files': ['bin/config-metawrap', 'bin/metaWRAP'], + 'dirs': [], +} + +sanity_check_commands = ["metaWRAP --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb new file mode 100644 index 0000000000..28077ad116 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -0,0 +1,47 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.11.0'), + ('Java', '11', '', True), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..54ab5e1ceb --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'CMakeMake' + +name = 'SPAdes' +version = '3.15.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://cab.spbu.ru/software/spades/' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['e93b43951a814dc7bd6a246e1e863bbad6aac4bfe1928569402c131b2af99d0d'] + +builddependencies = [ + ('CMake', '3.18.4'), +] +dependencies = [ + ('Python', '2.7.18'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('libreadline', '8.0'), +] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', + 'spades-ionhammer', 'spades-kmercount', 'spades.py']], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s.py', '--test')] + +moduleclass = 'bio' From 3972a575f47a6852f384b69fc3ade7ceebb5997d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Apr 2021 18:25:00 +0100 Subject: [PATCH 0774/2365] Remove download_dep_fail from scanpy EC --- easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb index e4e665c5d1..552707e13e 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb @@ -35,7 +35,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_list = [ ('tqdm', '4.60.0', { From 36f57e9c79568b685d0f809b94a676539848860b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 19:31:23 +0200 Subject: [PATCH 0775/2365] add missing checksums in SRPRISM 3.1.2 easyconfig --- easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb index d8ec072f09..41984431bd 100644 --- a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/ncbi/SRPRISM/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['93e6864b7ab18be96584950227426102b545db7d6d02762490a43e1610b7eb9b'] builddependencies = [('binutils', '2.35')] From d12d29f6cd7774fb1b42aa7644b0a5f8ba266719 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Apr 2021 19:33:20 +0200 Subject: [PATCH 0776/2365] add missing checksums in parallel 20210322 easyconfig --- .../easyconfigs/p/parallel/parallel-20210322-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/parallel/parallel-20210322-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20210322-GCCcore-10.2.0.eb index 198953d8b4..a5bb031caf 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20210322-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20210322-GCCcore-10.2.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['98f71b445a23a18bb4e9bce4f374b93e6a6d9decdf892be8d22459f224b85694'] builddependencies = [('binutils', '2.35')] From e595becc27291a6e55f09d6e7fcbe7e61c320e32 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 22 Apr 2021 22:43:46 +0200 Subject: [PATCH 0777/2365] add miceadds, visdat, UpSetR, naniar, stringdist, image.binarization to R-4.0.3-foss-2020b.eb --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index b27365ac40..7b91a735f1 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2803,6 +2803,24 @@ exts_list = [ ('DMCfun', '1.3.0', { 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], }), + ('miceadds', '3.11-6', { + 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], + }), + ('visdat', '0.5.3', { + 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('naniar', '0.6.0', { + 'checksums': ['9c93c64f51dd8c3002c930c276ef57651e91c8db12f885a03113753c604e7e54'], + }), + ('stringdist', '0.9.6.3', { + 'checksums': ['cd6d98f982e9ae7c4154a040c3a3f959bce19abf0229d64d22efef41f85b3f1b'], + }), + ('image.binarization', '0.1.1', { + 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], + }), ] moduleclass = 'lang' From 002480464e7137ff0851e0a583b45fb28b3362fd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 22 Apr 2021 22:44:47 +0200 Subject: [PATCH 0778/2365] add miceadds, visdat, UpSetR, naniar, stringdist, image.binarization to R-4.0.4-foss-2020b.eb --- .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index e3afe51d73..9f559db2ab 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2838,6 +2838,24 @@ exts_list = [ ('DMCfun', '1.3.0', { 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], }), + ('miceadds', '3.11-6', { + 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], + }), + ('visdat', '0.5.3', { + 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('naniar', '0.6.0', { + 'checksums': ['9c93c64f51dd8c3002c930c276ef57651e91c8db12f885a03113753c604e7e54'], + }), + ('stringdist', '0.9.6.3', { + 'checksums': ['cd6d98f982e9ae7c4154a040c3a3f959bce19abf0229d64d22efef41f85b3f1b'], + }), + ('image.binarization', '0.1.1', { + 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], + }), ] moduleclass = 'lang' From 59488e7f1e64dc93f1bae3d75d680a88b3febfb4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 22 Apr 2021 22:46:26 +0200 Subject: [PATCH 0779/2365] add all missing extensions from R-4.0.3-foss-2020b.eb to R-4.0.3-fosscuda-2020b.eb --- .../easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 4ac9ced88b..3f3ad2dbab 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2813,6 +2813,24 @@ exts_list = [ ('DMCfun', '1.3.0', { 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], }), + ('miceadds', '3.11-6', { + 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], + }), + ('visdat', '0.5.3', { + 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('naniar', '0.6.0', { + 'checksums': ['9c93c64f51dd8c3002c930c276ef57651e91c8db12f885a03113753c604e7e54'], + }), + ('stringdist', '0.9.6.3', { + 'checksums': ['cd6d98f982e9ae7c4154a040c3a3f959bce19abf0229d64d22efef41f85b3f1b'], + }), + ('image.binarization', '0.1.1', { + 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From a80853ea7faf5a21f06c459440abea5cd81d5825 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 22 Apr 2021 22:47:02 +0200 Subject: [PATCH 0780/2365] add all missing extensions from R-4.0.4-foss-2020b.eb to R-4.0.4-fosscuda-2020b.eb --- .../easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 20534135a0..dc0233f242 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2822,6 +2822,45 @@ exts_list = [ ('rnetcarto', '0.2.4', { 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], }), + ('DEoptim', '2.2-5', { + 'checksums': ['ae12dedcd4a43994e811e7285f8c12bfdb688e7c99d65515cf7e8cb6db13955a'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2013.9-1', { + 'checksums': ['1a1a399682a06a5fea3934985ebb1334005676c6a2a22d06f3c91c3923432908'], + }), + ('Rvmmin', '2018-4.17', { + 'checksums': ['d53ba7ab06596a47990caf101a50935b2b34402f9dd8414f098a873026ff1f56'], + }), + ('Rcgmin', '2013-2.21', { + 'checksums': ['a824a09c32d7565a3e30607c71333506d5b7197478fbe8b43f8a77dad6c12f0a'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '1.3.0', { + 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], + }), + ('miceadds', '3.11-6', { + 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], + }), + ('visdat', '0.5.3', { + 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('naniar', '0.6.0', { + 'checksums': ['9c93c64f51dd8c3002c930c276ef57651e91c8db12f885a03113753c604e7e54'], + }), + ('stringdist', '0.9.6.3', { + 'checksums': ['cd6d98f982e9ae7c4154a040c3a3f959bce19abf0229d64d22efef41f85b3f1b'], + }), + ('image.binarization', '0.1.1', { + 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From 43d48cc0d606e8e1406025c480a662b12322e56f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 22 Apr 2021 22:54:54 +0200 Subject: [PATCH 0781/2365] add Compress:Raw:Zlib to VEP-103.1-GCC-10.2.0.eb --- easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb index b53ccb6277..24e9111348 100644 --- a/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb @@ -31,6 +31,11 @@ exts_list = [ 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], }), + ('Compress::Raw::Zlib', '2.101', { + 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['9d1b9515e8277c1b007e33fad1fd0f18717d56bf647e3794d61289c45b1aabb2'], + }), ] moduleclass = 'bio' From a2694eebfde384d8395880d58dfa304cf5c9cd7d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 22 Apr 2021 22:58:55 +0200 Subject: [PATCH 0782/2365] explain presence of Compress:Raw:Zlib in VEP-103.1-GCC-10.2.0.eb --- easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb index 24e9111348..25ee10d70c 100644 --- a/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb @@ -32,6 +32,7 @@ exts_list = [ 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], }), ('Compress::Raw::Zlib', '2.101', { + # Perl v5.32.0 already provides this extension, but VEP needs a more recent version 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], 'checksums': ['9d1b9515e8277c1b007e33fad1fd0f18717d56bf647e3794d61289c45b1aabb2'], From 9d735b81bb11c2281ce99514a278f872c9cc6034 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Apr 2021 09:21:48 +0200 Subject: [PATCH 0783/2365] adding easyconfigs: Nim-1.4.6-GCCcore-10.2.0.eb --- .../n/Nim/Nim-1.4.6-GCCcore-10.2.0.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nim/Nim-1.4.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/Nim/Nim-1.4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/Nim/Nim-1.4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..58f3d9cdb0 --- /dev/null +++ b/easybuild/easyconfigs/n/Nim/Nim-1.4.6-GCCcore-10.2.0.eb @@ -0,0 +1,17 @@ +name = 'Nim' +version = '1.4.6' + +homepage = 'https://nim-lang.org/' +description = "Nim is a systems and applications programming language." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://nim-lang.org/download/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0fbc0f9282cffe85de99bc47bfa876525b9ddda2a2eae55c185a08804b98d3bd'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('libreadline', '8.0')] + +moduleclass = 'lang' From 0eb0d967f970bafc6bc4b53d7c214d5648591310 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Apr 2021 10:52:50 +0200 Subject: [PATCH 0784/2365] add missing patch + checksums for pigz 2.6 with GCCcore/10.2.0 --- easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-10.2.0.eb index 226510c6db..c97ee4199c 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-10.2.0.eb @@ -28,6 +28,11 @@ source_urls = [ 'https://zlib.net/pigz/fossils/', ] sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + '2eed7b0d7449d1d70903f2a62cd6005d262eb3a8c9e98687bc8cbb5809db2a7d', # pigz-2.6.tar.gz + '7e37175714d43c946373d07c522ec98a77c0f8572a9d448f759c41f6f060275d', # pigz-2.6_makefile.patch +] builddependencies = [ ('binutils', '2.35'), From d50c4f49e6d0cdcd7367a85d9ba7a721be63eb82 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 23 Apr 2021 13:16:42 +0200 Subject: [PATCH 0785/2365] adding easyconfigs: angsd-0.935-GCC-10.2.0.eb --- .../a/angsd/angsd-0.935-GCC-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/angsd/angsd-0.935-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.935-GCC-10.2.0.eb b/easybuild/easyconfigs/a/angsd/angsd-0.935-GCC-10.2.0.eb new file mode 100644 index 0000000000..35882a6104 --- /dev/null +++ b/easybuild/easyconfigs/a/angsd/angsd-0.935-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'angsd' +version = '0.935' + +homepage = 'http://www.popgen.dk/angsd' +description = """Program for analysing NGS data.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'ANGSD' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['15000281330fa59ddf745cb84eeaa653acf6da34a4ac6c3df7c5835d1d01ba16'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('HTSlib', '1.12'), +] + +files_to_copy = [ + (['angsd', 'misc/supersim', 'misc/thetaStat', 'misc/realSFS', 'misc/msToGlf', + 'misc/smartCount', 'misc/printIcounts', 'misc/contamination', 'misc/splitgl', + 'misc/NGSadmix', 'misc/contamination2', 'misc/haploToPlink', 'misc/ngsPSMC', + 'misc/ibs'], 'bin'), + 'doc', +] + +sanity_check_paths = { + 'files': ['bin/angsd'], + 'dirs': ['doc'], +} + +moduleclass = 'bio' From 1d8a9bcb6ba806f83d21f1052d117c7113ba4d84 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 23 Apr 2021 13:05:40 +0100 Subject: [PATCH 0786/2365] Remove `six` from extensions (already installed in Python) Remove Bottleneck, numexpr, pandas ECs (already installed in SciPy-bundle) Add Seaborn 0.11.1 for foss-2020b and use as dep --- .../s/Seaborn/Seaborn-0.11.1-foss-2020b.eb | 28 +++++++++++++++++++ .../s/scanpy/scanpy-1.7.2-foss-2020b.eb | 14 ++-------- 2 files changed, 31 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb new file mode 100644 index 0000000000..5b326ff282 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.11.1' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb index 552707e13e..c59ffcfa5b 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb @@ -25,33 +25,25 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('h5py', '3.1.0'), - ('matplotlib', '3.3.3'), ('networkx', '2.5'), ('numba', '0.52.0'), ('pandas', '1.2.4'), ('PyTables', '3.6.1'), ('statsmodels', '0.12.1'), ('scikit-learn', '0.23.2'), + ('Seaborn', '0.11.1'), + ('tqdm', '4.56.2'), ] use_pip = True exts_list = [ - ('tqdm', '4.60.0', { - 'checksums': ['ebdebdb95e3477ceea267decfc0784859aa3df3e27e22d23b83e9b272bf157ae'], - }), - ('seaborn', '0.11.1', { - 'checksums': ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'], - }), ('natsort', '7.1.1', { 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], }), ('anndata', '0.7.6', { 'checksums': ['a3cc67bba9a4cd4b5984aec64c4f577c2d5a4695f4064027f8e6a9dac1f508b2'], }), - ('six', '1.15.0', { - 'checksums': ['30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259'], - }), ('patsy', '0.5.1', { 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), @@ -97,7 +89,7 @@ exts_list = [ sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['igraph', 'natsort', 'scanpy', 'tqdm']], + 'files': ['bin/%s' % x for x in ['igraph', 'natsort', 'scanpy']], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } From 4a8f0a57f3a9bdfd639ad859e517b7470e9cfe48 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 23 Apr 2021 14:22:27 +0200 Subject: [PATCH 0787/2365] update on r-inla easyconfig --- .../r/Rmath/Rmath-4.0.4-foss-2020b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb new file mode 100644 index 0000000000..84c1c2001b --- /dev/null +++ b/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb @@ -0,0 +1,47 @@ +# Easyconfig for Rmath +# Author: Caspar van Leeuwen +# SURFsara, Amsterdam, The Netherlands + +easyblock = 'ConfigureMake' + +name = 'Rmath' +version = '4.0.4' + +homepage = "https://www.r-project.org/" +description = """Rmath is the standalone version of the R math library. + Rmath can be used in your own C/C++ routines.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s/'] +sources = ['R-%(version)s.tar.gz'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('cURL', '7.72.0'), + ('libreadline', '8.0'), + ('PCRE2', '10.35'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11') +] + +# Copied from R-3.3.1-intel-2016b.eb. +# Again, unsure if these affect R-math: R documentation doesn't specify. +configopts = "--with-pic --enable-threads --with-x=no --with-pcre1" + +# Since we're only installing Rmath anyway, we don't care about R packages. +configopts += " --with-recommended-packages=no" + +# To build Rmath, docs say you need to execute 'make' in src/nmath/standalone +# https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Configuration-options +prebuildopts = 'cd src/nmath/standalone;' +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': [('lib/libRmath.a', 'lib64/libRmath.so'), + ('lib/libRmath.%s' % SHLIB_EXT, 'lib64/libRmath.%s' % SHLIB_EXT), + 'include/Rmath.h'], + 'dirs': [] +} + +moduleclass = 'numlib' From 2d08172f37b1a820fc7d6fa96901b034ef3835df Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 23 Apr 2021 15:34:34 +0100 Subject: [PATCH 0788/2365] Add easyconfigs for igraph, python-igraph and leidenalg for foss 2020b Remove python-igraph and leidenalg from scanpy exts_list Add sanity check command for scanpy --- .../i/igraph/igraph-0.9.1-foss-2020b.eb | 44 +++++++++++++++ .../l/leidenalg/leidenalg-0.8.3-foss-2020b.eb | 46 ++++++++++++++++ .../python-igraph-0.9.0-foss-2020b.eb | 53 +++++++++++++++++++ .../s/scanpy/scanpy-1.7.2-foss-2020b.eb | 27 +++++----- 4 files changed, 157 insertions(+), 13 deletions(-) create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.9.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.9.1-foss-2020b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.9.1-foss-2020b.eb new file mode 100644 index 0000000000..227d6a8a2e --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.9.1-foss-2020b.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'CMakeMake' + +name = 'igraph' +version = '0.9.1' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['1902810650e8f9d98feefa3eca735db5a879416d00a08f68aad2ca07964cee9f'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('GLPK', '4.65'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), +] + +configopts = "--with-external-blas --with-external-lapack --with-external-glpk" + +# extra folder `igraph` is wrong, since all other software expects it to be in ./include folder directly +postinstallcmds = [ + 'mv %(installdir)s/include/igraph/* %(installdir)s/include/ && rmdir %(installdir)s/include/igraph ', +] + +sanity_check_paths = { + 'files': ['include/igraph%s.h' % x for x in ['', '_blas', '_constants', '_lapack', '_types', '_version']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb new file mode 100644 index 0000000000..b5307684eb --- /dev/null +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb @@ -0,0 +1,46 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'leidenalg' +version = '0.8.3' + +homepage = 'https://github.com/vtraag/leidenalg' +description = """Implementation of the Leiden algorithm for various quality +functions to be used with igraph in Python.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('PyYAML', '5.3.1'), + ('Bison', '3.7.1'), + ('libtool', '2.4.6'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('igraph', '0.9.1'), + ('python-igraph', '0.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ddt', '1.4.2', { + 'checksums': ['64a67366a2715e636b88694cc6075cc02db292f01098b8e385397c894d395378'], + }), + (name, version, { + 'checksums': ['84c2fa673390b62986e51258cbe048a49c163e516ee791b372c2779c928d8e7e'], + 'buildopts': '--use-pkg-config', + 'runtest': "python setup.py test", + 'testopts': '--use-pkg-config', + }), +] + +sanity_check_commands = ["python -c 'import leidenalg; import igraph as ig; " + "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), " + "leidenalg.ModularityVertexPartition)'"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb new file mode 100644 index 0000000000..792aba8a30 --- /dev/null +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'python-igraph' +version = '0.9.0' + +homepage = 'https://igraph.org/python' +description = """Python interface to the igraph high performance graph library, primarily aimed at complex network + research and analysis.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('igraph', '0.9.1'), + ('PyCairo', '1.20.0'), + ('Clang', '11.0.1'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), +] + +use_pip = True + +exts_list = [ + ('texttable', '1.6.3', { + 'checksums': ['ce0faf21aa77d806bbff22b107cc22cce68dc9438f97a2df32c93e9afa4ce436'], + }), + (name, version, { + 'installopts': '--install-option="--use-pkg-config" --install-option="--static"', + 'modulename': 'igraph', + 'patches': ['python-igraph-%(version)s_fix-igraph-libs.patch'], + 'checksums': [ + '7aa1d77fa02e27475eb4f14503f3cb342c3ed8990d9224640fd29c70797f2dd6', # python-igraph-0.9.0.tar.gz + # python-igraph-0.9.0_fix-igraph-libs.patch + '7af7a6e6a8b982ced7cdd939d82a98829512088744bebad34c714a3c4803f126', + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/igraph'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# cairo must be available for proper plotting support +sanity_check_commands = ["python -c 'from igraph.drawing.utils import find_cairo; cairo = find_cairo(); cairo.Context'"] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb index c59ffcfa5b..efa8b26016 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb @@ -27,12 +27,12 @@ dependencies = [ ('h5py', '3.1.0'), ('networkx', '2.5'), ('numba', '0.52.0'), - ('pandas', '1.2.4'), ('PyTables', '3.6.1'), ('statsmodels', '0.12.1'), ('scikit-learn', '0.23.2'), ('Seaborn', '0.11.1'), ('tqdm', '4.56.2'), + ('leidenalg', '0.8.3'), ] use_pip = True @@ -70,17 +70,17 @@ exts_list = [ ('sinfo', '0.3.1', { 'checksums': ['e1b2358808aded7b2ff00ea0cd4e6a2d978fb2a44ee9b15ac23d64a81bf62706'], }), - ('texttable', '1.6.3', { - 'checksums': ['ce0faf21aa77d806bbff22b107cc22cce68dc9438f97a2df32c93e9afa4ce436'], - }), - ('python-igraph', '0.9.1', { - 'modulename': 'igraph', - 'checksums': ['f1895a83c57180f03c50fb77334a4d5029327aefee14f03381e10d34a1794410'], - }), - ('leidenalg', '0.8.4', { - 'build_cmd': "build --no-pkg-config", - 'checksums': ['45764e0fc8829d23dee7698bd91d07c2027423d6309bd66b9711cdfecbcf8459'], - }), + #('texttable', '1.6.3', { + # 'checksums': ['ce0faf21aa77d806bbff22b107cc22cce68dc9438f97a2df32c93e9afa4ce436'], + #}), + #('python-igraph', '0.9.1', { + # 'modulename': 'igraph', + # 'checksums': ['f1895a83c57180f03c50fb77334a4d5029327aefee14f03381e10d34a1794410'], + #}), + #('leidenalg', '0.8.4', { + # 'build_cmd': "build --no-pkg-config", + # 'checksums': ['45764e0fc8829d23dee7698bd91d07c2027423d6309bd66b9711cdfecbcf8459'], + #}), (name, version, { 'checksums': ['ad5e7afdf1948753cd27f6f27ee904df1ce455855eec8520985effe86c53c630'], }), @@ -89,8 +89,9 @@ exts_list = [ sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['igraph', 'natsort', 'scanpy']], + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_check_commands = ["%(name)s --help"] moduleclass = 'bio' From 7ddddd76889bef78daec0d64d4ed58eb483b4b88 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 23 Apr 2021 15:41:42 +0100 Subject: [PATCH 0789/2365] Remove scanpy builddependencies (since various deps moved out of exts_list) --- .../s/scanpy/scanpy-1.7.2-foss-2020b.eb | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb index efa8b26016..f599ebcc9b 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb @@ -13,14 +13,6 @@ description = """Scanpy is a scalable toolkit for analyzing single-cell gene exp toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'openmp': True} -builddependencies = [ - ('pkg-config', '0.29.2'), - ('Autotools', '20200321'), - ('flex', '2.6.4'), - ('Bison', '3.7.1'), - ('CMake', '3.18.4'), -] - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -70,17 +62,6 @@ exts_list = [ ('sinfo', '0.3.1', { 'checksums': ['e1b2358808aded7b2ff00ea0cd4e6a2d978fb2a44ee9b15ac23d64a81bf62706'], }), - #('texttable', '1.6.3', { - # 'checksums': ['ce0faf21aa77d806bbff22b107cc22cce68dc9438f97a2df32c93e9afa4ce436'], - #}), - #('python-igraph', '0.9.1', { - # 'modulename': 'igraph', - # 'checksums': ['f1895a83c57180f03c50fb77334a4d5029327aefee14f03381e10d34a1794410'], - #}), - #('leidenalg', '0.8.4', { - # 'build_cmd': "build --no-pkg-config", - # 'checksums': ['45764e0fc8829d23dee7698bd91d07c2027423d6309bd66b9711cdfecbcf8459'], - #}), (name, version, { 'checksums': ['ad5e7afdf1948753cd27f6f27ee904df1ce455855eec8520985effe86c53c630'], }), From 6c6195f8ca694d0546e0102c065609206263fc4c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 23 Apr 2021 17:23:30 +0100 Subject: [PATCH 0790/2365] Add missing libtool build dependency to leidenalg --- .../easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb index f0e29a156c..66efa3a2fc 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb @@ -15,6 +15,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ('PyYAML', '5.3.1'), ('Bison', '3.7.1'), + ('libtool', '2.4.6'), ] dependencies = [ From b833f763acc28e424f7b41749ded45b567558813 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Apr 2021 12:09:14 +0100 Subject: [PATCH 0791/2365] adding easyconfigs: Seaborn-0.11.1-foss-2020b.eb, Seaborn-0.11.1-fosscuda-2020b.eb --- .../s/Seaborn/Seaborn-0.11.1-foss-2020b.eb | 28 +++++++++++++++++++ .../Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb new file mode 100644 index 0000000000..5b326ff282 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.11.1' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..6f3585c583 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.11.1' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 931d77862b68b03cde8d48d9166e9dcfca0a4891 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Apr 2021 15:06:07 +0100 Subject: [PATCH 0792/2365] Boost is moving download location as bintray is closing --- easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 2 +- .../easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index 9445b5ae8b..6d96a0ef07 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] patches = ['Boost-%(version)s-library_version_type_serialization.patch'] checksums = [ diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb index b201695628..49052e5479 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'iccifort', 'version': '2020.4.304'} # add C++ compiler option as workaround for "error: no instance of constructor .* matches the argument list" errors toolchainopts = {'pic': True, 'extra_cxxflags': '-DBOOST_ASIO_USE_TS_EXECUTOR_AS_DEFAULT=1'} -source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] patches = ['Boost-%(version)s-library_version_type_serialization.patch'] checksums = [ From dc99e1ef829c24f49347e8a7ea0eded9d79555b6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Apr 2021 15:08:00 +0100 Subject: [PATCH 0793/2365] Boost.Python: Boost is moving download location as bintray is closing --- .../b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb index b9d56af993..ca9a6e5edc 100644 --- a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb @@ -10,7 +10,7 @@ description = """Boost.Python is a C++ library which enables seamless interopera toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] patches = ['Boost-1.71.0_fix-Python3.patch'] checksums = [ From 6f1d8ad90455a61066d60214980a59d75092f624 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 25 Apr 2021 23:31:37 +0200 Subject: [PATCH 0794/2365] remove acceptance of NVHPC EULA by default --- easybuild/easyconfigs/n/NVHPC/NVHPC-21.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.2.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.2.eb index 81a0d1f4af..628b83138b 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.2.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.2.eb @@ -9,8 +9,8 @@ description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK ( toolchain = SYSTEM -# By downloading, you accept the HPC SDK Software License Agreement (https://docs.nvidia.com/hpc-sdk/eula/index.html) -accept_eula = True +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] local_tarball_tmpl = 'nvhpc_2021_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' sources = [local_tarball_tmpl % '%(arch)s'] From eae3e541b1f6d3a712f5907d2c048d771ea9765f Mon Sep 17 00:00:00 2001 From: Loris Bennett Date: Mon, 26 Apr 2021 08:42:21 +0200 Subject: [PATCH 0795/2365] adding easyconfigs: RAxML-NG-1.0.2-gompi-2020b.eb, googletest-1.10.0-GCCcore-10.2.0.eb --- .../googletest-1.10.0-GCCcore-10.2.0.eb | 29 +++++++ .../r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb | 87 +++++++++++++++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.10.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.10.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.10.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ff55b9164e --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.10.0-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.10.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['9dc9157a9a1551ec7a7e43daea9a694a0bb5fb8bec81235d8a1e6ef64c716dcb'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb new file mode 100644 index 0000000000..905f6060de --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb @@ -0,0 +1,87 @@ +easyblock = 'CMakeMakeCp' + +name = 'RAxML-NG' +version = '1.0.2' + +local_terrap_commit = '8af2e4c838c82329adf14fa8df2c341b757378af' +local_pllmod_commit = '4fd9592f469cd481771b9c7e8c33e223bfc0dfc0' +local_libpll_commit = 'f946d906bef1ac0ccc4380eb11fbceebfb0ca1e7' + +homepage = "https://github.com/amkozlov/raxml-ng" +description = """RAxML-NG is a phylogenetic tree inference tool which +uses maximum-likelihood (ML) optimality criterion. Its search heuristic + is based on iteratively performing a series of Subtree Pruning and Regrafting + (SPR) moves, which allows to quickly navigate to the best-known ML tree.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +local_extract_lib = 'tar --strip-components=1 -C %%(builddir)s/raxml-ng-%%(version)s/libs/%s -xzf %%s' +sources = [ + { + 'source_urls': ['https://github.com/amkozlov/raxml-ng/archive/'], + 'filename': '%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/amkozlov/terraphast-one/archive/'], + 'download_filename': '%s.tar.gz' % local_terrap_commit, + 'filename': 'terraphist-one-%(version)s.tar.gz', + 'extract_cmd': local_extract_lib % 'terraphast', + }, + { + 'source_urls': ['https://github.com/ddarriba/pll-modules/archive/'], + 'download_filename': '%s.tar.gz' % local_pllmod_commit, + 'filename': 'pll-modules-%(version)s.tar.gz', + 'extract_cmd': local_extract_lib % 'pll-modules', + }, + { + 'source_urls': ['https://github.com/xflouris/libpll-2/archive/'], + 'download_filename': '%s.tar.gz' % local_libpll_commit, + 'filename': 'libpll-2-%(version)s.tar.gz', + 'extract_cmd': local_extract_lib % 'pll-modules/libs/libpll', + }, +] +checksums = [ + 'bf629280f5b76cfc017b9accafc22760de3797d367fb9c8a8a2ec630bcec23fa', # 1.0.2.tar.gz + 'c0590e62f5ffb8b11551abcee2b43fb9454dcece2c87763ebe0d104de2eb541d', # terraphist-one-1.0.2.tar.gz + '0cc5dbff2d0be777191191fb531f1ec86de08664130b2ff3556b6b7fc7a09ae5', # pll-modules-1.0.2.tar.gz + 'd6adf56989b460e9658715e8a093f7cec4249e96ed5664c709b80d0aecade5f3', # libpll-2-1.0.2.tar.gz +] + +dependencies = [ + ('GMP', '6.2.0'), +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('googletest', '1.10.0'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), +] + +configopts = '-DUSE_MPI=ON ' +configopts += '-DUSE_GMP=ON ' + +build_type = 'Release' + +separate_build_dir = True + +# too much parallellism makes the build fail with: +# No rule to make target 'localdeps/lib/libterraces.a'; +# see https://github.com/amkozlov/raxml-ng/issues/108 +maxparallel = 10 + +runtest = 'test' + +files_to_copy = [ + (["bin/raxml-ng-mpi"], "bin"), +] + +sanity_check_paths = { + 'files': ['bin/raxml-ng-mpi'], + 'dirs': [], +} + +sanity_check_commands = ['raxml-ng-mpi -h'] + +moduleclass = 'bio' From af5ce8c0fe515e3bebb1ddbc682c60a692e620c9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 26 Apr 2021 08:11:44 +0100 Subject: [PATCH 0796/2365] Remove obsolete Python versionsuffix --- .../p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1d62246901 --- /dev/null +++ b/easybuild/easyconfigs/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'Pylint' +version = '2.7.4' + +homepage = 'https://www.pylint.org/' +description = """Pylint is a tool that checks for errors in Python code, tries to enforce + a coding standard and looks for code smells. It can also look for certain type errors, + it can recommend suggestions about how particular blocks can be refactored and + can offer you details about the code's complexity.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True + +exts_list = [ + ('setuptools_scm', '6.0.1', { + 'checksums': ['d1925a69cb07e9b29416a275b9fadb009a23c148ace905b2fb220649a6c18e92'], + }), + ('lazy-object-proxy', '1.6.0', { + 'modulename': 'lazy_object_proxy', + 'checksums': ['489000d368377571c6f982fba6497f2aa13c6d1facc40660963da62f5c379726'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('astroid', '2.5.3', { + 'checksums': ['ad63b8552c70939568966811a088ef0bc880f99a24a00834abd0e3681b514f91'], + }), + ('isort', '5.8.0', { + 'checksums': ['0a943902919f65c5684ac4e0154b1ad4fac6dcaa5d9f3426b732f1c8b5419be6'], + }), + ('pytest-runner', '5.3.0', { + 'modulename': 'ptr', + 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], + }), + ('mccabe', '0.6.1', { + 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], + }), + ('pylint', version, { + 'checksums': ['bd38914c7731cdc518634a8d3c5585951302b6e2b6de60fbb3f7a0220e21eeee'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pylint'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From d1b9dacf8255153d063e85414744213150370956 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 26 Apr 2021 08:14:15 +0100 Subject: [PATCH 0797/2365] Update toolchain version --- .../t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ab14afd56f --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.60.0' + +homepage = "https://github.com/tqdm/tqdm" +description = """A fast, extensible progress bar for Python and CLI""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ebdebdb95e3477ceea267decfc0784859aa3df3e27e22d23b83e9b272bf157ae'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From 0b234444aaf64bd284697512facebd49343ef764 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 26 Apr 2021 11:18:17 +0200 Subject: [PATCH 0798/2365] Add patches for PyTorch 1.7.1 avoiding failures on POWER and A100 --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 6 ++++++ 2 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index d270180023..ed86594a72 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -239,6 +239,7 @@ patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -288,6 +289,8 @@ checksums = [ # PyTorch-1.7.0_increase-distributed-test-timeout.patch '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_run-large-tests-on-GPU.patch + '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', ] excluded_tests = { diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 2debc8f748..165024fb70 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -252,6 +252,8 @@ patches = [ 'PyTorch-1.7.1_complex32.patch', 'PyTorch-1.7.1_bypass-nan-compare.patch', 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', + 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -312,6 +314,10 @@ checksums = [ '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', + # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch + '18ecad081a8c940add64040ad9698d3273366acf738a8a44eab1c793d3f49950', + # PyTorch-1.7.1_run-large-tests-on-GPU.patch + '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', ] excluded_tests = { From b8c27703b455a0ee43e0e97490944d4e138a1d2c Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 26 Apr 2021 12:30:28 +0200 Subject: [PATCH 0799/2365] Delete imkl-2020.4.304-gompi-2020b.eb removing unnecessary easyconfig --- .../i/imkl/imkl-2020.4.304-gompi-2020b.eb | 39 ------------------- 1 file changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb deleted file mode 100644 index 1f70515297..0000000000 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb +++ /dev/null @@ -1,39 +0,0 @@ -# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ - -name = 'imkl' -version = '2020.4.304' - -homepage = 'https://software.intel.com/mkl' -description = """Intel Math Kernel Library is a library of highly optimized, - extensively threaded math routines for science, engineering, and financial - applications that require maximum performance. Core math functions include - BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" - -toolchain = {'name': 'gompi', 'version': '2020b'} - -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] -sources = ['l_mkl_%(version)s.tgz'] -checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] - -dontcreateinstalldir = True - -components = ['intel-mkl'] - -license_file = HOME + '/licenses/intel/license.lic' - -interfaces = True - -postinstallcmds = [ - # extract the examples - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', -] - -modextravars = { - 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', -} - -moduleclass = 'numlib' From c25978592a532cf9619ecfd2e76d19e766bbaef6 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 26 Apr 2021 14:00:56 +0200 Subject: [PATCH 0800/2365] Revert "Delete imkl-2020.4.304-gompi-2020b.eb" This reverts commit b8c27703b455a0ee43e0e97490944d4e138a1d2c. revert` --- .../i/imkl/imkl-2020.4.304-gompi-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb new file mode 100644 index 0000000000..1f70515297 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.4.304' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' From 7ea2601e120deb6edd2b2082bbc88caadc805045 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 26 Apr 2021 15:17:44 +0200 Subject: [PATCH 0801/2365] checksums --- easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb index 84c1c2001b..c880502720 100644 --- a/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s/'] sources = ['R-%(version)s.tar.gz'] +checksums = ['523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e'] dependencies = [ ('bzip2', '1.0.8'), From edd4da1e5ee6d389935258f1e0153342b046bc16 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 27 Apr 2021 09:32:24 +0100 Subject: [PATCH 0802/2365] adding easyconfigs: R-keras-2.4.0-foss-2020b-R-4.0.4.eb, R-keras-2.4.0-fosscuda-2020b-R-4.0.4.eb --- .../R-keras-2.4.0-foss-2020b-R-4.0.4.eb | 49 +++++++++++++++++++ .../R-keras-2.4.0-fosscuda-2020b-R-4.0.4.eb | 49 +++++++++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-keras/R-keras-2.4.0-foss-2020b-R-4.0.4.eb create mode 100644 easybuild/easyconfigs/r/R-keras/R-keras-2.4.0-fosscuda-2020b-R-4.0.4.eb diff --git a/easybuild/easyconfigs/r/R-keras/R-keras-2.4.0-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/R-keras/R-keras-2.4.0-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..02ccc3c146 --- /dev/null +++ b/easybuild/easyconfigs/r/R-keras/R-keras-2.4.0-foss-2020b-R-4.0.4.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'R-keras' +version = '2.4.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/keras' +description = """ Interface to 'Keras' , a high-level neural networks 'API'. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('R', '4.0.4'), + ('TensorFlow', '2.4.1'), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} +exts_list = [ + ('config', '0.3.1', { + 'checksums': ['d48878be8f47041e4ffeaa449dd1e5f48f6174a4592e465913e72b6cf6b95f50'], + }), + ('tfruns', '1.5.0', { + 'checksums': ['898a45a5e8420af1542919874a26cf8c00ae12638e6842197773b818de648e12'], + }), + ('tensorflow', version, { + 'checksums': ['670ec0f2bc5de97b0916b4989ec4748a978ac2ceed097c993df51c5733a7207c'], + }), + ('keras', version, { + 'checksums': ['ad1ee6d6e09b7884c2e6b173ba7b1193f81592126e99195643ad06d48a2b7c01'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['config', 'tfruns', 'tensorflow', 'keras'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R-keras/R-keras-2.4.0-fosscuda-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/R-keras/R-keras-2.4.0-fosscuda-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..124e5addf5 --- /dev/null +++ b/easybuild/easyconfigs/r/R-keras/R-keras-2.4.0-fosscuda-2020b-R-4.0.4.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'R-keras' +version = '2.4.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/keras' +description = """ Interface to 'Keras' , a high-level neural networks 'API'. """ + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('R', '4.0.4'), + ('TensorFlow', '2.4.1'), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} +exts_list = [ + ('config', '0.3.1', { + 'checksums': ['d48878be8f47041e4ffeaa449dd1e5f48f6174a4592e465913e72b6cf6b95f50'], + }), + ('tfruns', '1.5.0', { + 'checksums': ['898a45a5e8420af1542919874a26cf8c00ae12638e6842197773b818de648e12'], + }), + ('tensorflow', version, { + 'checksums': ['670ec0f2bc5de97b0916b4989ec4748a978ac2ceed097c993df51c5733a7207c'], + }), + ('keras', version, { + 'checksums': ['ad1ee6d6e09b7884c2e6b173ba7b1193f81592126e99195643ad06d48a2b7c01'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['config', 'tfruns', 'tensorflow', 'keras'], +} + +moduleclass = 'math' From 4e8033a8f1c297e7e209cf93393b02b9de5e7baa Mon Sep 17 00:00:00 2001 From: Loris Bennett Date: Tue, 27 Apr 2021 10:34:35 +0200 Subject: [PATCH 0803/2365] Replace incorrect checksums --- .../easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb index 905f6060de..b18fbb2c5f 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb @@ -43,8 +43,8 @@ sources = [ checksums = [ 'bf629280f5b76cfc017b9accafc22760de3797d367fb9c8a8a2ec630bcec23fa', # 1.0.2.tar.gz 'c0590e62f5ffb8b11551abcee2b43fb9454dcece2c87763ebe0d104de2eb541d', # terraphist-one-1.0.2.tar.gz - '0cc5dbff2d0be777191191fb531f1ec86de08664130b2ff3556b6b7fc7a09ae5', # pll-modules-1.0.2.tar.gz - 'd6adf56989b460e9658715e8a093f7cec4249e96ed5664c709b80d0aecade5f3', # libpll-2-1.0.2.tar.gz + '64f58ed77d074818505cf032c3509482c2e00ba0636990131e05f8a148e1a3a9', # pll-modules-1.0.2.tar.gz + '0d9d93fb5057048ed966a30bf8e1de84def2fd25decc45e01094722c4dd92d48', # libpll-2-1.0.2.tar.gz ] dependencies = [ From 400e8e1ba9bd941a35b212a0aa8ee41a2cf6163f Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 27 Apr 2021 14:35:18 +0200 Subject: [PATCH 0804/2365] Update imkl-2020.4.304-gompi-2020b.eb correcting src for imkl --- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb index 1f70515297..d292d071b1 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] From e0232c6d3ceec03d7db20f1675fc5133d77a421f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 27 Apr 2021 16:50:15 +0200 Subject: [PATCH 0805/2365] adding easyconfigs: WannierTools-2.5.1-intel-2020b.eb and patches: WannierTools-2.5.1_fix_Makefile.patch --- .../WannierTools-2.5.1-intel-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb b/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb new file mode 100644 index 0000000000..ae59e3579f --- /dev/null +++ b/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'WannierTools' +version = '2.5.1' + +homepage = 'http://www.wanniertools.com' +description = """WannierTools is an open source software that studies the physical properties of given tight-binding model.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/quanshengwu/wannier_tools/archive'] +sources = ['V%(version)s.tar.gz'] +patches = ['WannierTools-2.5.1_fix_Makefile.patch'] +checksums = [ + '22aad8e95f2da07ac2dd892c2ca0438010779e6cc542e30f34ea5c3f580fd72c', # V2.5.1.tar.gz + '1752319cad40fc258c5b9753baa9db4ca1c5a4d931234164d66212c7ba92f7cb', # WannierTools-2.5.1_fix_Makefile.patch +] + +skipsteps = ['configure'] + +prebuildopts = 'cd src && ' +preinstallopts = prebuildopts + +# use -cpp -fallow-argument-mismatch -ffree-line-length-512 for GNU based compilers +# use -fpp for Intel based compilers +# We use the same Makefile regardless of toolchain due to the Makefile patch +buildopts = '-f Makefile.intel-mpi F90FLAGS="$F90FLAGS -fpp -DMPI" ' +installopts = '-f Makefile.intel-mpi PREFIX=%(installdir)s ' + +# No dependecies in the Makefile +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/wt.x'], + 'dirs': [] +} + +moduleclass = 'chem' From f4f21dd9879c03e103fe2dd2a0aae787df6d29d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Apr 2021 17:40:26 +0200 Subject: [PATCH 0806/2365] adding easyconfigs: gpustat-0.6.0-gcccuda-2020b.eb --- .../g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb new file mode 100644 index 0000000000..8734993b43 --- /dev/null +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'gpustat' +version = '0.6.0' + +homepage = 'https://github.com/wookayin/gpustat' +description = 'dstat-like utilization monitor for NVIDIA GPUs' + +toolchain = {'name': 'gcccuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True + +exts_list = [ + ('psutil', '5.8.0', { + 'checksums': ['0c9ccb99ab76025f2f0bbecf341d4656e9c1351db8cc8a03ccd62e318ab4b5c6'], + }), + ('blessings', '1.7', { + 'checksums': ['98e5854d805f50a5b58ac2333411b0482516a8210f23f43308baeb58d77c157d'], + }), + ('nvidia-ml-py3', '7.352.0', { + 'modulename': 'pynvml', + 'checksums': ['390f02919ee9d73fe63a98c73101061a6b37fa694a793abf56673320f1f51277'], + }), + (name, version, { + 'checksums': ['f69135080b2668b662822633312c2180002c10111597af9631bb02e042755b6c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gpustat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gpustat --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From 43d68354a9b35f7ab4f641c90268aa2af672adab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Apr 2021 18:38:58 +0200 Subject: [PATCH 0807/2365] adding easyconfigs: minimap2-2.18-GCCcore-10.2.0.eb --- .../minimap2/minimap2-2.18-GCCcore-10.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9f7b208cc9 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.18' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['7a55101d58ecaec545db51079ad82b214632dc697ee67290b6dc34cc70dbeeb4'] + +builddependencies = [('binutils', '2.35')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = ["minimap2 --help"] + +moduleclass = 'bio' From 63ebe88e5438d64f62911da31049395fdfafb9b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Apr 2021 19:01:05 +0200 Subject: [PATCH 0808/2365] adding easyconfigs: python-parasail-1.2.4-fosscuda-2020b.eb, parasail-2.4.3-GCC-10.2.0.eb --- .../p/parasail/parasail-2.4.3-GCC-10.2.0.eb | 27 ++++++++++++++++ .../python-parasail-1.2.4-fosscuda-2020b.eb | 32 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..9ad845641f --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.4.3' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +# https://github.com/jeffdaily/parasail +github_account = 'jeffdaily' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6f0cddcaaf7c00573e62a3b081a09380cb022b2ed6a3a138108f8823775ca026'] + +builddependencies = [('CMake', '3.18.4')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..0f02c50779 --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.2.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'] + +builddependencies = [ + ('parasail', '2.4.3'), +] +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' From b1d8d4d999d270682423a121777ddd727175f43d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Apr 2021 20:26:24 +0200 Subject: [PATCH 0809/2365] {bio}[fosscuda/2020b] Bonito v0.3.8, apex v20210420 w/ Python 3.8.6 --- .../a/apex/apex-20210420-fosscuda-2020b.eb | 33 +++++ .../b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb | 117 ++++++++++++++++++ 2 files changed, 150 insertions(+) create mode 100644 easybuild/easyconfigs/a/apex/apex-20210420-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/apex/apex-20210420-fosscuda-2020b.eb b/easybuild/easyconfigs/a/apex/apex-20210420-fosscuda-2020b.eb new file mode 100644 index 0000000000..9507c3802d --- /dev/null +++ b/easybuild/easyconfigs/a/apex/apex-20210420-fosscuda-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'apex' +local_commit = '082f999' +version = '20210420' + +homepage = 'https://github.com/nvidia/apex' +description = "A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/NVIDIA/apex/archive/'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'download_filename': '%s.tar.gz' % local_commit, +}] +checksums = ['a4a82b14ca95ec2068e85fdce5188d03c8eda92ac90a16bec46cd7e5e1534a53'] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', '1.7.1'), +] + +download_dep_fail = True +use_pip = True + +installopts = "--no-cache-dir --global-option='--cpp_ext' --global-option='--cuda_ext' --global-option='--pyprof'" + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from apex import amp'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb new file mode 100644 index 0000000000..b677ee8f20 --- /dev/null +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb @@ -0,0 +1,117 @@ +easyblock = 'PythonBundle' + +name = 'Bonito' +version = '0.3.8' + +homepage = 'https://github.com/nanoporetech/bonito' +description = "Convolution Basecaller for Oxford Nanopore Reads" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('h5py', '3.1.0'), + ('Mako', '1.1.3'), + ('PyYAML', '5.3.1'), + ('python-parasail', '1.2.4'), + ('tqdm', '4.56.2'), + ('apex', '20210420'), + ('minimap2', '2.18'), + ('CuPy', '8.5.0'), +] + +use_pip = True + +exts_list = [ + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('alembic', '1.5.8', { + 'checksums': ['e27fd67732c97a1c370c33169ef4578cf96436fa0e7dcfaeeef4a917d0737d56'], + }), + ('cmd2', '1.5.0', { + 'checksums': ['701a8c9975c4abc45e5d13906ab149f959f812869106347323a3f89ac0e82a62'], + }), + ('prettytable', '2.1.0', { + 'checksums': ['5882ed9092b391bb8f6e91f59bcdbd748924ff556bb7c634089d5519be87baa0'], + }), + ('cliff', '3.7.0', { + 'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ", + 'checksums': ['389c81960de13f05daf1cbd546f33199e86c518ba4266c79ec7a153a280980ea'], + }), + ('colorlog', '5.0.1', { + 'checksums': ['f17c013a06962b02f4449ee07cfdbe6b287df29efc2c9a1515b4a376f4e588ea'], + }), + ('greenlet', '1.0.0', { + 'checksums': ['719e169c79255816cdcf6dccd9ed2d089a72a9f6c42273aae12d55e8d35bdcf8'], + }), + ('SQLAlchemy', '1.4.11', { + 'checksums': ['4ad4044eb86fbcbdff2106e44f479fbdac703d77860b3e19988c8a8786e73061'], + }), + ('cmaes', '0.8.2', { + 'checksums': ['1c04ba23ded925ef13b96f42cfbd667a905ea5b80754c750e6448b9fcda96a5d'], + }), + ('optuna', '2.7.0', { + 'checksums': ['eb1595108ec444e840deb0037351074144fecb7a4eff6870fc11569ab782cfc6'], + }), + ('colorama', '0.4.4', { + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('importlib_metadata', '4.0.1', { + 'checksums': ['8c501196e49fb9df5df43833bdb1e4328f64847763ec8a50703148b73784d581'], + }), + ('stevedore', '3.3.0', { + 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], + }), + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '3.3.0', { + 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], + }), + ('fast-ctc-decode', '0.3.0', { + 'source_tmpl': 'fast_ctc_decode-%(version)s-cp38-cp38-manylinux2010_x86_64.whl', + 'unpack_sources': False, + 'checksums': ['623d83f8de5e02199a09bfe0160a1e477f0db8d4ab612b26a7e42c2a335b378c'], + }), + ('mappy', '2.18', { + 'checksums': ['18fffdb4b831cc3f5399b919b0942c640bf9a943ca22102ac446f53af3b905a8'], + }), + ('seqdist', '0.0.3', { + 'preinstallopts': "sed -i 's/cupy-cuda102//g' settings.ini && sed -i 's/[<>=]=[0-9].*//g' settings.ini && ", + 'checksums': ['bdbbea6ebba1c6dd6698d46e23ba7858f93a7cdf0c7cbc2ea66660291acb044f'], + }), + ('crf-beam', '0.0.1a0', { + 'modulename': 'kbeam', + 'sources': ['crf_beam-%(version)s-cp38-cp38-manylinux1_x86_64.whl'], + 'unpack_sources': False, + 'checksums': ['0cba80ff4d7f90595f498921cf904736e3bce558dba80de5611874d89e72312e'], + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'preinstallopts': "sed -i 's/[><=]=.*//g' requirements.txt && export PATH=%(installdir)s/bin:$PATH && ", + 'checksums': ['f18ec073c841bb0ccfe9049530df370ab0fb19931614e8ba37316acaa58639a1'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bonito'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bonito --help", + "bonito convert --help", + "bonito download --help", +] + +moduleclass = 'bio' From ba17e3aac055c41676b759b1b67cfbacc8dec244 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 27 Apr 2021 16:43:50 -0700 Subject: [PATCH 0810/2365] update hypothesis-6.7.0 --- .../hypothesis-6.7.0-GCCcore-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cf62caebaa --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '6.7.0' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a62eedc72630575f4c3f38e288a4bbc29ffdf91267bbadc0ba969c786ede1d70'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 18fa79a00b0237f772d5a66567dccc4f7ec8cb22 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 27 Apr 2021 18:08:46 -0700 Subject: [PATCH 0811/2365] {bio}[GCCcore/10.2.0] TagDust 2.33 --- .../t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..003fb9008b --- /dev/null +++ b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +# easybuild easyconfig +# +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +# John Dey +# +easyblock = 'ConfigureMake' + +name = 'TagDust' +version = '2.33' + +homepage = 'http://tagdust.sourceforge.net/' +description = """Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, + linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the + sequences to be mapped in downstream pipelines.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://sourceforge.net/projects/tagdust/files'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_extern.patch'] +checksums = [ + '8825e2975eae11e19033f233b5951517b5126bd19e049a500b1e048eaa215f84', # tagdust-2.33.tar.gz + 'dd8f861d0b6307d1f020f57a080fcefb683ac79916cad484c429df950c223524', # TagDust-2.33_extern.patch +] + +parallel = 1 + +builddependencies = [ + ('binutils', '2.35'), + ('Pandoc', '2.10', '', True), +] + +sanity_check_paths = { + 'dirs': [], + 'files': ['bin/tagdust'], +} + +sanity_check_commands = [('%(namelower)s', '--version')] +moduleclass = 'bio' From 6e941cdc296f56ae371bc2b12b42e8fa52f3035b Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 28 Apr 2021 10:00:23 +0200 Subject: [PATCH 0812/2365] OpenPGM pc file includes non-existent directory --- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb index d79856789c..239dad0b1c 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb @@ -20,7 +20,11 @@ toolchainopts = {'pic': True} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] +patches = ['OpenPGM-5.2.122-pkgconfig_includes.patch'] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch +] builddependencies = [ ('binutils', '2.35'), From 3fa5b4447f516b07e14d404107a9dd79fa1854ff Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 28 Apr 2021 10:30:29 +0200 Subject: [PATCH 0813/2365] Only update the latest versions with new patches --- .../o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb index 239dad0b1c..c5c3f86e07 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb @@ -20,15 +20,19 @@ toolchainopts = {'pic': True} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -patches = ['OpenPGM-5.2.122-pkgconfig_includes.patch'] +patches = [ + 'OpenPGM-5.2.122-pkgconfig_includes.patch', + 'OpenPGM-5.2.122-python3-compliant.patch' +] checksums = [ '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch ] builddependencies = [ ('binutils', '2.35'), - ('Python', '2.7.18'), + ('Python', '3.8.6'), ] start_dir = 'pgm' From d38b0706ecee1e30e51dfaebc258150850fa39da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Apr 2021 12:42:09 +0200 Subject: [PATCH 0814/2365] {numlib}[iimpi/2020.12] imkl v2021.1.1 --- easybuild/easyconfigs/i/iimpi/iimpi-2020.12.eb | 18 ++++++++++++++++++ .../i/imkl/imkl-2021.1.1-iimpi-2020.12.eb | 14 ++++++++++++++ 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2020.12.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2020.12.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2020.12.eb new file mode 100644 index 0000000000..9cf9d3045b --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2020.12.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2020.12' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_compver = '2021.1.2' +dependencies = [ + ('intel-compilers', local_compver), + ('impi', '2021.1.1', '', ('intel-compilers', local_compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb new file mode 100644 index 0000000000..737f7462d7 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb @@ -0,0 +1,14 @@ +name = 'imkl' +version = '2021.1.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2020.12'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17402/'] +sources = ['l_onemkl_p_%(version)s.52_offline.sh'] +checksums = ['818b6bd9a6c116f4578cda3151da0612ec9c3ce8b2c8a64730d625ce5b13cc0c'] + +moduleclass = 'numlib' From fbb0fc11ae60d8eacf6cecd66c85062f521822a0 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 28 Apr 2021 13:47:43 +0200 Subject: [PATCH 0815/2365] Disable tests failing with CUDA 11.2 driver --- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 165024fb70..0c835eba9d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -254,6 +254,7 @@ patches = [ 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', + 'PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -318,6 +319,8 @@ checksums = [ '18ecad081a8c940add64040ad9698d3273366acf738a8a44eab1c793d3f49950', # PyTorch-1.7.1_run-large-tests-on-GPU.patch '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', + # PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch + '752383efed8ac170acc77b5f3665b921f25af54aa965dbe3ad6f7df53f30778a', ] excluded_tests = { From cd921652fe00bbe1d80b66eb72ae9323209254d9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 28 Apr 2021 14:29:57 +0200 Subject: [PATCH 0816/2365] Disable tests failing with CUDA 11.2 driver - 3 --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 0c835eba9d..edcfaedf1c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -320,7 +320,7 @@ checksums = [ # PyTorch-1.7.1_run-large-tests-on-GPU.patch '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', # PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch - '752383efed8ac170acc77b5f3665b921f25af54aa965dbe3ad6f7df53f30778a', + '2a9df4face04798f51eee0db83d28a905ea7ac53569cf25ed9f049b0a547702e', ] excluded_tests = { From 189e99a139b587e38bb495d2d6a9b3f03221b81f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Apr 2021 14:31:41 +0200 Subject: [PATCH 0817/2365] fix moduleclass for impi 2021.1.2 easyconfig, should be 'mpi' --- .../i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb index 9f36c8608a..e94d38ae26 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb @@ -11,4 +11,4 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/1739 sources = ['l_mpi_oneapi_p_%(version)s.76_offline.sh'] checksums = ['8b7693a156c6fc6269637bef586a8fd3ea6610cac2aae4e7f48c1fbb601625fe'] -moduleclass = 'compiler' +moduleclass = 'mpi' From db2959e893525cc2cd7b7ba7d9b7b255b1745699 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 28 Apr 2021 12:45:31 +0000 Subject: [PATCH 0818/2365] adding easyconfigs: OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb --- .../OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb new file mode 100644 index 0000000000..0762e17f6c --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb @@ -0,0 +1,28 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.7' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 05d0bd2a47ffa556e3c522b78805120db7400195 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Wed, 28 Apr 2021 16:45:27 +0200 Subject: [PATCH 0819/2365] adding easyconfigs: magma-2.5.4-intelcuda-2020b.eb --- .../m/magma/magma-2.5.4-intelcuda-2020b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.5.4-intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.4-intelcuda-2020b.eb b/easybuild/easyconfigs/m/magma/magma-2.5.4-intelcuda-2020b.eb new file mode 100644 index 0000000000..8fe0d955a9 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.5.4-intelcuda-2020b.eb @@ -0,0 +1,37 @@ +easyblock = "CMakeMake" + +name = 'magma' +version = '2.5.4' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = ['magma-2.5.4_allow-all-sms.patch'] +checksums = [ + '7734fb417ae0c367b418dea15096aef2e278a423e527c615aab47f0683683b67', # magma-2.5.4.tar.gz + '4e47ecc080ff761866f179c9b383b8930e4daa2fcee1c2a48db585fc50531561', # magma-2.5.4_allow-all-sms.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0'] +# make sure both static and shared libs are built +configopts = [ + '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') +] + +sanity_check_paths = { + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From ff104e9b9fcac6d958f7319cf194a94aaffd0f97 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 28 Apr 2021 15:16:04 +0000 Subject: [PATCH 0820/2365] adding easyconfigs: librsb-1.2.0.9-GCC-10.2.0.eb --- .../l/librsb/librsb-1.2.0.9-GCC-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsb/librsb-1.2.0.9-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.2.0.9-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.2.0.9-GCC-10.2.0.eb new file mode 100644 index 0000000000..1e66ae9aa3 --- /dev/null +++ b/easybuild/easyconfigs/l/librsb/librsb-1.2.0.9-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'librsb' +version = '1.2.0.9' + +homepage = 'https://sourceforge.net/projects/librsb/' +description = """A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f421f5d572461601120933e3c1cfee2ca69e6ecc92cbb11baa4e86bdedd3d9fa'] + +dependencies = [ + ('zlib', '1.2.11') +] + +configopts = '--enable-openmp --enable-fortran-module-install' + +sanity_check_paths = { + 'files': ['bin/rsbench', 'lib/librsb.a', 'lib/librsb.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From c6fd59f8e395c65c6d799d3d45f1cfb83a00b3ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Apr 2021 21:10:56 +0200 Subject: [PATCH 0821/2365] remove psutil extension from easyconfig for gpustat 0.6.0 w/ gcccuda/2020b, already available through Python --- easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb index 8734993b43..aa1e4ba5b7 100644 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb @@ -15,9 +15,6 @@ dependencies = [ use_pip = True exts_list = [ - ('psutil', '5.8.0', { - 'checksums': ['0c9ccb99ab76025f2f0bbecf341d4656e9c1351db8cc8a03ccd62e318ab4b5c6'], - }), ('blessings', '1.7', { 'checksums': ['98e5854d805f50a5b58ac2333411b0482516a8210f23f43308baeb58d77c157d'], }), From cc7ab5dbe5e49d33b00091d01193d06fb63c12f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Apr 2021 21:20:30 +0200 Subject: [PATCH 0822/2365] adding easyconfigs: ABINIT-9.4.1-intel-2020b.eb --- .../a/ABINIT/ABINIT-9.4.1-intel-2020b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb new file mode 100644 index 0000000000..943b370cb5 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.4.1' + +homepage = 'https://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ec74133ef9d247cb6ad44c205675694919cf36d7f1682a9b85cae8bdecdc22a8'] + +builddependencies = [ + ('Python', '3.8.6'), +] +dependencies = [ + ('libxc', '4.3.4'), + ('netCDF-Fortran', '4.5.3'), + ('Wannier90', '3.1.0'), +] + +# Ensure MPI with intel wrappers. +configopts = '--with-mpi="yes" --enable-openmp="no" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# BLAS/Lapack from MKL +configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4. +configopts += 'with_netcdf="${EBROOTNETCDF}" ' +configopts += 'with_netcdf_fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += 'with_hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From 4189e56adc99c70ba76f3b1203081a37d3d10ad7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Apr 2021 09:01:03 +0200 Subject: [PATCH 0823/2365] remove 'unpack_sources = False' from recent easyconfigs that use a *.whl file as source --- easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb index ce0683e82d..d5a6b4d2ec 100644 --- a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb @@ -17,8 +17,6 @@ builddependencies = [ dependencies = [('Python', '3.8.6')] -unpack_sources = False - download_dep_fail = True use_pip = True From c5c049c6ab855059b7fffc43a238d94ead8a5f73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Apr 2021 09:33:14 +0200 Subject: [PATCH 0824/2365] also remove setting unpack_sources to False in recent easyconfigs that do so for specific extensions --- .../tensorflow-probability-0.12.1-foss-2020b.eb | 1 - .../tensorflow-probability-0.12.1-fosscuda-2020b.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb index 021eaa0106..a33fbf38cd 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb @@ -34,7 +34,6 @@ exts_list = [ 'modulename': 'tensorflow_probability', 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/probability/archive/'], - 'unpack_sources': False, 'checksums': ['1fe89e85fd053bf36e8645a5a1a53b729bc254cf1516bc224fcbd1e4ff50083a'], }), ] diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb index 3bd4385f27..28b222eb33 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb @@ -34,7 +34,6 @@ exts_list = [ 'modulename': 'tensorflow_probability', 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/probability/archive/'], - 'unpack_sources': False, 'checksums': ['1fe89e85fd053bf36e8645a5a1a53b729bc254cf1516bc224fcbd1e4ff50083a'], }), ] From 0c0ef1fa8ffb00e457e56b7c2d9fae50045cecac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85ke=20Sandgren?= Date: Thu, 29 Apr 2021 10:34:15 +0200 Subject: [PATCH 0825/2365] Update easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb Fix too long line. Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../w/WannierTools/WannierTools-2.5.1-intel-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb b/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb index ae59e3579f..64d7016da8 100644 --- a/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb @@ -4,7 +4,8 @@ name = 'WannierTools' version = '2.5.1' homepage = 'http://www.wanniertools.com' -description = """WannierTools is an open source software that studies the physical properties of given tight-binding model.""" +description = """WannierTools is an open source software that studies the physical properties of given tight-binding + model.""" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'usempi': True} From 9dc4853c0ca0b98254edc23a943fa3d73b33a64b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 30 Apr 2021 11:59:26 +0200 Subject: [PATCH 0826/2365] wget has a build dep on Perl --- easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb index c878ea314f..b553d12489 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb @@ -17,6 +17,7 @@ checksums = ['31cccfc6630528db1c8e3a06f6decf2a370060b982841cfab2b8677400a5092e'] builddependencies = [ ('binutils', '2.35'), ('pkg-config', '0.29.2'), + ('Perl', '5.32.0'), ] dependencies = [ ('PCRE', '8.44'), From 4936e2086ff59d9059fe82000b693236e7e036f0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 30 Apr 2021 13:07:08 +0200 Subject: [PATCH 0827/2365] adding easyconfigs: Kraken2-2.1.1-gompi-2020b.eb and patches: Kraken2-2.1.1_fix_installation_for_easybuild.patch --- .../k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb new file mode 100644 index 0000000000..f24d9c3b21 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'Kraken2' +version = '2.1.1' + +homepage = 'https://github.com/DerrickWood/kraken2/wiki' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# part is compiled with $CXX, the rest is in Perl +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['Kraken2-2.1.1_fix_installation_for_easybuild.patch'] +checksums = [ + '8f3e928cdb32b9e8e6f55b44703d1557b2a5fc3f30f63e8d16e465e19a81dee4', # v2.1.1.tar.gz + # Kraken2-2.1.1_fix_installation_for_easybuild.patch + '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11', +] + +dependencies = [ + ('Perl', '5.32.0'), + ('BLAST+', '2.11.0'), + ('wget', '1.20.3'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken2.sh %(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh', + 'build_db', 'build_gg_taxonomy.pl', 'build_kraken2_db.sh', 'build_rdp_taxonomy.pl', 'build_silva_taxonomy.pl', + 'classify', 'clean_db.sh', 'cp_into_tempfile.pl', 'download_genomic_library.sh', 'download_taxonomy.sh', + 'dump_table', 'estimate_capacity', 'kraken2', 'kraken2-build', 'kraken2-inspect', 'kraken2lib.pm', + 'lookup_accession_numbers.pl', 'make_seqid2taxid_map.pl', 'mask_low_complexity.sh', 'rsync_from_ncbi.pl', + 'scan_fasta_file.pl']], + 'dirs': [], +} + +moduleclass = 'bio' From 8041d7f4abacaacec756fbf53f1ce04bd6a97d49 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 30 Apr 2021 12:30:30 +0100 Subject: [PATCH 0828/2365] Add dependency on plotly.py, Seaborn easyconfigs Remove plotly, retrying and Seaborn from exts_list --- .../c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index e848444349..9fcb4e7cfd 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -20,8 +20,10 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('PyTorch', '1.7.1'), ('numba', '0.52.0'), + ('plotly', '4.14.3'), ('scikit-learn', '0.23.2'), ('matplotlib', '3.3.3'), + ('Seaborn', '0.11.1'), ] use_pip = True @@ -31,12 +33,6 @@ exts_list = [ ('colorlover', '0.3.0', { 'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'], }), - ('retrying', '1.3.3', { - 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], - }), - ('plotly', '4.14.3', { - 'checksums': ['7d8aaeed392e82fb8e0e48899f2d3d957b12327f9d38cdd5802bc574a8a39d91'], - }), ('cufflinks', '0.17.3', { 'checksums': ['48c1b3406dc030004121966489eebc5518cea70fd4e3f16379b491328501a644'], }), @@ -47,9 +43,6 @@ exts_list = [ 'checksums': ['3e3e5e526109866012a9da79f423c922edc379c6cac9bf65ea08fbb9dd93ff3a'], 'modulename': 'umap', }), - ('seaborn', '0.11.1', { - 'checksums': ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'], - }), (name.lower(), version, { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/zhonge/cryodrgn/archive'], From 06132c543a824b829acbca19f40b798f4b80e8fa Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 30 Apr 2021 12:32:56 +0100 Subject: [PATCH 0829/2365] Replace sanity_check_paths with sanity_check_commands --- .../easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index 9fcb4e7cfd..d44a539af4 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -50,9 +50,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} +sanity_check_commands = ["%(namelower)s --help"] moduleclass = 'chem' From 707d938ff404e508b4a5b67aec107085678a303f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 30 Apr 2021 13:56:26 +0100 Subject: [PATCH 0830/2365] Fix dependency name plotly -> plotly.py --- .../easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index d44a539af4..5d9c5f8d47 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -20,7 +20,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('PyTorch', '1.7.1'), ('numba', '0.52.0'), - ('plotly', '4.14.3'), + ('plotly.py', '4.14.3'), ('scikit-learn', '0.23.2'), ('matplotlib', '3.3.3'), ('Seaborn', '0.11.1'), From e63f722e727b198adedda19c03cc71be8e022a34 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 30 Apr 2021 17:04:47 +0200 Subject: [PATCH 0831/2365] adding easyconfigs: pysheds-0.2.7.1-foss-2020b.eb, pyproj-3.0.1-GCCcore-10.2.0.eb, rasterio-1.2.3-foss-2020b.eb --- .../p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb | 37 ++++++++++ .../p/pysheds/pysheds-0.2.7.1-foss-2020b.eb | 35 +++++++++ .../r/rasterio/rasterio-1.2.3-foss-2020b.eb | 71 +++++++++++++++++++ 3 files changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..55cfb0d3a0 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.0.1' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['bfbac35490dd17f706700673506eeb8170f8a2a63fb5878171d4e6eef242d141'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('PROJ', '7.2.1'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb new file mode 100644 index 0000000000..88589c72da --- /dev/null +++ b/easybuild/easyconfigs/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'pysheds' +version = '0.2.7.1' + +homepage = 'https://mattbartos.com/pysheds/' +description = "Simple and fast watershed delineation in python." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-image', '0.18.1'), + ('pyproj', '3.0.1'), + ('rasterio', '1.2.3'), +] + +use_pip = True + +# the latest pypi version of pysheds is currently behind the github one at 0.2.7 +exts_list = [ + ('geojson', '2.5.0', { + 'checksums': ['6e4bb7ace4226a45d9c8c8b1348b3fc43540658359f93c3f7e03efa9f15f658a'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/mdbartos/pysheds/archive/'], + 'checksums': ['1f086931b71af7a0770f38840a4ff61606a984da7246dd9bbc1143467ee9639d'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb b/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb new file mode 100644 index 0000000000..4416762b19 --- /dev/null +++ b/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'rasterio' +version = '1.2.3' + +homepage = 'https://github.com/mapbox/rasterio' +description = "Rasterio reads and writes geospatial raster data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('matplotlib', '3.3.3'), + ('GDAL', '3.2.1'), +] + +use_pip = True + +exts_list = [ + ('affine', '2.3.0', { + 'checksums': ['2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102'], + }), + ('attrs', '20.3.0', { + 'modulename': 'attr', + 'checksums': ['832aa3cde19744e49938b91fea06d69ecb9e649c93ba974535d08ad92164f700'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('botocore', '1.20.61', { + 'checksums': ['c765ddd0648e32b375ced8b82bfcc3f8437107278b2d2c73b7da7f41297b5388'], + }), + ('s3transfer', '0.4.2', { + 'checksums': ['cb022f4b16551edebbb31a377d3f09600dbada7363d8c5db7976e7f47732e1b2'], + }), + ('boto3', '1.17.61', { + 'checksums': ['35b099fa55f5db6e99a92855b9f320736121ae985340adfc73bc46fb443809e9'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('cligj', '0.7.1', { + 'checksums': ['b2f1f7247d59a5387bd3013a08b9ed6829e96fafa4a6e6292341efdb46fe6220'], + }), + ('snuggs', '1.4.7', { + 'checksums': ['501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b'], + }), + (name, version, { + 'checksums': ['d8c345e01052b70ac3bbbe100c83def813c0ab19f7412c2c98e553d03720c1c5'], + }), +] + +fix_python_shebang_for = ['bin/jp.py', 'bin/rio'] + +sanity_check_paths = { + 'files': ['bin/rio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "jp.py --help", + "rio --help", +] + +sanity_pip_check = True + +moduleclass = 'geo' From 1fa0e5cebb7e704d266c4b7b00553a83ae731437 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 30 Apr 2021 20:23:36 +0200 Subject: [PATCH 0832/2365] adding easyconfigs: Bowtie-1.3.0-GCC-10.2.0.eb --- .../b/Bowtie/Bowtie-1.3.0-GCC-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..8b2978402e --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.0-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Artistic v2.0 +# +# Notes:: +## + +name = 'Bowtie' +version = '1.3.0' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.zip'] +checksums = ['04e04d5f9a4a8cdee1fe58512588e95a173cf8395cf7d42136ecc76c1b8cab85'] + +dependencies = [ + ('tbb', '2020.3'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' From 1ee8489e021e06352e3d1dc801b747d572360346 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 30 Apr 2021 20:55:20 +0200 Subject: [PATCH 0833/2365] remove redundant extensions from rasterio --- .../easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb b/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb index 4416762b19..1589973f77 100644 --- a/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb @@ -21,10 +21,6 @@ exts_list = [ ('affine', '2.3.0', { 'checksums': ['2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102'], }), - ('attrs', '20.3.0', { - 'modulename': 'attr', - 'checksums': ['832aa3cde19744e49938b91fea06d69ecb9e649c93ba974535d08ad92164f700'], - }), ('jmespath', '0.10.0', { 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], }), @@ -37,9 +33,6 @@ exts_list = [ ('boto3', '1.17.61', { 'checksums': ['35b099fa55f5db6e99a92855b9f320736121ae985340adfc73bc46fb443809e9'], }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), ('click-plugins', '1.1.1', { 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], }), From 9b1bb1704782970b31dfdfb668b5d1500a2bfc13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 May 2021 09:46:08 +0200 Subject: [PATCH 0834/2365] adding easyconfigs: FastANI-1.33-GCC-10.2.0.eb, FastANI-1.33-iccifort-2020.4.304.eb --- .../f/FastANI/FastANI-1.33-GCC-10.2.0.eb | 45 +++++++++++++++++++ .../FastANI-1.33-iccifort-2020.4.304.eb | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.33-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-10.2.0.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-10.2.0.eb new file mode 100644 index 0000000000..63f4cc6433 --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-10.2.0.eb @@ -0,0 +1,45 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.33' + +homepage = "https://github.com/ParBLiSS/FastANI" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['FastANI-1.2-memcpy.patch'] +checksums = [ + 'fb392ffa3c7942091a06de05c56c8e250523723c39da65ae8f245e65e440a74b', # v1.33.zip + 'eebcf0b64c31ee360ca79136f644157064ac69747ed13cff70f5c9932c6bb0d5', # FastANI-1.2-memcpy.patch +] + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('GSL', '2.6'), + ('zlib', '1.2.11'), +] + +preconfigopts = 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': [] +} + +sanity_check_commands = ["fastANI --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.33-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..6fa29aa6ab --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-iccifort-2020.4.304.eb @@ -0,0 +1,45 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.33' + +homepage = "https://github.com/ParBLiSS/FastANI" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['FastANI-1.2-memcpy.patch'] +checksums = [ + 'fb392ffa3c7942091a06de05c56c8e250523723c39da65ae8f245e65e440a74b', # v1.33.zip + 'eebcf0b64c31ee360ca79136f644157064ac69747ed13cff70f5c9932c6bb0d5', # FastANI-1.2-memcpy.patch +] + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('GSL', '2.6'), + ('zlib', '1.2.11'), +] + +preconfigopts = 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': [] +} + +sanity_check_commands = ["fastANI --help"] + +moduleclass = 'bio' From 7a4ce4b4c86d85569ada912e86244ebef83976b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 May 2021 09:49:21 +0200 Subject: [PATCH 0835/2365] {bio}[intel/2020b] GTDB-Tk v1.5.0, HMMER v3.3.2, FastTree v2.1.11 w/ Python 3.8.6 --- .../FastTree-2.1.11-GCCcore-10.2.0.eb | 37 ++++++++++ .../g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb | 43 ++++++++++++ .../h/HMMER/HMMER-3.3.2-iimpi-2020b.eb | 68 +++++++++++++++++++ 3 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..598549d530 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = ['%(name)s-%(version)s.c'] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['source'] + +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb new file mode 100644 index 0000000000..0ff0be7b62 --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'GTDB-Tk' +version = '1.5.0' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/g/gtdbtk'] +sources = ['gtdbtk-%(version)s.tar.gz'] +checksums = ['3251b5c2ac1f6b904f4a57fd07a77302988d98d5f2a1cbe7b8232c7652dcfd0c'] + +dependencies = [ + ('Python', '3.8.6'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.3.3'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.56.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb new file mode 100644 index 0000000000..ea00c7b7ec --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb @@ -0,0 +1,68 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] + +builddependencies = [('Python', '3.8.6')] + +configopts = '--enable-mpi' + +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From 4600ac015777a1805f4c5a6860d2bb0468c5b7d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 2 May 2021 12:20:30 +0200 Subject: [PATCH 0836/2365] stick to gompi/iimpi toolchain for NetPIPE 5.1.4 --- .../n/NetPIPE/NetPIPE-5.1.4-gompi-2020b.eb | 41 +++++++++++++++++++ .../n/NetPIPE/NetPIPE-5.1.4-iimpi-2020b.eb | 41 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1.4-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1.4-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1.4-gompi-2020b.eb b/easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1.4-gompi-2020b.eb new file mode 100644 index 0000000000..fa9aaae018 --- /dev/null +++ b/easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1.4-gompi-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'NetPIPE' +version = '5.1.4' + +homepage = 'https://netpipe.cs.ksu.edu/' +description = """NetPIPE is a protocol independent communication performance benchmark that visually represents + the network performance under a variety of conditions.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://netpipe.cs.ksu.edu/download/'] +sources = ['NetPIPE-%(version)s.tar.gz'] +checksums = ['738abeb9665877332d4b0cada2f15f766259809d0e31a29e327bfbf86b7e0183'] + +local_common_buildopts = 'CC="$CC" CFLAGS="$CFLAGS -lrt -fcommon"' + +# possible values: disk, ibverbs, memcpy, mpi, shmem, tcp, theo +# shmem requires shmem.h (must be provided by OS?) +buildopts = [ + 'disk ' + local_common_buildopts, + 'ibverbs ' + local_common_buildopts, + 'memcpy ' + local_common_buildopts, + 'mpi ' + local_common_buildopts, + 'tcp ' + local_common_buildopts, + 'theo ' + local_common_buildopts, +] + +files_to_copy = [(['NP*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/NPdisk', 'bin/NPibverbs', 'bin/NPmemcpy', 'bin/NPmpi', 'bin/NPtcp', 'bin/NPtheo'], + 'dirs': [], +} + +sanity_check_commands = [ + "NPmpi --help", + "NPtcp --help", +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1.4-iimpi-2020b.eb b/easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1.4-iimpi-2020b.eb new file mode 100644 index 0000000000..73fab7b548 --- /dev/null +++ b/easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1.4-iimpi-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'NetPIPE' +version = '5.1.4' + +homepage = 'https://netpipe.cs.ksu.edu/' +description = """NetPIPE is a protocol independent communication performance benchmark that visually represents + the network performance under a variety of conditions.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} + +source_urls = ['https://netpipe.cs.ksu.edu/download/'] +sources = ['NetPIPE-%(version)s.tar.gz'] +checksums = ['738abeb9665877332d4b0cada2f15f766259809d0e31a29e327bfbf86b7e0183'] + +local_common_buildopts = 'CC="$CC" CFLAGS="$CFLAGS -lrt"' + +# possible values: disk, ibverbs, memcpy, mpi, shmem, tcp, theo +# shmem requires shmem.h (must be provided by OS?) +buildopts = [ + 'disk ' + local_common_buildopts, + 'ibverbs ' + local_common_buildopts, + 'memcpy ' + local_common_buildopts, + 'mpi ' + local_common_buildopts, + 'tcp ' + local_common_buildopts, + 'theo ' + local_common_buildopts, +] + +files_to_copy = [(['NP*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/NPdisk', 'bin/NPibverbs', 'bin/NPmemcpy', 'bin/NPmpi', 'bin/NPtcp', 'bin/NPtheo'], + 'dirs': [], +} + +sanity_check_commands = [ + "NPmpi --help", + "NPtcp --help", +] + +moduleclass = 'perf' From 14e61f2692ded222a97d4161141c3d0b3b2eae3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 2 May 2021 12:25:57 +0200 Subject: [PATCH 0837/2365] switch to PythonPackage easyblock for QUAST, since simplejson extension is included with Python dependency --- .../QUAST-5.0.2-foss-2020b-Python-2.7.18.eb | 22 ++++++++----------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb index e7f2fc926b..58f9709a65 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'QUAST' version = '5.0.2' @@ -12,6 +12,10 @@ assemblies, thus is suitable for comparison.""" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True} +source_urls = ['https://github.com/ablab/quast/archive/'] +sources = ['quast_%(version)s.tar.gz'] +checksums = ['9f30c03e0bfd261492fe6b72fb07645bdee5b29d741f75fc75857b6fa095d91d'] + dependencies = [ ('Python', '2.7.18'), ('Perl', '5.32.0'), @@ -20,23 +24,15 @@ dependencies = [ ('Boost', '1.74.0'), ] +download_dep_fail = True use_pip = True -exts_list = [ - ('simplejson', '3.17.2', { - 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], - }), - (name, version, { - 'install_target': 'install_full', - 'modulename': 'quast_libs', - 'source_tmpl': 'quast_%(version)s.tar.gz', - 'source_urls': ['https://github.com/ablab/quast/archive/'], - 'checksums': ['9f30c03e0bfd261492fe6b72fb07645bdee5b29d741f75fc75857b6fa095d91d'], - }), -] +install_target = 'install_full' postinstallcmds = ["cd %(installdir)s/bin && ln -s quast.py quast"] +options = {'modulename': 'quast_libs'} + sanity_check_paths = { 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 57641c7b325eac0b9ed3142e6c5dc7b1e973efa5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 2 May 2021 15:39:02 +0200 Subject: [PATCH 0838/2365] {geo}[intel/2020b] xESMF v0.3.0 (+ dependencies) w/ Python 3.8.6 --- .../e/ESMF/ESMF-8.0.1-intel-2020b.eb | 31 +++++++++++++++++ .../e/ESMPy/ESMPy-8.0.1-intel-2020b.eb | 34 +++++++++++++++++++ .../netCDF-C++4-4.3.1-iimpi-2020b.eb | 25 ++++++++++++++ .../x/xESMF/xESMF-0.3.0-intel-2020b.eb | 26 ++++++++++++++ 4 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020b.eb create mode 100644 easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-intel-2020b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-intel-2020b.eb new file mode 100644 index 0000000000..dccfd612ef --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.1-intel-2020b.eb @@ -0,0 +1,31 @@ +name = 'ESMF' +version = '8.0.1' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['%%(name)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '9172fb73f3fe95c8188d889ee72fdadb4f978b1d969e1d8e401e8d106def1d84', # ESMF_8_0_1.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +dependencies = [ + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('netCDF-C++4', '4.3.1'), +] + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb b/easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb new file mode 100644 index 0000000000..b9da3e2f02 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'ESMPy' +version = '8.0.1' + +homepage = 'https://earthsystemmodeling.org/esmpy' +description = "Earth System Modeling Framework (ESMF) Python Interface" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['ESMF_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['9172fb73f3fe95c8188d889ee72fdadb4f978b1d969e1d8e401e8d106def1d84'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy, mpi4py + ('ESMF', version), +] + +start_dir = 'src/addon/ESMPy' + +download_dep_fail = True + +# ESMPy's setup.py script doesn't support using "pip install" +use_pip = False + +buildopts = "--ESMFMKFILE=$EBROOTESMF/lib/esmf.mk" + +options = {'modulename': 'ESMF'} + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020b.eb new file mode 100644 index 0000000000..8ca2e42891 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.7.4')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-intel-2020b.eb b/easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-intel-2020b.eb new file mode 100644 index 0000000000..6777e058f4 --- /dev/null +++ b/easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-intel-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'xESMF' +version = '0.3.0' + +homepage = 'https://xesmf.readthedocs.io' +description = "xESMF: Universal Regridder for Geospatial Data" + +toolchain = {'name': 'intel', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['66b6deb37f43749df06819fc2003bbd394207617cf7d8fd9dafe655d7af7b94c'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy, scipy + ('ESMPy', '8.0.1'), + ('xarray', '0.16.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'geo' From 102279b8f483ef6b247067a0b1bf0fc898da73dc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 3 May 2021 14:32:23 +0200 Subject: [PATCH 0839/2365] Use install_pip and clean up changes done by inject-checksum --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 11 ++++--- .../p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 30 +++++++------------ 2 files changed, 16 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index c343b9d7ea..591c3feab6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -28,6 +28,8 @@ dependencies = [ osdependencies = [OS_PKG_OPENSSL_DEV] +install_pip = True + exts_default_options = { 'download_dep_fail': True, 'sanity_pip_check': True, @@ -38,19 +40,16 @@ exts_default_options = { # order is important! # package versions updated 13 October 2020, to the most recent versions still supporting Python 2.x exts_list = [ - ('pip', '20.3.4', { - 'pip_ignore_installed': False, - 'source_tmpl': SOURCE_WHL, - 'checksums': ['217ae5161a0e08c0fb873858806e3478c9775caffce5168b50ec885e358c199d'], - }), ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], - 'pip_ignore_installed': False, }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], }), + ('pip', '20.3.4', { + 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], + }), ('nose', '1.3.7', { 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index ed6f449a50..74d7a4c702 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -34,9 +34,7 @@ dependencies = [ osdependencies = [OS_PKG_OPENSSL_DEV] -# symlink 'pip' command to 'pip3' that is included with Python installation -# required so we can update pip to version included in extensions, using pip -installopts = " && ln -s %(installdir)s/bin/pip3 %(installdir)s/bin/pip" +install_pip = True exts_default_options = { 'download_dep_fail': True, @@ -49,19 +47,16 @@ exts_default_options = { # order is important! # package versions updated 13 October 2020 exts_list = [ - ('pip', '20.2.3', { - 'pip_ignore_installed': False, - 'source_tmpl': SOURCE_WHL, - 'checksums': ['0f35d63b7245205f4060efe1982f5ea2196aa6e5b26c07669adcf800e2542026'], - }), ('setuptools', '50.3.0', { 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['39060a59d91cf5cf403fa3bacbb52df4205a8c3585e0b9ba4b30e0e19d4c4b18'], - 'pip_ignore_installed': False, }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], }), + ('pip', '20.2.3', { + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), ('nose', '1.3.7', { 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), @@ -333,10 +328,6 @@ exts_list = [ ('intreehooks', '1.0', { 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], }), - ('crashtest', '0.3.1', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], - }), ('pylev', '1.3.0', { 'checksums': ['063910098161199b81e453025653ec53556c1be7165a9b7c50be2f4d57eae1c3'], }), @@ -348,10 +339,6 @@ exts_list = [ 'source_tmpl': SOURCE_WHL, 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], }), - ('jeepney', '0.4.3', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['d6c6b49683446d2407d2fe3acb7a368a77ff063f9182fe427da15d622adc24cf'], - }), ('SecretStorage', '3.1.2', { 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], }), @@ -408,8 +395,7 @@ exts_list = [ 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], }), ('ptyprocess', '0.6.0', { - 'source_tmpl': SOURCE_WHL, - 'checksums': ['d7cc528d76e76342423ca640335bd3633420dc1366f258cb31d05e865ef5ca1f'], + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], }), ('lockfile', '0.12.2', { 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], @@ -421,6 +407,12 @@ exts_list = [ ('poetry', '1.1.3', { 'checksums': ['49eae89e2c44b0323214d0bbcefc21ebe3a19baa44db98eefabd4db9e82c7253'], }), + ('crashtest', '0.3.1', { + 'checksums': ['42ca7b6ce88b6c7433e2ce47ea884e91ec93104a4b754998be498a8e6c3d37dd'], + }), + ('jeepney', '0.4.3', { + 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], + }), ('fsspec', '0.8.4', { 'checksums': ['e1e494d4814f6804769f3c7bfd7a722a15113cc0339d14755297f09306b8f21f'], }), From 562548ea633fb5381e3a6e44178f782859a931a0 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 3 May 2021 15:16:52 +0200 Subject: [PATCH 0840/2365] Exclude test_nn (failing on A100) --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index edcfaedf1c..03f193e6e4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -330,6 +330,8 @@ excluded_tests = { # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! # https://github.com/pytorch/pytorch/issues/43209 'test_quantization', + # Fails with A100 cards due to precision issues: https://github.com/pytorch/pytorch/issues/52278 + 'test_nn', ] } From 182ed17226ae6273f56729005b6e7861c03608a2 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 3 May 2021 16:51:43 +0200 Subject: [PATCH 0841/2365] add missing Pandoc dependency for DROP 1.0.3 --- easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb index 6361cbff22..83694e1330 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -23,6 +23,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix ('SAMtools', '1.11'), ('BCFtools', '1.11'), + ('Pandoc', '2.13', '', True), ] # added ext_postinstallcmds to pandoc: import fails if pandoc/definitions dir is not installed From 98a80ec54b7b50d7c34b5411b825e34229dfb366 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 3 May 2021 18:12:40 +0200 Subject: [PATCH 0842/2365] adding easyconfigs: Gurobi-9.0.3-GCCcore-10.2.0.eb, Gurobi-9.0.3.eb, Gurobi-9.1.2-GCCcore-10.2.0.eb, Gurobi-9.1.2.eb and patches: Gurobi-9.0.1_use-eb-python-gurobi-shell.patch --- .../g/Gurobi/Gurobi-9.0.3-GCCcore-10.2.0.eb | 37 +++++++++++++++++++ .../g/Gurobi/Gurobi-9.1.2-GCCcore-10.2.0.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d0177b1ef1 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +name = 'Gurobi' +version = '9.0.3' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch'] +checksums = [ + '4dfdb5fb1ca3bed5a230dd74b9da45d86abae934e6781d14dcfbc97c1c47dc2f', # gurobi9.0.3_linux64.tar.gz + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01', # Gurobi-9.0.1_use-eb-python-gurobi-shell.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +license_file = HOME + '/licenses/%(name)s.lic' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c505ea66ee --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +name = 'Gurobi' +version = '9.1.2' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch'] +checksums = [ + '7f60bd675f79476bb2b32cd632aa1d470f8246f2b033b7652d8de86f6e7e429b', # gurobi9.1.2_linux64.tar.gz + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01', # Gurobi-9.0.1_use-eb-python-gurobi-shell.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +license_file = HOME + '/licenses/%(name)s.lic' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' From a01c55e1bc8d4fca1a8c5a494a2f98b8fb74d4d2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 3 May 2021 18:16:41 +0200 Subject: [PATCH 0843/2365] patch gurobi shell in Gurobi-9.1.1-GCCcore-10.2.0.eb --- .../easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb index 9e05e99db0..4c39fc6168 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] sources = ['%(namelower)s%(version)s_linux64.tar.gz'] -checksums = ['ba57a83656bf6ab481e1114f5596664385a88a35a47ae51aa2ac307f58aaa44a'] +patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch'] +checksums = [ + 'ba57a83656bf6ab481e1114f5596664385a88a35a47ae51aa2ac307f58aaa44a', # gurobi9.1.1_linux64.tar.gz + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01', # Gurobi-9.0.1_use-eb-python-gurobi-shell.patch +] builddependencies = [ ('binutils', '2.35'), @@ -21,8 +25,6 @@ dependencies = [ ('Python', '3.8.6'), ] -sanity_check_commands = ["gurobi_cl --help"] - license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' moduleclass = 'math' From 2c7a6063f4b58e72288ef039328ec759a5fa84df Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 3 May 2021 18:18:28 +0200 Subject: [PATCH 0844/2365] remove bundled python in Gurobi-9.1.1-GCCcore-10.2.0.eb --- .../easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb index 4c39fc6168..890b1c101c 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb @@ -25,6 +25,13 @@ dependencies = [ ('Python', '3.8.6'), ] +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + moduleclass = 'math' From 2b627511d7997ebc3943624a598733436af88b92 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 May 2021 19:10:06 +0200 Subject: [PATCH 0845/2365] adding easyconfigs: loompy-3.0.6-intel-2020b.eb --- .../l/loompy/loompy-3.0.6-intel-2020b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb new file mode 100644 index 0000000000..bd5b98eef7 --- /dev/null +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'loompy' +version = '3.0.6' + +homepage = 'https://loompy.org/' +description = "Python implementation of the Loom file format, an efficient file format for large omics datasets" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('numba', '0.52.0'), +] + +use_pip = True + +exts_list = [ + ('numpy_groupies', '0.9.13', { + 'checksums': ['7b17b291322353f07c51598512d077e3731da0a048cfa8f738f3460d1ef0658d'], + }), + (name, version, { + 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], + }), +] + +sanity_check_paths = { + 'files': ['bin/loompy'], + 'dirs': ['lib/python3.8/site-packages'], +} + +sanity_check_commands = ["loompy --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From a3e1fc1c388d2f5ae081f5fae2cb72c94b9b770a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 3 May 2021 21:31:20 +0200 Subject: [PATCH 0846/2365] Update easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb --- easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb index bd5b98eef7..64f5e58792 100644 --- a/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb @@ -28,7 +28,7 @@ exts_list = [ sanity_check_paths = { 'files': ['bin/loompy'], - 'dirs': ['lib/python3.8/site-packages'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = ["loompy --help"] From c8c6fafe08f288237a65f4b217e75c233c2d1cf8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 3 May 2021 20:36:43 +0100 Subject: [PATCH 0847/2365] remove unneeded PYPI_LOWER_SOURCE --- easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb index e991128da6..44daa4b563 100644 --- a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb @@ -9,7 +9,6 @@ cellular electrophysiology.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['393ebc85413bd1b573909736caeadd9d7757f41cceb7bd29f3b30f5107237cba'] From be4de94dd3ea2a43a076b5cbd1b966c6a53bfec0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 May 2021 09:36:48 +0200 Subject: [PATCH 0848/2365] don't skip source step in FastTree easyconfig --- .../f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb index 598549d530..149902edb0 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb @@ -18,14 +18,12 @@ toolchainopts = {'openmp': True} # HTTPS cert error: # hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... source_urls = ['http://www.microbesonline.org/fasttree/'] -sources = ['%(name)s-%(version)s.c'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] builddependencies = [('binutils', '2.35')] -skipsteps = ['source'] - -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] From 817e9907e6218d259ecc43a3416f9000e3507b68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 May 2021 09:51:15 +0200 Subject: [PATCH 0849/2365] add trivial sanity check command to FastTree easyconfig --- .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb index 149902edb0..f3c470d682 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb @@ -32,4 +32,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['FastTree'] + moduleclass = 'bio' From bf065f69b481f68e8785815338e7def0f1d52954 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 May 2021 10:00:52 +0200 Subject: [PATCH 0850/2365] check output of FastTree sanity check command via stderr --- .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb index f3c470d682..11318dc50b 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb @@ -32,6 +32,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ['FastTree'] +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] moduleclass = 'bio' From cdb336b57bf3d77af76a59b3891308ea2a7cfbc9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 4 May 2021 10:45:52 +0200 Subject: [PATCH 0851/2365] Exclude test_nn on POWER --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index ed86594a72..ae12b291b7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -294,6 +294,10 @@ checksums = [ ] excluded_tests = { + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/57533 + 'test_nn', + ], '': [ # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', From 5e14acb3aba32706bfd126f73e8adf42adac8665 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 4 May 2021 11:23:18 +0100 Subject: [PATCH 0852/2365] adding easyconfigs: scikit-allel-1.3.2-foss-2020b.eb, zarr-2.8.1-foss-2020b.eb, bcolz-1.2.1-foss-2020b.eb --- .../b/bcolz/bcolz-1.2.1-foss-2020b.eb | 45 +++++++++++++++++++ .../scikit-allel-1.3.2-foss-2020b.eb | 32 +++++++++++++ .../z/zarr/zarr-2.8.1-foss-2020b.eb | 41 +++++++++++++++++ 3 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/z/zarr/zarr-2.8.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb b/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb new file mode 100644 index 0000000000..405d6aad61 --- /dev/null +++ b/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = "PythonPackage" + +name = 'bcolz' +version = '1.2.1' + +homepage = 'https://bcolz.blosc.org/en/latest/' +description = """bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. + Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. + It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, + but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_fix-deprecation.patch', +] +checksums = [ + 'c017d09bb0cb5bbb07f2ae223a3f3638285be3b574cb328e91525b2880300bd1', # bcolz-1.2.1.tar.gz + '90e3525c3254ab0c6b45a170423b8a4a17764fc27fa47ff45ff8465169375d35', # bcolz-1.2.1_fix-deprecation.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('Blosc', '1.21.0'), + ('dask', '2021.2.0'), + ('SciPy-bundle', '2020.11'), + ('PyTables', '3.6.1'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "BLOSC_DIR=$EBROOTBLOSC" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["python -c 'import bcolz; bcolz.test()'"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb new file mode 100644 index 0000000000..ed61424ed7 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'scikit-allel' +version = '1.3.2' + +homepage = 'https://scikit-allel.readthedocs.io/en/latest/' +description = """This package provides utilities for exploratory analysis of large scale genetic variation data. + It is based on numpy, scipy and other general-purpose Python scientific libraries.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['fcb2932038033557fa2ccdf485b54eea3d8a06a2b0a5692a3dc1130b21bb301a'] + +dependencies = [ + ('Python', '3.8.6'), + ('Seaborn', '0.11.1'), + ('h5py', '3.1.0'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('dask', '2021.2.0'), + ('bcolz', '1.2.1'), + ('zarr', '2.8.1'), +] + +use_pip = True + +options = {'modulename': 'allel'} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.8.1-foss-2020b.eb b/easybuild/easyconfigs/z/zarr/zarr-2.8.1-foss-2020b.eb new file mode 100644 index 0000000000..31ce9c5cb0 --- /dev/null +++ b/easybuild/easyconfigs/z/zarr/zarr-2.8.1-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = "PythonBundle" + +name = 'zarr' +version = '2.8.1' + +homepage = 'https://zarr.readthedocs.io/en/stable/' +description = """Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, + designed for use in parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +exts_list = [ + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('fasteners', '0.16', { + 'checksums': ['c995d8c26b017c5d6a6de9ad29a0f9cdd57de61ae1113d28fac26622b06a0933'], + }), + ('monotonic', '1.6', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/atdt/monotonic/archive'], + 'checksums': ['9609c249aed584fd714811014870650d08d6f6414402b5a190663c49bf83b221'], + }), + ('numcodecs', '0.7.3', { + 'checksums': ['022b12ad83eb623ec53f154859d49f6ec43b15c36052fa864eaf2d9ee786dd85'], + }), + (name, version, { + 'checksums': ['138e5f64bbaf7aece6da1f229b611a7a04742e15358dde49c6e9bae8404a3bf2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 3d10a20cd58b709f6a77be59a88e1ad0442ff040 Mon Sep 17 00:00:00 2001 From: jfgrimm <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 4 May 2021 12:07:47 +0100 Subject: [PATCH 0853/2365] Update scikit-allel-1.3.2-foss-2020b.eb add download_dep_fail to scikit-allel --- .../easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb index ed61424ed7..092fe559f0 100644 --- a/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb @@ -23,6 +23,7 @@ dependencies = [ ('zarr', '2.8.1'), ] +download_dep_fail = True use_pip = True options = {'modulename': 'allel'} From 62aa985aeb66b6c44f8cd8a1f30d91aae8853915 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 May 2021 14:29:51 +0200 Subject: [PATCH 0854/2365] add versionsuffix to Pandoc 2.13 to indicate target architecture + use %(arch)s Pandoc dependency for DROP --- easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb index 83694e1330..87ce950277 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -23,7 +23,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix ('SAMtools', '1.11'), ('BCFtools', '1.11'), - ('Pandoc', '2.13', '', True), + ('Pandoc', '2.13', '-%(arch)s', True), ] # added ext_postinstallcmds to pandoc: import fails if pandoc/definitions dir is not installed From db78b1022f4e4658b7c149fb2e41be5eeb496d7a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 May 2021 15:25:26 +0200 Subject: [PATCH 0855/2365] also use patch for DMCfun extension in easyconfig for R 4.0.4 with fosscuda/2020b --- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index dc0233f242..b1828ac9b6 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2841,7 +2841,12 @@ exts_list = [ 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], }), ('DMCfun', '1.3.0', { - 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], + 'patches': ['DMCfun-1.3.0_fix-parallel-detect.patch'], + 'checksums': [ + '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz + # DMCfun-1.3.0_fix-parallel-detect.patch + '96cccbe650dfab5619e3b6e782062ab72e9f1038ddf05b439dd097e1d8a59a79', + ], }), ('miceadds', '3.11-6', { 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], From 7f602a11a4b7b158a2c947478c48997b9dac6a4d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Wed, 5 May 2021 10:51:59 +0200 Subject: [PATCH 0856/2365] Fix missing parenthesis --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 768a7781eb..6aff6f9491 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2805,7 +2805,7 @@ exts_list = [ 'checksums': [ '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz # DMCfun-1.3.0_fix-parallel-detect.patch - '96cccbe650dfab5619e3b6e782062ab72e9f1038ddf05b439dd097e1d8a59a79', + '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', ], }), ('miceadds', '3.11-6', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 7e29daee9e..30ea18f1da 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2815,7 +2815,7 @@ exts_list = [ 'checksums': [ '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz # DMCfun-1.3.0_fix-parallel-detect.patch - '96cccbe650dfab5619e3b6e782062ab72e9f1038ddf05b439dd097e1d8a59a79', + '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', ], }), ('miceadds', '3.11-6', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 61087d5b2b..c6f63d1be4 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2840,7 +2840,7 @@ exts_list = [ 'checksums': [ '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz # DMCfun-1.3.0_fix-parallel-detect.patch - '96cccbe650dfab5619e3b6e782062ab72e9f1038ddf05b439dd097e1d8a59a79', + '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', ], }), ('miceadds', '3.11-6', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index b1828ac9b6..18c8d8a60e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2845,7 +2845,7 @@ exts_list = [ 'checksums': [ '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz # DMCfun-1.3.0_fix-parallel-detect.patch - '96cccbe650dfab5619e3b6e782062ab72e9f1038ddf05b439dd097e1d8a59a79', + '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', ], }), ('miceadds', '3.11-6', { From 0771d31e192e1c1269ccb3b35ca492384151acbe Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 May 2021 10:57:02 +0200 Subject: [PATCH 0857/2365] Exclude test_utils on POWER because test_bottleneck fails when run in EasyBuild --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index ae12b291b7..439cb3cbc5 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -297,6 +297,8 @@ excluded_tests = { 'POWER': [ # https://github.com/pytorch/pytorch/issues/57533 'test_nn', + # Fails for unknown reasons when run within EB but not when run manually + 'test_utils', ], '': [ # Test from this suite timeout often. The process group backend is deprecated anyway From 4f93fdf09cfc813b7c3f0f0911ccfdebdfbd6826 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 5 May 2021 16:51:54 +0200 Subject: [PATCH 0858/2365] adding easyconfigs: XlsxWriter-1.4.0-GCCcore-10.2.0.eb --- .../XlsxWriter-1.4.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..eb57ec2b02 --- /dev/null +++ b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'XlsxWriter' +version = '1.4.0' + +homepage = 'https://xlsxwriter.readthedocs.io/' +description = "A Python module for creating Excel XLSX files" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['82be5a58c09bdc2ff8afc25acc815c465275239ddfc56d6e7b2a7e6c5d2e213b'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/vba_extract.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['vba_extract.py --help'] + +sanity_pip_check = True + +moduleclass = 'tools' From ce1b56733b8fd818ca92348d710e3f2923b21482 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 5 May 2021 17:15:03 +0100 Subject: [PATCH 0859/2365] Add lassosum extension to R/4.0.3, R/4.0.4 --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 25 +++++++++---------- .../easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 5 ++++ .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 5 ++++ .../easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 5 ++++ 4 files changed, 27 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 6aff6f9491..e0d8f6aea9 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -1694,7 +1694,7 @@ exts_list = [ 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], 'checksums': [ 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz - '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch ], }), ('diveRsity', '1.9.90', { @@ -2169,13 +2169,12 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.1', { 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], @@ -2289,8 +2288,7 @@ exts_list = [ 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], }), ('rda', '1.0.2-2.1', { - 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', - 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], }), ('sampling', '2.8', { 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], @@ -2386,9 +2384,9 @@ exts_list = [ 'checksums': ['a0282a054d0e6ab310ec7edcffa953b77c7e4a858d9ac7028aab1b4fb4ce8cf3'], }), ('V8', '3.4.0', { - 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], - 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], }), ('rstan', '2.21.2', { 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], @@ -2651,13 +2649,9 @@ exts_list = [ 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), ('gWidgets2tcltk', '1.0-6', { - 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... 'modulename': False, + 'preinstallopts': "xvfb-run ", + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], }), ('mgsub', '1.7.2', { 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], @@ -2826,6 +2820,11 @@ exts_list = [ ('image.binarization', '0.1.1', { 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 30ea18f1da..fbed579c88 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2843,6 +2843,11 @@ exts_list = [ ('RViennaCL', '1.7.1.8', { 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index c6f63d1be4..4f78e77a11 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2861,6 +2861,11 @@ exts_list = [ ('image.binarization', '0.1.1', { 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 18c8d8a60e..5a91968ee9 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2873,6 +2873,11 @@ exts_list = [ ('RViennaCL', '1.7.1.8', { 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), ] moduleclass = 'lang' From 99158c895676da35eeebfaab5eb95829c5b8bac5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 5 May 2021 17:22:28 +0100 Subject: [PATCH 0860/2365] Add GenABEL to R-bundle-Bioconductor --- .../R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index 3c687feedc..3edd386e47 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -1014,6 +1014,12 @@ exts_list = [ ('FRASER', '1.2.1', { 'checksums': ['37562b7e92fd95feb950f160b38427f23a9e31729fa0783b441fc74fc45f7120'], }), + ('GenABEL', '1.8-0', { + 'checksums': ['434fc806b918738ec67171a37a47099d1706332819317e368fe0ccb8f149a469'], + }), + ('GenABEL.data', '1.0.0', { + 'checksums': ['2c28d5df63ae13545cf7aea6ce5f22ae1bbb58219fdaed6c1d5d5affc072c65c'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From b85edbe3be2bae29deee5df6226b554c6a1ec1d8 Mon Sep 17 00:00:00 2001 From: spottho1 Date: Wed, 5 May 2021 20:37:20 +0200 Subject: [PATCH 0861/2365] Latest availble EC is for v1.3.0 and foss/2018b. Don't know if something changed that makes it obsolete, but it was requested at our site - so here we are. --- .../gdc-client-1.6.0-GCCcore-10.2.0.eb | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f41142ccf5 --- /dev/null +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,85 @@ +easyblock = 'PythonBundle' + +name = 'gdc-client' +version = '1.6.0' + +homepage = 'https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool' +description = """The gdc-client provides several convenience functions over + the GDC API which provides general download/upload via HTTPS.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + + +dependencies = [ + ('Python', '3.8.6'), + ('libxslt', '1.1.34'), + ('libyaml', '0.2.5'), +] + +exts_defaultclass = 'PythonPackage' +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_list = [ + ('cryptography', '2.8', { + 'checksums': ['3cda1f0ed8747339bbdf71b9f38ca74c7b592f24f65cdb3ab3765e4b02871651'], + }), + ('jsonschema', '2.6.0', { + 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], + }), + ('lxml', '4.4.2', { + 'checksums': ['eff69ddbf3ad86375c344339371168640951c302450c5d3e9936e98d6459db06'], + }), + ('ndg-httpsclient', '0.5.0', { + 'modulename': 'ndg', + 'source_tmpl': 'ndg_httpsclient-%(version)s.tar.gz', + 'checksums': ['c009f5430790936b3a97eaf9f968516664d97e146ab2bda991f0caadb7cc088b'], + }), + ('pyasn1', '0.4.3', { + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), + ('pyOpenSSL', '18.0.0', { + 'modulename': 'OpenSSL', + 'checksums': ['6488f1423b00f73b7ad5167885312bb0ce410d3312eb212393795b53c8caa580'], + }), + ('PyYAML', '3.13', { + 'modulename': 'yaml', + 'checksums': ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'], + }), + ('intervaltree', '3.0.2', { + 'checksums': ['cb4f61c81dcb4fea6c09903f3599015a83c9bdad1f0bbd232495e6681e19e273'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('idna', '2.8', { + 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], + }), + ('requests', '2.22.0', { + 'checksums': ['11e007a8a2aa0323f5a921e9e6a2d7e4e67d9877e85773fba9ba6419025cbeb4'], + }), + ('python-utils', '2.5.6', { + 'modulename': 'python_utils', + 'checksums': ['352d5b1febeebf9b3cdb9f3c87a3b26ef22d3c9e274a8ec1e7048ecd2fac4349'], + }), + ('progressbar2', '3.43.1', { + 'modulename': 'progressbar', + 'checksums': ['87a403d2f80f6e48b7b55559feae5c75b903941f55189b22207b574fe5e62276'], + }), + (name, version, { + 'modulename': 'gdc_client', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/NCI-GDC/gdc-client/archive'], + 'checksums': ['491da966d344b144233d828c82175871803f270ce35c9fd81bc03e48859c0d82'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/gdc-client'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From df081850566dc800cf5e5e9f027f2e755cdb6cd3 Mon Sep 17 00:00:00 2001 From: spottho1 Date: Wed, 5 May 2021 20:53:09 +0200 Subject: [PATCH 0862/2365] remove download_dep_fail --- .../easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb index f41142ccf5..a28d27aed6 100644 --- a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb @@ -19,7 +19,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('cryptography', '2.8', { From 43757c47ce56ce018b6cfc926838100e8185a768 Mon Sep 17 00:00:00 2001 From: spottho1 Date: Wed, 5 May 2021 21:07:59 +0200 Subject: [PATCH 0863/2365] add binutils to builddependencies --- .../easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb index a28d27aed6..14bff7b300 100644 --- a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb @@ -9,6 +9,7 @@ description = """The gdc-client provides several convenience functions over toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '3.8.6'), From aa877324ab4808b3402171f1a8e3218c6e60a251 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 6 May 2021 10:02:44 +0200 Subject: [PATCH 0864/2365] adding easyconfigs: dm-reverb-0.2.0-foss-2020b.eb and patches: dm-reverb-0.2.0_eb-build-environment.patch --- .../d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb new file mode 100644 index 0000000000..ff68784fc6 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb @@ -0,0 +1,38 @@ +name = 'dm-reverb' +version = '0.2.0' + +homepage = 'https://github.com/deepmind/reverb' +description = """ +Reverb is an efficient and easy-to-use data storage and transport system +designed for machine learning research. Reverb is primarily used as an +experience replay system for distributed reinforcement learning algorithms but +the system also supports multiple data structure representations such as FIFO, +LIFO, and priority queues.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/deepmind/reverb/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_eb-build-environment.patch'] +checksums = [ + '6bbb136afd3abadc0f825eff7aedcd05609bb292ab54fe21e31001e30f3e7cbc', # v0.2.0.tar.gz + '7b4b6a26de157cf7bffaf1d680b020fe192f33a6127aadddaefc380eaa1fb109', # dm-reverb-0.2.0_eb-build-environment.patch +] + +builddependencies = [ + ('Bazel', '3.7.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('TensorFlow', '2.4.1'), +] + +# Bundled upb sets -Werror, failing on any warning. Disable for harmless warnings +buildopts = "--copt='-Wno-error=stringop-truncation'" + +sanity_pip_check = True + +options = {'modulename': 'reverb'} + +moduleclass = 'lib' From f6f1e5d38eea349b365141fcd6aee7e18d942452 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 6 May 2021 10:33:09 +0200 Subject: [PATCH 0865/2365] adding easyconfigs: ccache-4.2.1.eb --- .../easyconfigs/c/ccache/ccache-4.2.1.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.2.1.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.2.1.eb b/easybuild/easyconfigs/c/ccache/ccache-4.2.1.eb new file mode 100644 index 0000000000..7db922f043 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.2.1.eb @@ -0,0 +1,39 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.2.1' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['320d2b17d2f76393e5d4bb28c8dee5ca783248e9cd23dff0654694d60f8a4b62'] + +osdependencies = [('glibc-static', 'libc6-dev')] + +local_gccver = '10.2.0' +builddependencies = [ + ('GCC', local_gccver), + ('CMake', '3.18.4', '', ('GCCcore', local_gccver)), + ('Ninja', '1.10.1', '', ('GCCcore', local_gccver)), + ('zstd', '1.4.5', '', ('GCCcore', local_gccver)), +] + +preconfigopts = 'LDFLAGS="-static"' +configopts = '-DENABLE_DOCUMENTATION=OFF -DENABLE_IPO=ON -DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a"' + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' From 856fc66d9263bacefc469a7f991d4483655af5ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 May 2021 15:35:08 +0200 Subject: [PATCH 0866/2365] adding easyconfigs: Biopython-1.78-fosscuda-2020b.eb --- .../Biopython-1.78-fosscuda-2020b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.78-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-fosscuda-2020b.eb new file mode 100644 index 0000000000..41f07d6177 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-fosscuda-2020b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.78' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From 170b95aff1c701043da59283fbe246bfbf2fd5a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 May 2021 15:35:39 +0200 Subject: [PATCH 0867/2365] adding easyconfigs: MDTraj-1.9.5-fosscuda-2020b.eb --- .../m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..8a14999b77 --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb @@ -0,0 +1,43 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.5' + +homepage = 'https://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('zlib', '1.2.11'), +] + +use_pip = True +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.0.5', { + 'checksums': ['b079a7d0b9fbc8a92850277b664bb582991ef5ac399b3607e695569148f6c784'], + }), + # must be astunparse < 1.6.3 with Python 3.8, see https://github.com/mdtraj/mdtraj/pull/1621 + ('astunparse', '1.6.2', { + 'checksums': ['dab3e426715373fd76cd08bb1abe64b550f5aa494cf1e32384f26fd60961eb67'], + }), + ('mdtraj', version, { + 'checksums': ['f22c28c9dd51aa0f8692078dd3c2c7a338a7ca27cbd9aaeb669a60361e95adc4'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' From f601619e92f6b5c1f3046ff4d0cdddf53caa15cd Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 7 May 2021 18:08:24 +0200 Subject: [PATCH 0868/2365] use ARCH constant to avoid different Pandoc easyconfigs for different architectures --- easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb index 87ce950277..83694e1330 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -23,7 +23,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix ('SAMtools', '1.11'), ('BCFtools', '1.11'), - ('Pandoc', '2.13', '-%(arch)s', True), + ('Pandoc', '2.13', '', True), ] # added ext_postinstallcmds to pandoc: import fails if pandoc/definitions dir is not installed From cc9c4c7be239e26c975e57a1b38bcd281089f829 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 7 May 2021 17:53:08 +0100 Subject: [PATCH 0869/2365] Fix order of genABEL and genABEL.data --- .../R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index 3edd386e47..282c70617f 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -1014,12 +1014,12 @@ exts_list = [ ('FRASER', '1.2.1', { 'checksums': ['37562b7e92fd95feb950f160b38427f23a9e31729fa0783b441fc74fc45f7120'], }), - ('GenABEL', '1.8-0', { - 'checksums': ['434fc806b918738ec67171a37a47099d1706332819317e368fe0ccb8f149a469'], - }), ('GenABEL.data', '1.0.0', { 'checksums': ['2c28d5df63ae13545cf7aea6ce5f22ae1bbb58219fdaed6c1d5d5affc072c65c'], }), + ('GenABEL', '1.8-0', { + 'checksums': ['434fc806b918738ec67171a37a47099d1706332819317e368fe0ccb8f149a469'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From f2b6a5592819922fe5ee5424c132b4fc4dc8762f Mon Sep 17 00:00:00 2001 From: spottho1 Date: Fri, 7 May 2021 20:22:49 +0200 Subject: [PATCH 0870/2365] get rid of exts_defaultclass and modextrapaths (since already set by default) --- .../g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb index 14bff7b300..10bf3fc560 100644 --- a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb @@ -17,7 +17,6 @@ dependencies = [ ('libyaml', '0.2.5'), ] -exts_defaultclass = 'PythonPackage' use_pip = True sanity_pip_check = True @@ -75,8 +74,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/gdc-client'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 9ef92aabe824e629c656bb872c60bb37dae6d4f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 May 2021 12:03:05 +0200 Subject: [PATCH 0871/2365] add patch for rhdf5filters extension in Bioconductor 3.12 bundle to fix installation on aarch64 (fixes #12817) --- .../R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb index 3c687feedc..0d5e70f9ad 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -328,7 +328,12 @@ exts_list = [ 'checksums': ['48c81620346c1c652d15098d1c90df749a28ca747ade82d2a1e276191fc1d691'], }), ('rhdf5filters', '1.2.0', { - 'checksums': ['58df019a2c8626cc236ebe19d44b830a6c3b5f787ea4090d5b57454a88d676cb'], + 'patches': ['rhdf5filters-1.2.0_fix-configure-aarch64.patch'], + 'checksums': [ + '58df019a2c8626cc236ebe19d44b830a6c3b5f787ea4090d5b57454a88d676cb', # rhdf5filters_1.2.0.tar.gz + # rhdf5filters-1.2.0_fix-configure-aarch64.patch + '01d00415dcf41d7ca331b69ef7b3d99834719474ef1da8f66a540d027e24da5b', + ], }), ('rhdf5', '2.34.0', { 'checksums': ['11d70b8d8284d4b7a6beb4c5b65abd42451e46d04f65dfc82bf265a677c8952a'], From f6b32023696d67a008e91400af540eb411555d62 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 May 2021 15:32:09 +0200 Subject: [PATCH 0872/2365] reinstate author credit in ChecKM easyconfig --- .../c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb index 889126fb59..b5127b17c5 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb @@ -1,3 +1,7 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + easyblock = 'PythonPackage' name = 'CheckM' From 03a1ca8691c88deddf936fe305fea1a3dfb50c5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 May 2021 15:33:09 +0200 Subject: [PATCH 0873/2365] stick to GCC toolchain for taxator-tk --- .../taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..d8f225d930 --- /dev/null +++ b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'taxator-tk' +version = '1.3.3' + +homepage = 'https://github.com/fungs/taxator-tk' +description = "A set of programs for the taxonomic analysis of nucleotide sequence data" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/fungs/taxator-tk/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c1da90bee42337a994c66653208c820b7b0d203093981eaec4eef0a9f6fdd156'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('SeqAn', '2.4.0'), + ('Boost', '1.74.0'), +] + +separate_build_dir = True + +buildopts = "&& mkdir -p %(installdir)s/bin" +buildopts += " && cp -a {alignments-filter,binner,taxator,taxknife,unittest_ncbitaxonomy} %(installdir)s/bin/" + +skipsteps = ['install'] + +sanity_check_paths = { + 'files': ['bin/alignments-filter', 'bin/binner', 'bin/taxator', 'bin/taxknife', 'bin/unittest_ncbitaxonomy'], + 'dirs': [], +} + +sanity_check_commands = ["taxator --help"] + +moduleclass = 'bio' From 4303b289af6550cf041f757e16ef9b66a902a079 Mon Sep 17 00:00:00 2001 From: jfgrimm <65227842+jfgrimm@users.noreply.github.com> Date: Mon, 10 May 2021 14:49:50 +0100 Subject: [PATCH 0874/2365] Update bcolz-1.2.1-foss-2020b.eb --- easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb b/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb index 405d6aad61..f9ba69782d 100644 --- a/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb @@ -35,7 +35,7 @@ preinstallopts = "BLOSC_DIR=$EBROOTBLOSC" sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = ["python -c 'import bcolz; bcolz.test()'"] From a832ad4e31f665cd1b03b54ae476070ff7317b58 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 10 May 2021 16:30:07 +0200 Subject: [PATCH 0875/2365] adding easyconfigs: GDRCopy-2.2-GCCcore-10.2.0.eb, GDRCopy-2.2-GCCcore-10.3.0.eb --- .../g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..85810e2394 --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.2' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e4be119809391b18c735346d24b3b398dd9421cbff47ef12befbae40d61da45f'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +# This easyconfig only installs the library of GDRCopy. Please keep in mind +# that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] + +local_envopts = "prefix=%(installdir)s" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib %s" % local_envopts +install_cmd = "make lib_install" +installopts = local_envopts + +sanity_check_paths = { + 'files': ['lib/libgdrapi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 4b27e54555c92ed080681eedcd1cd83df825620d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 May 2021 19:29:37 +0200 Subject: [PATCH 0876/2365] adding easyconfigs: kallisto-0.46.1-iimpi-2020b.eb --- .../k/kallisto/kallisto-0.46.1-iimpi-2020b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb new file mode 100644 index 0000000000..491b5541b7 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.46.1' + +homepage = 'https://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'pachterlab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231'] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), +] + +dependencies = [('HDF5', '1.10.7')] + +preconfigopts = "cd ../%(name)s-%(version)s/ext/htslib/ && autoreconf && cd - &&" + +parallel = 1 + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' From 48fe6d4c3ac8f76d1c2ca6d66416acd46937c2e1 Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Mon, 10 May 2021 21:31:38 +0200 Subject: [PATCH 0877/2365] adding easyconfigs: CDO-1.9.10-foss-2020b.eb, YAXT-0.9.0-gompi-2020b.eb --- .../y/YAXT/YAXT-0.9.0-gompi-2020b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb new file mode 100644 index 0000000000..9d9730518a --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.9.0' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.dkrz.de/redmine/attachments/download/498/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d3673e88c1cba3b77e0821393b94b5952d8ed7dc494305c8cf93e7ebec19483c'] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' From 392a2392678c40a857469988dcfcc2e83e534d95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 May 2021 09:34:44 +0200 Subject: [PATCH 0878/2365] adding easyconfigs: GROMACS-2021.2-fosscuda-2020b.eb --- .../GROMACS/GROMACS-2021.2-fosscuda-2020b.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..13d039f411 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb @@ -0,0 +1,87 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.2' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI builds. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', +] +checksums = [ + 'd940d865ea91e78318043e71f229ce80d32b0dc578d64ee5aa2b1a4be801aadb', # gromacs-2021.2.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch + '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From da7c46131bb904884c68aef20a0171cca762e3f7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 11 May 2021 13:18:32 +0200 Subject: [PATCH 0879/2365] Fix mis-optimization on POWER --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index 439cb3cbc5..4bccd93ead 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -239,6 +239,7 @@ patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', ] checksums = [ @@ -289,6 +290,8 @@ checksums = [ # PyTorch-1.7.0_increase-distributed-test-timeout.patch '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + '3f6398e26110c2c38c848e09ab1e6d29e28bbef4ce47b3203c2d3e803f4c9769', # PyTorch-1.7.1_run-large-tests-on-GPU.patch '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 03f193e6e4..b2a585bac7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -251,6 +251,7 @@ patches = [ 'PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch', 'PyTorch-1.7.1_complex32.patch', 'PyTorch-1.7.1_bypass-nan-compare.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', @@ -313,6 +314,8 @@ checksums = [ 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', '6028bff2be720cf70acad2129db60fd10872e02c9e460c72bb274228cf90b320', # PyTorch-1.7.1_complex32.patch '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + '3f6398e26110c2c38c848e09ab1e6d29e28bbef4ce47b3203c2d3e803f4c9769', # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch From a4ab7db00862d73e23af620b33ce4d01e74ac606 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 11 May 2021 14:13:20 +0200 Subject: [PATCH 0880/2365] Fixup last patch --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index 4bccd93ead..cf4efa342e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -291,7 +291,7 @@ checksums = [ '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch - '3f6398e26110c2c38c848e09ab1e6d29e28bbef4ce47b3203c2d3e803f4c9769', + '472362281f2a2df026985f54d8efe5180ea29d5190afa2cd56ecfe228b28b3eb', # PyTorch-1.7.1_run-large-tests-on-GPU.patch '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index b2a585bac7..12984784ee 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -315,7 +315,7 @@ checksums = [ '6028bff2be720cf70acad2129db60fd10872e02c9e460c72bb274228cf90b320', # PyTorch-1.7.1_complex32.patch '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch - '3f6398e26110c2c38c848e09ab1e6d29e28bbef4ce47b3203c2d3e803f4c9769', + '472362281f2a2df026985f54d8efe5180ea29d5190afa2cd56ecfe228b28b3eb', # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch From c5596ca5d908c76264a453134c6253e2f27592aa Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 11 May 2021 16:10:34 +0200 Subject: [PATCH 0881/2365] Fixup last patch --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index cf4efa342e..b15bc1b536 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -291,7 +291,7 @@ checksums = [ '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch - '472362281f2a2df026985f54d8efe5180ea29d5190afa2cd56ecfe228b28b3eb', + 'fc66465d31c9d3b874189d589770abc7adb0c11016124e442ae1dbf0ec52455b', # PyTorch-1.7.1_run-large-tests-on-GPU.patch '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 12984784ee..843c2aeabf 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -315,7 +315,7 @@ checksums = [ '6028bff2be720cf70acad2129db60fd10872e02c9e460c72bb274228cf90b320', # PyTorch-1.7.1_complex32.patch '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch - '472362281f2a2df026985f54d8efe5180ea29d5190afa2cd56ecfe228b28b3eb', + 'fc66465d31c9d3b874189d589770abc7adb0c11016124e442ae1dbf0ec52455b', # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch From 0c4cf8126759ba73698bc2e8102cfff1411505af Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 11 May 2021 17:04:33 +0200 Subject: [PATCH 0882/2365] Relax precision in tests for A100 --- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 843c2aeabf..d41ca2497f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -254,6 +254,7 @@ patches = [ 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', + 'PyTorch-1.7.1_relax_precision_in_test_nn.patch', 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', 'PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch', ] @@ -320,6 +321,8 @@ checksums = [ '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch '18ecad081a8c940add64040ad9698d3273366acf738a8a44eab1c793d3f49950', + # PyTorch-1.7.1_relax_precision_in_test_nn.patch + '4089bd3d2ee1939108ed9ebe9cd98da306df626ea6e59fac52fa877a5ea8a163', # PyTorch-1.7.1_run-large-tests-on-GPU.patch '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', # PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch From 2c61c4d294caea3badd7d1811a642455e1920be9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 May 2021 21:02:26 +0200 Subject: [PATCH 0883/2365] enable sanity_pip_check in CONCOCT easyconfig --- .../c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb index d1d4b72dc2..9c7b23d10c 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb @@ -42,4 +42,6 @@ sanity_check_paths = { sanity_check_commands = ["concoct --help"] +sanity_pip_check = True + moduleclass = 'bio' From 1e3922bd5cd013d676da131b4827640564ffec29 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 12 May 2021 00:14:40 +0200 Subject: [PATCH 0884/2365] add dependencies on protobuf, snappy and zlib to dm-reverb v0.2.0 --- .../easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb index ff68784fc6..aa3a70ea80 100644 --- a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb @@ -26,6 +26,9 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), ('TensorFlow', '2.4.1'), + ('protobuf', '3.14.0'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), ] # Bundled upb sets -Werror, failing on any warning. Disable for harmless warnings From 52c10f74b42204a7acfee90f945bcfd6a83e5f55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 May 2021 09:41:35 +0200 Subject: [PATCH 0885/2365] restore comments/checksums that were removed unintentionally in R v4.0.3 easyconfig --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index e0d8f6aea9..c349c0338d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2169,12 +2169,13 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.1', { 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], @@ -2288,7 +2289,8 @@ exts_list = [ 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.8', { 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], @@ -2384,9 +2386,9 @@ exts_list = [ 'checksums': ['a0282a054d0e6ab310ec7edcffa953b77c7e4a858d9ac7028aab1b4fb4ce8cf3'], }), ('V8', '3.4.0', { - 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', - 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', }), ('rstan', '2.21.2', { 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], @@ -2649,9 +2651,13 @@ exts_list = [ 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), ('gWidgets2tcltk', '1.0-6', { - 'modulename': False, - 'preinstallopts': "xvfb-run ", 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, }), ('mgsub', '1.7.2', { 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], From 8b5e8037ccd0a5d30270c381d26c0d2006a2cbc3 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 12 May 2021 10:43:44 +0200 Subject: [PATCH 0886/2365] Adding scikit-image into intelcuda-2020b --- .../b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb | 39 ++++++++++ .../d/dask/dask-2021.2.0-intelcuda-2020b.eb | 73 +++++++++++++++++++ .../networkx/networkx-2.5-intelcuda-2020b.eb | 24 ++++++ .../PyWavelets-1.1.1-intelcuda-2020b.eb | 25 +++++++ .../scikit-image-0.18.1-intelcuda-2020b.eb | 48 ++++++++++++ 5 files changed, 209 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb new file mode 100644 index 0000000000..513e9f6b2f --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.2.3' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('Pillow', '8.0.1'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), +] + +use_pip = True + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + (name, version, { + 'checksums': ['c4a3f97afe5f525019dd58ee8c4e3d43f53fe1b1ac264ccaae9b02c07b2abc17'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb new file mode 100644 index 0000000000..b012d3c660 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2021.2.0' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('SciPy-bundle', '2020.11'), + ('bokeh', '2.2.3'), +] + +use_pip = True + +exts_list = [ + ('fsspec', '0.8.7', { + 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('locket', '0.2.1', { + 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + }), + ('partd', '1.1.0', { + 'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.0.0', { + 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + (name, version, { + 'checksums': ['e7054b8d685205e95c789900ae87d6174550180cbe38a3cb1142e10c73004c22'], + }), + ('distributed', version, { + 'checksums': ['9150b99b2c28e7c238c486b117154abd545c6990080d084aaff02f803f86f75e'], + }), + ('dask-mpi', '2.21.0', { + 'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.7.2', { + 'checksums': ['1767f4146b2663d9d2eaef62b882a86e1df0bccdb8ae68ae3e5e546aa6796d35'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb new file mode 100644 index 0000000000..d6967a10d7 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.5' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb new file mode 100644 index 0000000000..5dda1d5325 --- /dev/null +++ b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'PyWavelets' +version = '1.1.1' + +homepage = 'https://pywavelets.readthedocs.io' +description = "PyWavelets is open source wavelet transform software for Python." + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'pywt'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb new file mode 100644 index 0000000000..3169f709e7 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.18.1' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('Pillow', '8.0.1'), + ('networkx', '2.5'), + ('dask', '2021.2.0'), + ('PyWavelets', '1.1.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('imageio', '2.9.0', { + 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.3.0', { + 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], + }), + ('tifffile', '2021.2.1', { + 'checksums': ['6793787742e18cf2116bc65e17c51cd9c14cd27a4a6033a8ddd5bf801a637615'], + }), + (name, version, { + 'modulename': 'skimage', + 'patches': ['scikit-image-%(version)s_fix-README-cache-perms.patch'], + 'preinstallopts': "sed -i 's/-fopenmp//g' setup.py && ", + 'checksums': [ + 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], + }), +] + +moduleclass = 'vis' From e2e341f40844289bc46e2e90cec83341323351c8 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 12 May 2021 10:49:13 +0200 Subject: [PATCH 0887/2365] Adding scikit-build into intel-2020b toolchains --- .../scikit-build-0.11.1-intel-2020b.eb | 29 +++++++++++++++++++ .../scikit-build-0.11.1-intelcuda-2020b.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb new file mode 100644 index 0000000000..be3e7b09c4 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.11.1' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.5.0', { + 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], + }), + (name, version, { + 'modulename': 'skbuild', + 'checksums': ['da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb new file mode 100644 index 0000000000..6ed9c54bce --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.11.1' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.5.0', { + 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], + }), + (name, version, { + 'modulename': 'skbuild', + 'checksums': ['da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c'], + }), +] + +moduleclass = 'lib' From 2f368bc67949331600f07cda3c860b1b206af357 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 12 May 2021 11:05:32 +0200 Subject: [PATCH 0888/2365] Adding astropy-4.2.1 into intel-cuda-2020b --- .../astropy/astropy-4.2.1-intelcuda-2020b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb new file mode 100644 index 0000000000..d452a246b3 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '1.7.3', { + 'modulename': 'erfa', + 'checksums': ['6cf3a645d63e0c575a357797903eac5d2c6591d7cdb89217c8c4d39777cf18cb'], + }), + ('extension-helpers', '0.1', { + 'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'], + }), + (name, version, { + 'checksums': ['ed483e472241153daec45f4b0c318c2c63d9f47305b78e6e63d32fc388c18427'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], +} + +moduleclass = 'astro' From d807b3d0b7348ad9536459fa29c060a8bd743bdd Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 12 May 2021 11:43:26 +0200 Subject: [PATCH 0889/2365] Removing old style Python prefix from 2020b easyconfig --- easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb index d452a246b3..8479d0024e 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'astropy' version = '4.2.1' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.astropy.org/' description = """The Astropy Project is a community effort to develop From a17cdbe9512ff63ffe565bf0bcf38a9cd0f57ca1 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 12 May 2021 11:51:34 +0200 Subject: [PATCH 0890/2365] Adding netCDF to iimpic-2020b --- .../n/netCDF/netCDF-4.7.4-iimpic-2020b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpic-2020b.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpic-2020b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpic-2020b.eb new file mode 100644 index 0000000000..e21bf6a3c6 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpic-2020b.eb @@ -0,0 +1,38 @@ +name = 'netCDF' +version = '4.7.4' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpic', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['netCDF-%(version)s_fix-ocdebug.patch'] +checksums = [ + '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b', # v4.7.4.tar.gz + '94c9883005f189a4551947e04191a68199cf4cdcada4b2d313115720fb4690e9', # netCDF-4.7.4_fix-ocdebug.patch +] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('cURL', '7.72.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From ba6c159d97f8a523ce64eb257213af1717ac77c8 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 12 May 2021 13:54:45 +0200 Subject: [PATCH 0891/2365] Disable usNIC by default in libfabric --- .../l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb index e95e33215a..7837e771aa 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb @@ -27,7 +27,12 @@ builddependencies = [ osdependencies = [OS_PKG_IBVERBS_DEV] # Disable deprecated "sockets" provider -configopts = "--disable-sockets" +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(['libnl3-devel', 'libnl3-dev']) +configopts += "--disable-usnic " sanity_check_paths = { 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + From 05775843b2572dc0f64a5fdf62962ef98a58b2c4 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 12 May 2021 14:00:25 +0200 Subject: [PATCH 0892/2365] Append a tuple not a list --- .../easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb index 7837e771aa..d7da6e3a9e 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb @@ -31,7 +31,7 @@ configopts = "--disable-sockets " # Disable usNIC provider by default as this requires specific osdependencies # If you want to enable this provider you need to uncomment the following line: -# osdependencies.append(['libnl3-devel', 'libnl3-dev']) +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) configopts += "--disable-usnic " sanity_check_paths = { From 1b0935e20146a099eb46c74412a5ee8774a176f5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 12 May 2021 18:01:27 +0200 Subject: [PATCH 0893/2365] Reenable test_nn after adding the patch --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index d41ca2497f..73d92f7ca8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -336,8 +336,6 @@ excluded_tests = { # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! # https://github.com/pytorch/pytorch/issues/43209 'test_quantization', - # Fails with A100 cards due to precision issues: https://github.com/pytorch/pytorch/issues/52278 - 'test_nn', ] } From b1b5342f09dccf43bc63f3461f06c4bf45e98ed4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 12 May 2021 18:27:23 +0200 Subject: [PATCH 0894/2365] adding easyconfigs: gemmi-0.4.5-GCCcore-10.2.0.eb --- .../g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e2eeaa64d5 --- /dev/null +++ b/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/05 +easyblock = 'CMakePythonPackage' + +name = 'gemmi' +version = '0.4.5' + +homepage = 'https://gemmi.readthedocs.io/' +description = """ +Gemmi is a library, accompanied by a set of programs, developed primarily for +use in macromolecular crystallography (MX). For working with: + +macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files), refinement +restraints (CIF files), reflection data (MTZ and mmCIF formats), data on a 3D +grid (electron density maps, masks, MRC/CCP4 format) crystallographic symmetry. +Parts of this library can be useful in structural bioinformatics (for symmetry- +aware analysis of protein models), and in other molecular-structure sciences +that use CIF files (we have the fastest open-source CIF parser). +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'opt': True} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['af462dbb3a2a144b1437700637e78c0365a5273dc5bffadeea80f73765ab15c7'] + +github_account = 'project-gemmi' + +runtest = 'cpptest ftest ftest_grid test' + +configopts = '-DUSE_PYTHON=1 ' +configopts += '-DUSE_FORTRAN=1 ' +configopts += '-DPYTHON_INSTALL_DIR=%(installdir)s/lib/python%(pyshortver)s/site-packages ' + +builddependencies = [ + ('pybind11', '2.6.0'), + ('CMake', '3.18.4') +] +dependencies = [('Python', '3.8.6')] + +sanity_check_paths = { + 'files': ['bin/gemmi'], + 'dirs': ['bin', 'lib', 'include/gemmi'] +} + +moduleclass = 'bio' From 3edbb78b78ea9b821f73d43875c0fe5a4bca2db7 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 12 May 2021 20:27:01 +0200 Subject: [PATCH 0895/2365] Update gemmi-0.4.5-GCCcore-10.2.0.eb add binutils builddep --- easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb index e2eeaa64d5..f4b0e66ba3 100644 --- a/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb @@ -34,7 +34,8 @@ configopts += '-DPYTHON_INSTALL_DIR=%(installdir)s/lib/python%(pyshortver)s/site builddependencies = [ ('pybind11', '2.6.0'), - ('CMake', '3.18.4') + ('CMake', '3.18.4'), + ('binutils','2.35') ] dependencies = [('Python', '3.8.6')] From 4b15ab023f037e2ae7bc937ab5aeef33c6d95b19 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 12 May 2021 21:32:02 +0200 Subject: [PATCH 0896/2365] Update gemmi-0.4.5-GCCcore-10.2.0.eb fix style --- easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb index f4b0e66ba3..c45a19e3d0 100644 --- a/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb @@ -35,7 +35,7 @@ configopts += '-DPYTHON_INSTALL_DIR=%(installdir)s/lib/python%(pyshortver)s/site builddependencies = [ ('pybind11', '2.6.0'), ('CMake', '3.18.4'), - ('binutils','2.35') + ('binutils', '2.35') ] dependencies = [('Python', '3.8.6')] From a55cc3c511cbbf0324aee69a5ef6c9c8ef557d55 Mon Sep 17 00:00:00 2001 From: Richard Lawrence Date: Thu, 13 May 2021 12:00:53 -0500 Subject: [PATCH 0897/2365] Update Xerces-C++ to GCCcore 10.2.0 --- .../Xerces-C++-3.2.3-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..103ab67e6e --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Xerces-C++' +version = '3.2.3' + +homepage = 'https://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['fb96fc49b1fb892d1e64e53a6ada8accf6f0e6d30ce0937956ec68d39bd72c7e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('cURL', '7.72.0'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.so'], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' From 671e356cc046ed2b9cc4170647ddf240f89f924b Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 14 May 2021 14:08:12 +0200 Subject: [PATCH 0898/2365] Use gompi and iimpi toolchains instead of foss and intel. --- .../libGridXC/libGridXC-0.9.6-gompi-2020b.eb | 34 +++++++++++++++++++ .../libGridXC/libGridXC-0.9.6-iimpi-2020b.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb new file mode 100644 index 0000000000..a46d4f4f17 --- /dev/null +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libGridXC' +version = '0.9.6' + +homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' +description = """A library to compute the exchange and correlation energy + and potential in spherical (i.e. atoms) or periodic systems.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/uploads/e6e4ec1e3ec648a45b3613e724c7be04'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee513eeb08b631e2efaaea62e73d85b6fbf204da85963be785915802e5497463'] + +local_common_configopts = "--enable-static --enable-shared --enable-multiconfig --with-libxc" + +configopts = [ + local_common_configopts + " --without-mpi", + local_common_configopts + " CC=$MPICC FC=$MPIFC CXX=$MPICXX --with-mpi", +] + +dependencies = [('libxc', '4.3.4')] + +sanity_check_paths = { + 'files': + ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], + 'dirs': ['include'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb new file mode 100644 index 0000000000..3c9d3dbdce --- /dev/null +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libGridXC' +version = '0.9.6' + +homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' +description = """A library to compute the exchange and correlation energy + and potential in spherical (i.e. atoms) or periodic systems.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/uploads/e6e4ec1e3ec648a45b3613e724c7be04'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee513eeb08b631e2efaaea62e73d85b6fbf204da85963be785915802e5497463'] + +local_common_configopts = "--enable-static --enable-shared --enable-multiconfig --with-libxc" + +configopts = [ + local_common_configopts + " --without-mpi", + local_common_configopts + " CC=$MPICC FC=$MPIFC CXX=$MPICXX --with-mpi", +] + +dependencies = [('libxc', '4.3.4')] + +sanity_check_paths = { + 'files': + ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], + 'dirs': ['include'], +} + +moduleclass = 'phys' From 8e1cfbb4267711f56d0db0e46f63594fbd300c85 Mon Sep 17 00:00:00 2001 From: Richard Lawrence Date: Fri, 14 May 2021 09:43:37 -0500 Subject: [PATCH 0899/2365] use SHLIB_EXT in Xerces-C++-3.2.3-GCCcore-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb index 103ab67e6e..3d942f68bf 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ runtest = 'test' sanity_check_paths = { 'files': ['bin/XInclude', 'include/xercesc/xinclude/XIncludeUtils.hpp', - 'lib/libxerces-c-3.2.so'], + 'lib/libxerces-c-3.2.%s' % SHLIB_EXT], 'dirs': ['bin', 'include', 'lib'] } From 9b7a9c9caf5e8158cb64775fceaacfbea8243e39 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 15 May 2021 09:41:30 +0100 Subject: [PATCH 0900/2365] Add IceLake detection to OpenBLAS 0.3.12 and 0.3.15 --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index 6f432e2a0d..f3346d9db0 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-0.3.15_icelake-detection.patch', ] checksums = [ '65a7d3a4010a4e3bd5c0baa41a234797cd3a1735449a4a5902129152601dc57b', # v0.3.12.tar.gz @@ -23,6 +24,7 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch '4b3ab7260975ea2cfd7460731c0201b2c1e374cd83ae90d55b8da3e670633ba0', + '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', # OpenBLAS-0.3.15_icelake-detection.patch ] # extensive testing can be enabled by uncommenting the line below From 98da512aa45f42f555cf6833b573b47b752dc71d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 16 May 2021 16:57:45 +0200 Subject: [PATCH 0901/2365] fix checksum for MaxBin 2.2.7 --- easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb index cec4e9e46b..65c321a169 100644 --- a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['e40c8db96efe3d132a179e740208099105f231a8e10f95ef286631423472fda7'] +checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] builddependencies = [('binutils', '2.35')] From 27cddc9f9dcf2312044d86cbc0a5a12752483252 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 16 May 2021 19:37:40 +0200 Subject: [PATCH 0902/2365] run 'make clean' before building FragGeneScan Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb index 4f843adbc4..1b21dae3e0 100644 --- a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb @@ -18,6 +18,7 @@ dependencies = [("Perl", "5.32.0")] fix_perl_shebang_for = ['*.pl'] +prebuildopts = "make clean && " buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] From de4b9e93f8c16658e447819619c87d8812d98913 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 May 2021 09:08:27 +0200 Subject: [PATCH 0903/2365] clean up KronaTools easyconfig + enhance sanity check, add missing checksums for KronaTools, MetaBAT and metaWRAP --- .../KronaTools-2.8-GCCcore-10.2.0.eb | 29 ++++++++++--------- .../MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 1 + .../metaWRAP-1.3-foss-2020b-Python-2.7.18.eb | 1 + 3 files changed, 17 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb index f1ccf12fc5..4838f91cda 100644 --- a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb @@ -5,7 +5,7 @@ # This build also links updateTaxonomy.sh and updateAccessions.sh in the bin folder # so users can install their own Taxonomy database -easyblock = 'Binary' +easyblock = 'Tarball' name = 'KronaTools' version = '2.8' @@ -17,24 +17,25 @@ several Bioinformatics tools as well as from text and XML files.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] -sources = [{ - 'filename': '%(name)s-%(version)s.tar', - 'extract_cmd': 'tar xvf %s -C %(installdir)s/../', -}] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['56efc028b6226a1aea8ec4e9f049836b07d4833e7e4d5b9189118ed51a47c9c0'] -extract_sources = True - -builddependencies = [('binutils', '2.35')] dependencies = [('Perl', '5.32.0')] -install_cmd = 'cd %(installdir)s/../%(name)s-%(version)s; ./install.pl --prefix=%(installdir)s; ' -install_cmd += 'cd %(installdir)s/bin; ' -install_cmd += 'ln -s ../../%(name)s-%(version)s/updateTaxonomy.sh . ;' -install_cmd += 'ln -s ../../%(name)s-%(version)s/updateAccessions.sh . ' +postinstallcmds = [ + "cd %(installdir)s && ./install.pl --prefix=%(installdir)s;", + "cd %(installdir)s/bin && ln -s ../updateAccessions.sh . && ln -s ../updateTaxonomy.sh .", +] sanity_check_paths = { - 'files': ['bin/ktClassifyBLAST', 'bin/ktImportBLAST', 'bin/ktImportTaxonomy'], - 'dirs': [], + 'files': ['bin/ktClassifyBLAST', 'bin/ktImportBLAST', 'bin/ktImportTaxonomy', + 'bin/updateAccessions.sh', 'bin/updateTaxonomy.sh'], + 'dirs': ['data', 'img', 'scripts'], } +sanity_check_commands = [ + "updateAccessions.sh --help", + "ktImportText", +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index e98f41bec9..827c80520e 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb index 5b92735029..bb979fb26e 100644 --- a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/bxlab/metaWRAP/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['ffdbccf340dc0b1ebd0ad6f222e3bdef1e22bbd6e4e5156bf93500a3a834dd52'] builddependencies = [ ('Java', '11', '', True), From cbd7ea2eaa33532197b11e0e0888d945d48ee27f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 May 2021 12:09:12 +0200 Subject: [PATCH 0904/2365] {bio}[GCCcore/10.2.0] pyfaidx v0.5.9.5 w/ Python 3.8.6 --- .../CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb | 6 ++-- .../pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 2 files changed, 32 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb index 33289f4880..d6aa968a71 100644 --- a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb @@ -19,6 +19,7 @@ dependencies = [ ('Pillow', '8.0.1'), ('Pysam', '0.16.0.1'), ('PyYAML', '5.3.1'), + ('pyfaidx', '0.5.9.5'), ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', versionsuffix), ] @@ -27,9 +28,6 @@ exts_list = [ ('reportlab', '3.5.66', { 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], }), - ('pyfaidx', '0.5.9.5', { - 'checksums': ['9965644c5bd62bedc0ff7f336cbb2baef6406a36b4ec5c786b199872ce46192b'], - }), ('pomegranate', '0.13.5', { 'checksums': ['b1b803fa18c8a8ca4a8fd2824573914bbff7574e3dc6be770ab68efd00503341'], }), @@ -49,7 +47,7 @@ use_pip = True sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["cnvkit.py", "faidx"]], + 'files': ['bin/cnvkit.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b4502d6142 --- /dev/null +++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pyfaidx' +version = '0.5.9.5' + +homepage = 'https://pypi.python.org/pypi/pyfaidx' +description = "pyfaidx: efficient pythonic random access to fasta subsequences" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9965644c5bd62bedc0ff7f336cbb2baef6406a36b4ec5c786b199872ce46192b'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From eab640b1f2c7fcba6520ef7c593ce20001eb6651 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 17 May 2021 11:47:09 +0100 Subject: [PATCH 0905/2365] Add UCX dependency to OneAPI versions of impi --- .../i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb index e94d38ae26..1a0fbe3b03 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb @@ -11,4 +11,6 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/1739 sources = ['l_mpi_oneapi_p_%(version)s.76_offline.sh'] checksums = ['8b7693a156c6fc6269637bef586a8fd3ea6610cac2aae4e7f48c1fbb601625fe'] +dependencies = [('UCX', '1.9.0')] + moduleclass = 'mpi' From 4600920d69e45b0a10d75610406dc8541ced0bfa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 May 2021 15:07:17 +0200 Subject: [PATCH 0906/2365] adding easyconfigs: RegTools-0.5.2-foss-2020b.eb --- .../r/RegTools/RegTools-0.5.2-foss-2020b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2020b.eb b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2020b.eb new file mode 100644 index 0000000000..522791e91e --- /dev/null +++ b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2020b.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'RegTools' +version = '0.5.2' + +homepage = 'https://regtools.readthedocs.org' +description = """RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a +regulatory and splicing context.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/griffithlab/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['24d3bc18174237e0fc2d0330839c8dc21c97cdb7d6e528c518188c10f17f3e7e'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +# required by included scripts +dependencies = [ + ('Python', '3.8.6'), + ('R', '4.0.3'), +] + +# 'make install' is not supported... +install_cmd = "mkdir %(installdir)s/bin && cp -a regtools %(installdir)s/bin/ && " +install_cmd += "cp -a %(builddir)s/regtools-%(version)s/scripts %(installdir)s/" + +sanity_check_paths = { + 'files': ['bin/regtools'], + 'dirs': ['scripts'], +} + +sanity_check_commands = ["regtools --help"] + +moduleclass = 'bio' From bf099ac4ca19801d1bae25b70b7c57d4f9f49fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 May 2021 15:16:59 +0200 Subject: [PATCH 0907/2365] adding easyconfigs: HPL-2.3-intel-2020.12.eb, intel-2020.12.eb --- .../h/HPL/HPL-2.3-intel-2020.12.eb | 21 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2020.12.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020.12.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2020.12.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020.12.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020.12.eb new file mode 100644 index 0000000000..8aabdc2f01 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020.12.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2020.12'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/intel/intel-2020.12.eb b/easybuild/easyconfigs/i/intel/intel-2020.12.eb new file mode 100644 index 0000000000..ce1386acf6 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2020.12.eb @@ -0,0 +1,21 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2020.12' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_compver = '2021.1.2' +local_gccver = '10.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.35', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_compver), + ('impi', '2021.1.1', '', ('intel-compilers', local_compver)), + ('imkl', '2021.1.1', '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From 1982b4dc5c15d0693a6b6275226f476027e788b4 Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Mon, 17 May 2021 16:13:48 +0200 Subject: [PATCH 0908/2365] lower cdo toolchain to gompi --- .../c/CDO/CDO-1.9.10-gompi-2020b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2020b.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2020b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2020b.eb new file mode 100644 index 0000000000..1821dbe769 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.9.10' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/24638/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc39c89bbb481d7b3945a06c56a8492047235f46ac363c4f0d980fccdde6677e'] + +dependencies = [ + ('HDF5', '1.10.7'), + ('netCDF', '4.7.4'), + ('YAXT', '0.9.0'), + ('ecCodes', '2.20.0'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES" + +# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && " + +sanity_check_paths = { + 'files': ['bin/cdo'], + 'dirs': [], +} + +moduleclass = 'data' From 2aaa69d626f8426b5df7385e94fafb8dd4ccda81 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 17 May 2021 18:04:23 +0200 Subject: [PATCH 0909/2365] Update alias patch --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index b15bc1b536..2b9c404e04 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -291,7 +291,7 @@ checksums = [ '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch - 'fc66465d31c9d3b874189d589770abc7adb0c11016124e442ae1dbf0ec52455b', + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', # PyTorch-1.7.1_run-large-tests-on-GPU.patch '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 73d92f7ca8..d014c83683 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -316,7 +316,7 @@ checksums = [ '6028bff2be720cf70acad2129db60fd10872e02c9e460c72bb274228cf90b320', # PyTorch-1.7.1_complex32.patch '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch - 'fc66465d31c9d3b874189d589770abc7adb0c11016124e442ae1dbf0ec52455b', + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch From 355287b288fd939e72484998af9cb0394993f7ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 May 2021 09:03:35 +0200 Subject: [PATCH 0910/2365] add PyYAML dependency for RegTools --- easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2020b.eb b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2020b.eb index 522791e91e..9c668e77d1 100644 --- a/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2020b.eb @@ -20,6 +20,7 @@ builddependencies = [ # required by included scripts dependencies = [ ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), # required by create_IGVsessions.py script ('R', '4.0.3'), ] From 219b6a74a42a64caae748ca060297af007c3f483 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 18 May 2021 16:44:44 +0800 Subject: [PATCH 0911/2365] override Makefile with hardcoded CC=cc in UnZip easyconfigs --- easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb index 43ecaaf041..07c853d36a 100644 --- a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ skipsteps = ['configure'] -buildopts = '-f unix/Makefile D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' +buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' buildopts += 'LF2="$LDFLAGS" ' # Note: CF is multiple lines buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' From e3672454f8962886d57cefb8a8f9649f72824668 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 18 May 2021 11:12:55 +0200 Subject: [PATCH 0912/2365] adding easyconfigs: Nilearn-0.7.1-foss-2020b.eb --- .../n/NiBabel/NiBabel-3.2.1-foss-2020b.eb | 46 +++++++++++++++++++ .../n/Nilearn/Nilearn-0.7.1-foss-2020b.eb | 28 +++++++++++ .../p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb | 28 +++++++++++ 3 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb new file mode 100644 index 0000000000..5ee1fef6ce --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '3.2.1' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Pillow', '8.0.1'), + ('pydicom', '2.1.2'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['4d2ff9426b740011a1c916b54fc25da9348282e727eaa2ea163f42e00f1fc29e'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb new file mode 100644 index 0000000000..01da8bf51a --- /dev/null +++ b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Nilearn' +version = '0.7.1' + +homepage = 'https://nilearn.github.io/' +description = """Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.8.6'), + ('NiBabel', '3.2.1'), + ('scikit-learn', '0.23.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7d182f0b70 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.1.2' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'pydicom' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e7cfbc4a997e327583bee047b7c9340845328373d088e776cf9565e47609a1a3'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From e1be2e32910ab92c8a99e596a7a62e60117efb59 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 May 2021 13:43:16 +0200 Subject: [PATCH 0913/2365] adding easyconfigs: antiSMASH-5.2.0-foss-2020b.eb, GlimmerHMM-3.0.4c-GCC-10.2.0.eb, HMMER2-2.3.2-GCC-10.2.0.eb, MUSCLE-3.8.1551-GCC-10.2.0.eb and patches: antiSMASH-5.2.0_Biopython-1.78.patch --- .../a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb | 91 +++++++++++++++++++ .../GlimmerHMM-3.0.4c-GCC-10.2.0.eb | 45 +++++++++ .../h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb | 27 ++++++ .../m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 30 ++++++ 4 files changed, 193 insertions(+) create mode 100644 easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb new file mode 100644 index 0000000000..57fe702e6c --- /dev/null +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -0,0 +1,91 @@ +easyblock = 'PythonBundle' + +name = 'antiSMASH' +version = '5.2.0' + +homepage = 'https://github.com/antismash/antismash' +description = """antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary + metabolite biosynthesis gene clusters in bacterial and fungal genomes.""" + +docurls = ['https://docs.antismash.secondarymetabolites.org'] + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('DIAMOND', '2.0.7'), + ('FastTree', '2.1.11'), + ('GlimmerHMM', '3.0.4c'), + ('HMMER2', '2.3.2'), + ('HMMER', '3.3.2'), + ('MUSCLE', '3.8.1551'), + ('BLAST+', '2.11.0'), + ('prodigal', '2.6.3'), + ('Biopython', '1.78'), + ('matplotlib', '3.3.3'), + ('scikit-learn', '0.23.2'), +] + +# install MEME as a component in this installation, +# since antiSMASH requires very specific old version +# see https://docs.antismash.secondarymetabolites.org/install/#full-manual-install +components = [ + ('MEME', '4.11.2', { + 'source_urls': ['http://meme-suite.org/meme-software/%(version)s/'], + 'sources': ['meme_%(version)s_2.tar.gz'], + 'checksums': ['377238c2a9dda64e01ffae8ecdbc1492c100df9b0f84132d50c1cf2f68921b22'], + 'easyblock': 'ConfigureMake', + 'start_dir': 'meme_%(version)s', + 'buildopts': 'CFLAGS="$CFLAGS -std=gnu89 -DUNIX -D__USE_FIXED_PROTOTYPES__ -fcommon"', + }), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('helperlibs', '0.2.1', { + 'checksums': ['4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732'], + }), + ('pysvg-py3', '0.2.2.post3', { + 'modulename': 'pysvg', + 'checksums': ['a1183aa5d89871298c11f25d28640edc3798b6ed1e2b2a95c30d35985d6431d0'], + }), + ('bcbio-gff', '0.6.6', { + 'modulename': 'BCBio.GFF', + 'checksums': ['74c6920c91ca18ed9cb872e9471c0be442dad143d8176345917eb1fefc86bc37'], + }), + ('pyScss', '1.3.7', { + 'modulename': 'scss', + 'checksums': ['f1df571569021a23941a538eb154405dde80bed35dc1ea7c5f3e18e0144746bf'], + }), + (name, version, { + 'source_urls': ['https://github.com/antismash/antismash/archive/'], + 'source_tmpl': '%s.tar.gz' % '-'.join(version.split('.')), + 'patches': ['antiSMASH-%(version)s_Biopython-1.78.patch'], + 'checksums': [ + 'a6fae892e46fd945701dda4640d07467e2d0ab37913d29da403127833bc77291', # 5-2-0.tar.gz + '4ca5d671085761c5f86719603fa3bbd0e82b7b52deefe8cac6eb4a3973825f16', # antiSMASH-5.2.0_Biopython-1.78.patch + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/antismash', 'bin/meme'], + 'dirs': [], +} + +sanity_check_commands = [ + # 'meme -h' exits with non-zero exit status, so use 'grep' to check for pattern + "meme -h 2>&1 | grep 'Usage:[ \t]*meme'", + "antismash --version", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb new file mode 100644 index 0000000000..947e4cda9a --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + 'trained_dir', 'README', 'train/readme.train', +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = [('%(namelower)s -h')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..496d7c1314 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'HMMER2' +version = '2.3.2' + +homepage = 'http://hmmer.org' +description = """HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://eddylab.org/software/hmmer'] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4'] + +postinstallcmds = ["cd %(installdir)s/bin && for cmd in $(ls); do mv ${cmd} ${cmd}2; done"] + +local_cmd_suffixes = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'index', 'pfam', 'search'] + +sanity_check_paths = { + 'files': ['bin/hmm%s2' % x for x in local_cmd_suffixes], + 'dirs': ['man'], +} + +sanity_check_commands = ["hmm%s2 -h" % x for x in local_cmd_suffixes] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb new file mode 100644 index 0000000000..75cf15432a --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = "3.8.1551" + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.drive5.com/muscle/'] +sources = ['%(namelower)s_src_%(version)s.tar.gz'] +checksums = ['c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e'] + +# use correct compiler flags + +# don't use -static when linking, since that implies requiring glibc-static to be installed +buildopts = 'CFLAGS="$CXXFLAGS" LDLIBS="-lm"' + +files_to_copy = [(["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%(namelower)s"], + 'dirs': [], +} + +moduleclass = 'bio' From 4f863ffd042265ea00e5d521a19e73c3573a18cf Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 18 May 2021 13:50:27 +0200 Subject: [PATCH 0914/2365] adding easyconfigs: Nipype-1.6.0-foss-2020b.eb --- .../n/Nipype/Nipype-1.6.0-foss-2020b.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb new file mode 100644 index 0000000000..b4ace4a205 --- /dev/null +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb @@ -0,0 +1,87 @@ +easyblock = 'PythonBundle' + +name = 'Nipype' +version = '1.6.0' + +homepage = 'https://nipype.readthedocs.io' +description = """Nipype is a Python project that provides a uniform interface to existing neuroimaging software and + facilitates interaction between these packages within a single workflow.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('lxml', '4.6.2'), + ('networkx', '2.5'), + ('NiBabel', '3.2.1'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('traits', '6.2.0', { + 'checksums': ['16fa1518b0778fd53bf0547e6a562b1787bf68c8f6b7995a13bd1902529fdb0c'], + }), + ('pydot', '1.4.2', { + 'checksums': ['248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d'], + }), + ('pydotplus', '2.0.2', { + 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('isodate', '0.6.0', { + 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], + }), + ('rdflib', '5.0.0', { + 'checksums': ['78149dd49d385efec3b3adfbd61c87afaf1281c30d3fcaf1b323b34f603fb155'], + }), + ('prov', '2.0.0', { + 'checksums': ['b6438f2195ecb9f6e8279b58971e02bc51814599b5d5383366eef91d867422ee'], + }), + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + ('pytest-forked', '1.3.0', { + 'modulename': 'pytest_forked', + 'checksums': ['6aa9ac7e00ad1a539c41bec6d21011332de671e938c7637378ec9710204e37ca'], + }), + ('apipkg', '1.5', { + 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], + }), + ('execnet', '1.8.0', { + 'checksums': ['b73c5565e517f24b62dea8a5ceac178c661c4309d3aa0c3e420856c072c411b4'], + }), + ('pytest-xdist', '2.2.1', { + 'modulename': 'xdist', + 'checksums': ['718887296892f92683f6a51f25a3ae584993b06f7076ce1e1fd482e59a8220a2'], + }), + ('ci-info', '0.2.0', { + 'checksums': ['dd70632c977feb8797b1e633507166b64ad5f57183cebb2b0ea56934abba4616'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('etelemetry', '0.2.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3e304ea9070902e6367282369cb8eaae05f4beef9313820053cc03f611bd1e29'], + }), + ('nipype', version, { + 'preinstallopts': "sed -i'' 's/.*neurdflib.*//g' nipype/info.py && ", + 'checksums': ['bc56ce63f74c9a9a23c6edeaf77631377e8ad2bea928c898cc89527a47f101cf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/nipypecli'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import nipype.interfaces'"] + +sanity_pip_check = True + +moduleclass = 'vis' From 67326514342cee600567555664967b4f1cbe31a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 May 2021 14:32:39 +0200 Subject: [PATCH 0915/2365] update to muParser 2.3.2 + remove R versionsuffix for R-INLA --- .../muParser/muParser-2.3.2-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/muParser/muParser-2.3.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.3.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d7822f8a35 --- /dev/null +++ b/easybuild/easyconfigs/m/muParser/muParser-2.3.2-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'muParser' +version = '2.3.2' + +homepage = 'https://beltoforion.de/article.php?a=muparser' + +description = """ + muParser is an extensible high performance math expression parser library + written in C++. It works by transforming a mathematical expression into + bytecode and precalculating constant parts of the expression. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/beltoforion/muparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b35fc84e3667d432e3414c8667d5764dfa450ed24a99eeef7ee3f6647d44f301'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = "-DENABLE_SAMPLES=OFF -DBUILD_SHARED_LIBS=ON" + +sanity_check_paths = { + 'files': ['include/muParser.h', 'lib/libmuparser.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' From 8cad2a454524a0187569763cdf9800f25961cf71 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 May 2021 14:40:44 +0200 Subject: [PATCH 0916/2365] fix configure option for Rmath when using PRCE2 as dependency --- easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb index c880502720..5f67afb26f 100644 --- a/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/Rmath/Rmath-4.0.4-foss-2020b.eb @@ -28,7 +28,7 @@ dependencies = [ # Copied from R-3.3.1-intel-2016b.eb. # Again, unsure if these affect R-math: R documentation doesn't specify. -configopts = "--with-pic --enable-threads --with-x=no --with-pcre1" +configopts = "--with-pic --enable-threads --with-x=no --with-pcre2" # Since we're only installing Rmath anyway, we don't care about R packages. configopts += " --with-recommended-packages=no" From 4b34d9f234aac2f09ae230ce498af8306f9b13db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 May 2021 16:13:55 +0200 Subject: [PATCH 0917/2365] drop 'v' from cell2location version, add missing Bison build dependency, use proper numba dependency --- ...cell2location-0.05-alpha-fosscuda-2020b.eb | 132 ++++++++++++++++++ 1 file changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb new file mode 100644 index 0000000000..a85c5f0689 --- /dev/null +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -0,0 +1,132 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'cell2location' +version = '0.05-alpha' +local_nodejsver = '-nodejs-12.19.0' + +homepage = 'https://github.com/BayraktarLab/cell2location/' +description = """Comprehensive mapping of tissue cell architecture via integrated +single cell and spatial transcriptomics (cell2location model)""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('Bison', '3.7.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Java', '11', '', True), + ('SciPy-bundle', '2020.11'), + ('leidenalg', '0.8.3'), + ('hyperopt', '0.2.5'), + ('CMake', '3.18.4'), + ('dill', '0.3.3'), + ('IPython', '7.18.1'), + ('Seaborn', '0.11.1'), + ('matplotlib', '3.3.3'), + ('libgpuarray', '0.7.6'), + ('PyMC3', '3.11.1'), + ('request', '2.88.1', local_nodejsver), + ('PyTables', '3.6.1'), + ('PyTorch', '1.7.1'), + ('statsmodels', '0.12.1'), + ('numba', '0.52.0'), + ('Theano', '1.1.2', '-PyMC'), + ('umap-learn', '0.4.6'), + ('pyro-api', '0.1.2'), + ('pyro-ppl', '1.5.2'), +] + +preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " + +use_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('get_version', '2.1', { + 'use_pip': False, + 'checksums': ['8156b526c2557537b8ca82241fa2b82b3da25939627398f6567dee31ba9725bc'], + }), + ('legacy-api-wrap', '1.2', { + 'use_pip': False, + 'checksums': ['034a44612da7e9943d3964363a98937ab54d55e3301075374abe0d521eb8101b'], + }), + ('descartes', '1.1.0', { + 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], + }), + ('mizani', '0.7.1', { + 'checksums': ['97eea665d17fdc6c827b832925c094839e1ef7bf65b3aa47105e772b6eca9b0a'], + }), + ('anndata', '0.7.5', { + 'checksums': ['2113a7463388013023f153e1a1446add4182883e3320b6e37dda18ee6210e038'], + }), + ('ipykernel', '5.3.4', { + 'checksums': ['9b2652af1607986a1b231c62302d070bc0534f564c393a5d9d130db9abbbe89d'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('natsort', '7.1.0', { + 'checksums': ['33f3f1003e2af4b4df20908fe62aa029999d136b966463746942efbfc821add3'], + }), + ('palettable', '3.3.0', { + 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], + }), + ('scanpy', '1.6.0', { + 'checksums': ['542d1f1fc0471e7312d4349142e1c2eee4a465cd514fe4e3337be166f425fa55'], + }), + ('louvain', '0.7.0', { + 'checksums': ['9734fc6bf8c15546d685a8c6d7d7ca0574cad4cb641e9ca91c3334028658f7c6'], + }), + ('loompy', '3.0.6', { + 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], + }), + ('bbknn', '1.3.12', { + 'checksums': ['7dc5257baa278fc92349ac7865674ce70802dc4e3afdafed87a099dff9e91159'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.1', { + 'checksums': ['e1b2358808aded7b2ff00ea0cd4e6a2d978fb2a44ee9b15ac23d64a81bf62706'], + }), + ('plotnine', '0.7.0', { + 'checksums': ['8ee67cbf010ccea32670760e930b7b02177030a89ccdf85e35d156a96ce36cd3'], + }), + ('numpy-groupies', '0.9.13', { + 'modulename': 'numpy_groupies', + 'source_tmpl': 'numpy_groupies-%(version)s.tar.gz', + 'checksums': ['7b17b291322353f07c51598512d077e3731da0a048cfa8f738f3460d1ef0658d'], + }), + ('annoy', '1.17.0', { + 'checksums': ['9891e264041d1dcf3af42f67fbb16cb273c5404bc8c869d0915a3087f71d58dd'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['2df1fe2b2b4ec5fcebc6c1d6146ce0cd79115bd14059b0ae882a41f1029a4efc'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/loompy', 'bin/scanpy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From d108b09a97a20930750db9ccf7cef74805bb7275 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 May 2021 17:13:33 +0200 Subject: [PATCH 0918/2365] add missing source URL for cell2location + rename source tarball on download --- .../c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index a85c5f0689..7d60fb1c61 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -117,7 +117,8 @@ exts_list = [ 'checksums': ['9891e264041d1dcf3af42f67fbb16cb273c5404bc8c869d0915a3087f71d58dd'], }), (name, version, { - 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/BayraktarLab/cell2location/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['2df1fe2b2b4ec5fcebc6c1d6146ce0cd79115bd14059b0ae882a41f1029a4efc'], }), ] From bb33188d9f49708ebe815007a94965f0fe158276 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 May 2021 17:04:09 +0200 Subject: [PATCH 0919/2365] update to latest carputils commit + bump openCARP dependency to version 6.0 --- .../carputils-20210513-foss-2020b.eb | 74 +++++++++++++++++++ .../o/openCARP/openCARP-6.0-foss-2020b.eb | 38 ++++++++++ 2 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/c/carputils/carputils-20210513-foss-2020b.eb create mode 100644 easybuild/easyconfigs/o/openCARP/openCARP-6.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/carputils/carputils-20210513-foss-2020b.eb b/easybuild/easyconfigs/c/carputils/carputils-20210513-foss-2020b.eb new file mode 100644 index 0000000000..ee94dbf3d2 --- /dev/null +++ b/easybuild/easyconfigs/c/carputils/carputils-20210513-foss-2020b.eb @@ -0,0 +1,74 @@ +easyblock = 'PythonBundle' + +name = 'carputils' +local_commit = '8658b24c' +version = '20210513' + +homepage = 'https://git.opencarp.org/openCARP/carputils' +description = "carputils is a Python framework for generating and running openCARP examples." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('openCARP', '6.0'), + ('matplotlib', '3.3.3'), + ('PyTables', '3.6.1'), + ('meshtool', '16'), + ('meshalyzer', '2.2'), +] + +use_pip = True + +# version restrictions are too strict, so strip them out +local_carputils_preinstallopts = "sed -i 's/[=><]=[0-9].*//g' requirements.py3.txt && " +# inject proper version, to prevent installing carputils with 0.0.0 as version... +local_carputils_preinstallopts += """sed -i 's/ description=/ version="0.0.1-pre", description=/g' setup.py && """ + +exts_list = [ + ('common', '0.1.2', { + 'checksums': ['3dfa982670abefc870043b239eaa0ecd860be7aa952b1931c1356b426ff8c76a'], + }), + ('doxypypy', '0.8.8.6', { + 'checksums': ['627571455c537eb91d6998d95b32efc3c53562b2dbadafcb17e49593e0dae01b'], + }), + ('pyDOE', '0.3.8', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + 'modulename': 'pyDOE', + }), + (name, version, { + 'source_urls': ['https://git.opencarp.org/openCARP/carputils/-/archive/%s/' % local_commit], + 'sources': [{'download_filename': 'carputils-%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['fb218a5f0a1148da3b05fc0e1625e0494aab9d462ff56baa7cb15bd4ef5f95ab'], + 'preinstallopts': local_carputils_preinstallopts, + }), +] + +fix_python_shebang_for = ['bin/*'] + +postinstallcmds = [ + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "%(installdir)s/bin/cusettings %(installdir)s/settings.yaml", + # location to openCARP bin subdirectory + r'sed -i "s@^\([ ]*CPU: \).*@\1$EBROOTOPENCARP/bin@" %(installdir)s/settings.yaml', + r'sed -i "s@^\(MESHTOOL_DIR: \).*@\1$EBROOTMESHTOOL/bin@" %(installdir)s/settings.yaml', + r'sed -i "s@^\(MESHALYZER_DIR: \).*@\1$EBROOTMESHALYZER@" %(installdir)s/settings.yaml', + r'sed -i "s@^\(REGRESSION_REF: \).*@\1/path/to/carp-tests-reference@" %(installdir)s/settings.yaml', + r'sed -i "s/^\(EMAIL: \).*/\1 example@email.com/" %(installdir)s/settings.yaml', + r'sed -i "s@^\(REGRESSION_TEMP: \).*@#\1 /tmp@" %(installdir)s/settings.yaml', +] + +sanity_check_paths = { + 'files': ['bin/carphelp', 'bin/carptests', 'bin/cusettings'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["carphelp --help"] + +sanity_pip_check = True + +modextravars = {'CARPUTILS_SETTINGS': '%(installdir)s/settings.yaml'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/openCARP/openCARP-6.0-foss-2020b.eb b/easybuild/easyconfigs/o/openCARP/openCARP-6.0-foss-2020b.eb new file mode 100644 index 0000000000..12b4155a3d --- /dev/null +++ b/easybuild/easyconfigs/o/openCARP/openCARP-6.0-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMakeCp' + +name = 'openCARP' +version = '6.0' + +homepage = 'https://opencarp.org' +description = "openCARP is an open cardiac electrophysiology simulator for in-silico experiments." + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://git.opencarp.org/openCARP/openCARP/-/archive/v%(version)s/'] +sources = ['openCARP-v%(version)s.tar.gz'] +patches = ['openCARP-3.2_build-info.patch'] +checksums = [ + '280f6dd2f5968e02e1f981f52cbd94da2ebb8d8fd00eb274d2fca6b566f40afb', # openCARP-v6.0.tar.gz + '43004c7dee2981677c4316c32ce20080ad2e70760d53981aaaaba55ebc659e8c', # openCARP-3.2_build-info.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('gengetopt', '2.23'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('PETSc', '3.14.4'), + ('zlib', '1.2.11'), +] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bench', 'igbapd', 'igbextract', 'igbhead', 'igbops', 'mesher', 'openCARP']], + 'dirs': [], +} + +moduleclass = 'bio' From 2a4217087ea99f3f58d6d7661d470c330d747d74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 May 2021 19:20:23 +0200 Subject: [PATCH 0920/2365] adding easyconfigs: impi-2019.12.320-iccifort-2020.4.304.eb --- .../impi-2019.12.320-iccifort-2020.4.304.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..a5ba5409ff --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2019.12.320' + +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17836/'] +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['8108fbf2353a9f1926036bb67647b65c0e4933a3eb66e1dc933960e5b055f320'] + +dependencies = [ + # needed by libfabric provider MLX introduced in Intel MPI v2019.6, + # https://software.intel.com/en-us/articles/improve-performance-and-stability-with-intel-mpi-library-on-infiniband + ('UCX', '1.9.0'), +] + +dontcreateinstalldir = True + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = True + +modextravars = { + # to enable SLURM integration with srun (site-specific) + # 'I_MPI_PMI_LIBRARY': 'libpmi2.so', +} + +# may be needed if you enable I_MPI_PMI_LIBRARY above +# osdependencies = [('slurm-libpmi')] + +moduleclass = 'mpi' From 3e46af3486c7c72683a0a92eb76deb711e67eb36 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 19 May 2021 14:53:34 +0200 Subject: [PATCH 0921/2365] adding easyconfigs: TensorFlow-2.5.0-fosscuda-2020b.eb and patches: TensorFlow-2.5.0_add-default-shell-env.patch, TensorFlow-2.5.0_add-protobuf-deps.patch, TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch, TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch, TensorFlow-2.5.0_remove-keras-nightly-dependency.patch --- .../TensorFlow-2.5.0-fosscuda-2020b.eb | 207 ++++++++++++++++++ 1 file changed, 207 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..ba58d8927e --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -0,0 +1,207 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.5.0' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), + ('NCCL', '2.8.3', '-CUDA-11.1.1', True), + ('Python', '3.8.6'), + ('h5py', '3.1.0'), + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +exts_default_options = { + 'sanity_pip_check': True, +} +use_pip = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('google-auth', '1.30.0', { + 'modulename': 'google.auth', + 'checksums': ['9ad25fba07f46a628ad4d0ca09f38dcb262830df2ac95b217f9b0129c9e42206'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.4', { + 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], + }), + ('Werkzeug', '2.0.0', { + 'checksums': ['3389bbfe6d40c6dd25e6d3f974155163c8b3de5bbda6a89342d4ab93fae80ba0'], + }), + ('absl-py', '0.12.0', { + 'modulename': 'absl', + 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.34.1', { + 'modulename': 'grpc', + 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], + }), + ('tensorboard_plugin_wit', '1.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard_plugin_profile', '2.4.0', { + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-default-shell-env.patch', + 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.5.0_remove-keras-nightly-dependency.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + 'checksums': [ + '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch + 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', + # TensorFlow-2.5.0_remove-keras-nightly-dependency.patch + '41f0fabbaed1fc0de5b8427f1b12cd359f2361b7c0e3cd81ba862a24e3f14327', + ], + }), +] + +moduleclass = 'lib' From 7a6fedf61a3cb81a7c537c5a1539650734cf2329 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 20 May 2021 14:49:21 +0200 Subject: [PATCH 0922/2365] {compiler}[AOMP/13.0-2] Add updated AOMP compiler module This is an updated version of the PR #12018. This PR updates the version to `13.0-2`. In addition this PR adds an improved patch which should force the built modules to pick up the EasyBuild installed version of `gcc`. This module requires the `aomp.py` EasyBlock to build. --- .../a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8b3302a846 --- /dev/null +++ b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Jørgen Nordmoen +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'AOMP' +version = '13.0-2' + +homepage = 'https://github.com/ROCm-Developer-Tools/aomp' +description = "AMD fork of LLVM, setup for OpenMP offloading to Accelerators" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/ROCm-Developer-Tools/aomp/releases/download/rel_%(version)s/'] +sources = ['aomp-%(version)s.tar.gz'] +patches = ['build_aomp-%(version)s.patch'] +checksums = [ + '0256a84aefcbf7c49112f068321b84e0620f4c43a9d490c64d820e40658e0d67', # aomp-13.0-2.tar.gz + '1deca48ec55e74b091731e48ce54097b88620062ed0cb05de1dc9d56c2016a21', # build_aomp-13.0-2.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.35'), + ('libffi', '3.3'), + ('numactl', '2.0.13'), +] + +sanity_check_paths = { + 'files': ['bin/clang', 'bin/ld.lld', 'include/omp.h'], + 'dirs': ['amdgcn', 'bin', 'include', 'lib'], +} + +moduleclass = 'compiler' From dbada405d2813925eeb6ea33049881721e151c9a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 20 May 2021 15:15:43 +0200 Subject: [PATCH 0923/2365] Removed non ASCII character from name --- easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb index 8b3302a846..3db59cebf1 100644 --- a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # -# Authors:: Jørgen Nordmoen +# Authors:: Jorgen Nordmoen # License:: GPLv2 or later, MIT, three-clause BSD. # $Id$ ## From 6c7355d477022dde4e78c29dcb6331549d4553c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 May 2021 17:02:15 +0200 Subject: [PATCH 0924/2365] use BFD linker for ccache 4.2.1 to fix build on CentOS/RHEL 8 --- easybuild/easyconfigs/c/ccache/ccache-4.2.1.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.2.1.eb b/easybuild/easyconfigs/c/ccache/ccache-4.2.1.eb index 7db922f043..c367614071 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.2.1.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.2.1.eb @@ -27,8 +27,11 @@ builddependencies = [ ('zstd', '1.4.5', '', ('GCCcore', local_gccver)), ] -preconfigopts = 'LDFLAGS="-static"' -configopts = '-DENABLE_DOCUMENTATION=OFF -DENABLE_IPO=ON -DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a"' +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-static -fuse-ld=bfd"' +configopts = '-DENABLE_DOCUMENTATION=OFF -DENABLE_IPO=ON -DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a" ' +# disable hunt for faster linker, since using ld.gold may fail (on CentOS 8, for example) +configopts += '-DUSE_FASTER_LINKER=OFF' sanity_check_paths = { 'files': ['bin/ccache'], From 55e74d262de5a5065bedc355af6ccfba005b88d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 May 2021 21:02:03 +0200 Subject: [PATCH 0925/2365] fix test step for libxc 4.3.4 and 5.1.x when using RPATH linking --- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb | 8 ++++++-- .../l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb | 4 ++++ easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb | 8 ++++++-- easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb | 8 ++++++-- 4 files changed, 22 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb index 1bd1ee4c45..2d16f4413b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb @@ -30,6 +30,8 @@ builddependencies = [ separate_build_dir = True +parallel = 1 + local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" # perform iterative build to get both static and shared libraries @@ -38,6 +40,10 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + runtest = 'test' sanity_check_paths = { @@ -46,6 +52,4 @@ sanity_check_paths = { 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], } -parallel = 1 - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb index a07e6e4dbc..81cacc26ca 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb @@ -46,6 +46,10 @@ configopts = [ parallel = 1 +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + runtest = 'test' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb index e38add051d..e62a0ad0fa 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb @@ -28,6 +28,12 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + runtest = 'test' sanity_check_paths = { @@ -36,6 +42,4 @@ sanity_check_paths = { 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], } -parallel = 1 - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb index 59a421a6ea..8aa007ac6f 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb @@ -28,6 +28,12 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + runtest = 'test' sanity_check_paths = { @@ -36,6 +42,4 @@ sanity_check_paths = { 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], } -parallel = 1 - moduleclass = 'chem' From 44cb5ab38a5d766d3f42255d3dd1ff4da4849317 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 May 2021 09:48:13 +0200 Subject: [PATCH 0926/2365] add R versionsuffix to R-INLA, since it requires R 4.0.4 --- .../R-INLA-21.05.02-foss-2020b-R-4.0.4.eb | 89 +++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..2760903f45 --- /dev/null +++ b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb @@ -0,0 +1,89 @@ +easyblock = 'Bundle' + +name = 'R-INLA' +version = '21.05.02' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://www.r-inla.org' +description = "R-INLA is a package in R that do approximate Bayesian inference for Latent Gaussian Models." + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('R', '4.0.4'), + ('GSL', '2.6'), + ('zlib', '1.2.11'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('METIS', '5.1.0'), + ('muParser', '2.3.2'), + ('Rmath', '%(rver)s'), + ('X11', '20201008'), +] + +default_easyblock = 'ConfigureMake' +# all components are installed from the same source tarball +default_component_specs = { + 'source_urls': ['https://github.com/hrue/r-inla/archive/refs/tags/'], + 'sources': [{'download_filename': 'Version_%s.tar.gz' % version, 'filename': 'R-INLA-%s.tar.gz' % version}], + 'skipsteps': ['configure'], + 'checksums': ['7e2f6f92ca36739ae8f948697491572cf62191955f74bbf495703e0e1ffb88a6'], +} + +local_gmrflib_buildopts = ' -C r-inla-*/gmrflib PREFIX=%(installdir)s CC="$CC" FC="$FC" ' +local_gmrflib_buildopts += ' FLAGS="$CXXFLAGS -DINLA_LINK_WITH_OPENBLAS " ' + +local_inla_buildopts = '-C r-inla-*/inlaprog PREFIX=%(installdir)s ' +local_inla_buildopts += ' CC="$CC" CXX="$CXX" FC="$FC" ' +local_inla_buildopts += ' FLAGS="$CXXFLAGS -DINLA_LINK_WITH_OPENBLAS"' + +components = [ + ('taucs', version, { + 'easyblock': 'MakeCp', + 'prebuildopts': "cd r-inla-*/extlibs && tar xvfz taucs-2.2--my-fix.tgz && cd taucs-2.2--my-fix && ", + 'buildopts': 'CC="$CC" CFLAGS="$CFLAGS" FC="$FC" FFLAGS="$FFLAGS" LIBBLAS="$LIBBLAS" LIBLAPACK="$LIBLAPACK"', + 'files_to_copy': [(['r-inla-*/extlibs/taucs-2.2--my-fix/lib/linux/libtaucs.a'], 'lib')], + }), + ('fmesher', version, { + 'buildopts': '-C r-inla-*/fmesher PREFIX=%(installdir)s CC="$CC" CXX="$CXX" FLAGS="$CXXFLAGS -std=c++11"', + 'installopts': '-C r-inla-*/fmesher PREFIX=%(installdir)s', + }), + ('GMRFLib', version, { + 'buildopts': local_gmrflib_buildopts, + 'installopts': '-C r-inla-*/gmrflib PREFIX=%(installdir)s', + }), + ('rinla', version, { + 'checksums': default_component_specs['checksums'] + [ + 'c88e22739d1238414d10a5473a99dbc8fa6ccf811f2e6dc7701e015025f62f07', + ], + 'patches': ['R-INLA-%(version)s-foss-2020b-remove-hardcoding.patch'], + 'easyblock': 'RPackage', + 'start_dir': 'r-inla-Version_%s/rinla' % version, + }), + (name, version, { + 'checksums': default_component_specs['checksums'] + [ + '3a71c714f230c4af6729898c8f2a11f6c3c73e14b3c02534c8ed2b16f385843b', + ], + 'patches': ['R-INLA-%(version)s-skip-binaries.patch'], + 'prebuildopts': 'export CPATH=$EBROOTR/lib64/R/include/:$CPATH && ', + 'buildopts': local_inla_buildopts, + 'installopts': '-C r-inla-*/inlaprog PREFIX=%(installdir)s', + }), +] + +postinstallcmds = ['ln -s %(installdir)s/bin/inla %(installdir)s/INLA/bin/linux/64bit/inla'] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': ['bin/fmesher', 'bin/inla', 'lib/libGMRFLib.a', 'lib/libGMRFLib-geo.a', 'lib/libtaucs.a'], + 'dirs': ['doc', 'include/GMRFLib'], +} + +sanity_check_commands = [ + "fmesher -h", + "inla -h", + "Rscript -e 'library(INLA)'", +] + +moduleclass = 'math' From 685326cc86575b83ffd3e7bb278b9e876d50a28d Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Fri, 21 May 2021 11:21:03 +0100 Subject: [PATCH 0927/2365] Create GeneMark-ET-4.65-GCCcore-10.2.0.eb Updated for latest versions of GeneMark, GCCcore and Perl5. --- .../GeneMark-ET-4.65-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2d0158f1b0 --- /dev/null +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'GeneMark-ET' +version = '4.65' + +homepage = 'http://exon.gatech.edu/GeneMark' +description = "Eukaryotic gene prediction suite with automatic training" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# download via http://exon.gatech.edu/GeneMark/license_download.cgi +sources = ['gmes_linux_64.tar.gz'] +checksums = ['62ea2dfa1954ab25edcc118dbeaeacf15924274fb9ed47bc54716cfd15ad04fe'] + +dependencies = [('Perl', '5.32.0')] + +fix_perl_shebang_for = ['*.pl'] + +sanity_check_paths = { + 'files': ['gmes.cfg', 'gmes_petap.pl'], + 'dirs': ['lib'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 7dfeae2e9bdfc6dfcb0b733dfe7463491db62c6e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 21 May 2021 14:03:30 +0100 Subject: [PATCH 0928/2365] adding easyconfigs: TRF-4.09.1-GCCcore-9.3.0.eb, TRF-4.09.1-GCCcore-10.2.0.eb --- .../t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9faf26915e --- /dev/null +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'TRF' +version = '4.09.1' + +homepage = 'https://tandem.bu.edu/trf/trf.html' +description = """Tandem Repeats Finder: a program to analyze DNA sequences.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'Benson-Genomics-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s -v"] + +moduleclass = 'bio' From b538c1e94d7030bb307f1b0259ba18fc7c5bf34b Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Fri, 21 May 2021 14:47:33 +0100 Subject: [PATCH 0929/2365] Update GeneMark-ET-4.65-GCCcore-10.2.0.eb Made changes recommended by reviewer. --- .../g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb index 2d0158f1b0..f6cc1e0092 100644 --- a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb @@ -9,7 +9,8 @@ description = "Eukaryotic gene prediction suite with automatic training" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} # download via http://exon.gatech.edu/GeneMark/license_download.cgi -sources = ['gmes_linux_64.tar.gz'] +# rename gmes_linux_64.tar.gz to gmes_linux_64-4.65.tar.gz +sources = ['gmes_linux_64-%(version)s.tar.gz'] checksums = ['62ea2dfa1954ab25edcc118dbeaeacf15924274fb9ed47bc54716cfd15ad04fe'] dependencies = [('Perl', '5.32.0')] From 6dea454a1f426bac126a37d78e3db5dc1f4614fd Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 21 May 2021 15:02:37 +0100 Subject: [PATCH 0930/2365] Add checksums --- easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb index 9faf26915e..9f5d55cc2a 100644 --- a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} github_account = 'Benson-Genomics-Lab' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] builddependencies = [ ('binutils', '2.35'), From 86ca29cc0a0e5a77252be9d85892dcd39ddbde42 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 21 May 2021 16:03:49 +0200 Subject: [PATCH 0931/2365] Add foss version and patches --- .../TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 202 ++++++++++++++++++ .../TensorFlow-2.5.0-fosscuda-2020b.eb | 12 +- 2 files changed, 210 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb new file mode 100644 index 0000000000..02180159e4 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -0,0 +1,202 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.5.0' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('Python', '3.8.6'), + ('h5py', '3.1.0'), + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +exts_default_options = { + 'sanity_pip_check': True, +} +use_pip = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('google-auth', '1.30.0', { + 'modulename': 'google.auth', + 'checksums': ['9ad25fba07f46a628ad4d0ca09f38dcb262830df2ac95b217f9b0129c9e42206'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.4', { + 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], + }), + ('Werkzeug', '2.0.0', { + 'checksums': ['3389bbfe6d40c6dd25e6d3f974155163c8b3de5bbda6a89342d4ab93fae80ba0'], + }), + ('absl-py', '0.12.0', { + 'modulename': 'absl', + 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.34.1', { + 'modulename': 'grpc', + 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], + }), + ('tensorboard_plugin_wit', '1.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard_plugin_profile', '2.4.0', { + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + ('keras_nightly', '2.5.0.dev2021032900', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-default-shell-env.patch', + 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-compilation-on-ppc.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + 'checksums': [ + '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-compilation-on-ppc.patch + 'e408251d6bd8cbd811e5d1244e211621f17b64d22fd18fd6ec1a59edb8e0460d', + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index ba58d8927e..049feeb9c2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -142,6 +142,10 @@ exts_list = [ ('portpicker', '1.3.1', { 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], }), + ('keras_nightly', '2.5.0.dev2021032900', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], + }), (name, version, { 'patches': [ 'TensorFlow-2.1.0_fix-cuda-build.patch', @@ -150,8 +154,8 @@ exts_list = [ 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-compilation-on-ppc.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', - 'TensorFlow-2.5.0_remove-keras-nightly-dependency.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -196,10 +200,10 @@ exts_list = [ '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-compilation-on-ppc.patch + 'e408251d6bd8cbd811e5d1244e211621f17b64d22fd18fd6ec1a59edb8e0460d', # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch - 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', - # TensorFlow-2.5.0_remove-keras-nightly-dependency.patch - '41f0fabbaed1fc0de5b8427f1b12cd359f2361b7c0e3cd81ba862a24e3f14327', + 'e8159e92e68e88095a553dd4eb1d4354861e35bcdac32f938a055bc1e69dd82e', ], }), ] From 029072d62f03c33de4cfee009a406d7c79ce7525 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 May 2021 17:57:24 +0100 Subject: [PATCH 0932/2365] correct the patch and apply it earlier in the R-INLA install --- .../r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb index 2760903f45..2d9520f22f 100644 --- a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb @@ -45,6 +45,10 @@ components = [ 'files_to_copy': [(['r-inla-*/extlibs/taucs-2.2--my-fix/lib/linux/libtaucs.a'], 'lib')], }), ('fmesher', version, { + 'checksums': default_component_specs['checksums'] + [ + '51b7dbdc79a01a0ff1da3b2aa4f18569b8bc921573f6f6ecc7f107c935ef72ea', + ], + 'patches': ['R-INLA-%(version)s-skip-binaries.patch'], 'buildopts': '-C r-inla-*/fmesher PREFIX=%(installdir)s CC="$CC" CXX="$CXX" FLAGS="$CXXFLAGS -std=c++11"', 'installopts': '-C r-inla-*/fmesher PREFIX=%(installdir)s', }), @@ -61,10 +65,6 @@ components = [ 'start_dir': 'r-inla-Version_%s/rinla' % version, }), (name, version, { - 'checksums': default_component_specs['checksums'] + [ - '3a71c714f230c4af6729898c8f2a11f6c3c73e14b3c02534c8ed2b16f385843b', - ], - 'patches': ['R-INLA-%(version)s-skip-binaries.patch'], 'prebuildopts': 'export CPATH=$EBROOTR/lib64/R/include/:$CPATH && ', 'buildopts': local_inla_buildopts, 'installopts': '-C r-inla-*/inlaprog PREFIX=%(installdir)s', From 0584b1aa15c35b7e51eb756c5a71f3b955b122d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 22 May 2021 20:40:06 +0200 Subject: [PATCH 0933/2365] add missing xproto build dependency to imake easyconfig --- .../i/imake/imake-1.0.8-GCCcore-10.2.0.eb | 6 +++- .../x/xproto/xproto-7.0.31-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 2 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb index 98c68c4297..773071072b 100644 --- a/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-10.2.0.eb @@ -13,7 +13,11 @@ source_urls = ['https://artfiles.org/x.org/pub/individual/util/'] sources = [SOURCE_TAR_GZ] checksums = ['8178a09bfef33ad5f61cb5cb62283df7d3a5682f014507d2e7cfd922485a5c00'] -builddependencies = [('binutils', '2.35')] +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), + ('xproto', '7.0.31'), +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ccmakedep', 'cleanlinks', 'imake', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..56ff7cb84e --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = 'https://www.freedesktop.org/wiki/Software/xlibs' +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + ('binutils', '2.35'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' From 7a612ac2283b39109ee3899c671a778df75be543 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 24 May 2021 10:16:55 +0200 Subject: [PATCH 0934/2365] remove postinstallcmds from imkl 2020.x easyconfigs, easyblock not installs examples --- .../i/imkl/imkl-2020.4.304-gompi-2020b.eb | 13 ------------- .../i/imkl/imkl-2020.4.304-iimpi-2020b.eb | 13 ------------- .../i/imkl/imkl-2020.4.304-iimpic-2020b.eb | 13 ------------- .../i/imkl/imkl-2020.4.304-iompi-2020b.eb | 13 ------------- 4 files changed, 52 deletions(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb index d292d071b1..541c3c12ae 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb @@ -23,17 +23,4 @@ license_file = HOME + '/licenses/intel/license.lic' interfaces = True -postinstallcmds = [ - # extract the examples - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', -] - -modextravars = { - 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', -} - moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb index 9675315f1d..e1f7dd0c3f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb @@ -23,17 +23,4 @@ license_file = HOME + '/licenses/intel/license.lic' interfaces = True -postinstallcmds = [ - # extract the examples - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', -] - -modextravars = { - 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', -} - moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb index e26a6afff2..a350ab4a6e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb @@ -23,17 +23,4 @@ license_file = HOME + '/licenses/intel/license.lic' interfaces = True -postinstallcmds = [ - # extract the examples - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', -] - -modextravars = { - 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', -} - moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb index 7536b65853..89d0c991d8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb @@ -23,17 +23,4 @@ license_file = HOME + '/licenses/intel/license.lic' interfaces = True -postinstallcmds = [ - # extract the examples - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', -] - -modextravars = { - 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', -} - moduleclass = 'numlib' From 2686bc06f245856e88be0b721340b70e30a0ffbb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 24 May 2021 10:59:10 +0200 Subject: [PATCH 0935/2365] Nilearn: Add missing checksum --- easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb index 01da8bf51a..0dacbc3487 100644 --- a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb @@ -9,6 +9,7 @@ description = """Nilearn is a Python module for fast and easy statistical learni toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] +checksums = ['8b1409a5e1f0f6d1a1f02555c2f11115a2364f45f1e57bcb5fb3c9ea11f346fa'] dependencies = [ ('Python', '3.8.6'), From d5d0e7a1560731256cfb758430f041e96d077783 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 24 May 2021 18:26:54 +0200 Subject: [PATCH 0936/2365] replace hardcoded -march=native with $CXXFLAGS in meshtool easyconfig --- easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb b/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb index cc3f7d844b..be07346800 100644 --- a/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb @@ -13,6 +13,8 @@ source_urls = ['https://bitbucket.org/aneic/meshtool/get/'] sources = ['v%(version)s.tar.gz'] checksums = ['822e715b363603dfe320b4b530ad4a77cc5ecd0ccb692d77e01b6ecfe7da9d38'] +prebuildopts = 'sed -i "s/-march=native/$CXXFLAGS/g" switches.def && ' + files_to_copy = [(['meshtool'], 'bin')] sanity_check_paths = { From d77978d1ebfb7a737d85eb8ce8b0393c46af646b Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 25 May 2021 10:35:44 +0100 Subject: [PATCH 0937/2365] update checksum --- .../easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb index 2d9520f22f..7601b307f5 100644 --- a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb @@ -46,7 +46,7 @@ components = [ }), ('fmesher', version, { 'checksums': default_component_specs['checksums'] + [ - '51b7dbdc79a01a0ff1da3b2aa4f18569b8bc921573f6f6ecc7f107c935ef72ea', + '9ec131a8a470ea2614be77f917c0d66eacecbba4b511c90d6427059fe2c36b51', ], 'patches': ['R-INLA-%(version)s-skip-binaries.patch'], 'buildopts': '-C r-inla-*/fmesher PREFIX=%(installdir)s CC="$CC" CXX="$CXX" FLAGS="$CXXFLAGS -std=c++11"', From e609732dfb922a26561ecee7cb91141f6bd5d71d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Tue, 25 May 2021 11:44:58 +0200 Subject: [PATCH 0938/2365] Added necessary runtime dependency on 'ncurses' --- easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb index 3db59cebf1..4577ff337d 100644 --- a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb @@ -32,6 +32,7 @@ builddependencies = [ dependencies = [ ('binutils', '2.35'), ('libffi', '3.3'), + ('ncurses', '6.2'), ('numactl', '2.0.13'), ] From 71a2eab7684701ec13f6e6c89140b45b756b3776 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 25 May 2021 11:49:22 +0200 Subject: [PATCH 0939/2365] capitalize name; sanity_check_commands --- .../easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb new file mode 100644 index 0000000000..c3feca2d8a --- /dev/null +++ b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb @@ -0,0 +1,47 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/05 +easyblock = 'PythonPackage' + +name = 'CSB' +version = '1.2.5' + +homepage = 'https://github.com/csb-toolbox' +description = """Computational Structural Biology Toolbox +CSB is a python library and application framework, which can be used to solve +problems in the field of structural bioinformatics. If you are a +bioinformatician, software engineer or a researcher working in this field, +chances are you may find something useful here. Our package consists of a few +major components: +1. Core class library - object-oriented, granular, with an emphasis on design +and clean interfaces. +2. Application framework - console applications ("protocols"), which consume +objects from the core library in order to build something executable (and +hopefully useful). +3. Test framework - ensures that the library actually works. +""" +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/csb-toolbox/CSB/releases/download/R-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3f05924acaca6673f94fc430965eabfe59a0c9b2cbdda8c1cb50a43ffe83f254'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +sanity_check_commands = ['csb-%s -h' % x for x in [ + 'bfit', 'bfite', 'buildhmm', 'csfrag', 'embd', + 'hhfrag', 'hhsearch', 'precision', 'promix', 'test']] + +sanity_check_paths = { + 'files': ['bin/csb-%s' % x for x in [ + 'bfit', 'bfite', 'buildhmm', 'csfrag', 'embd', + 'hhfrag', 'hhsearch', 'precision', 'promix', 'test']], + 'dirs': ["lib/python%(pyshortver)s/site-packages"] +} + +moduleclass = 'bio' From f56fc76a6539abdaaf84a1a3436e716c0517ec49 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Tue, 25 May 2021 12:39:13 +0200 Subject: [PATCH 0940/2365] adding easyconfigs: CVXOPT-1.2.6-foss-2020b.eb --- .../c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb new file mode 100644 index 0000000000..be6d64350b --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'CVXOPT' +version = '1.2.6' + +homepage = 'https://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['CVXOPT-1.2.1-fix-setup-py.patch'] +checksums = [ + 'a4c433706fd0ad9d47e7f222773a7f7601766fb8e74b633524b3c3fce29aa73e', # cvxopt-1.2.6.tar.gz + '85d8475098895e9af45f330489a712b5b944489c5fb4a6c67f59bef8fed4303d', # CVXOPT-1.2.1-fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('GSL', '2.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' +preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' + +installopts = ' --no-binary cvxopt' + +sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && nosetests'] + +moduleclass = 'math' From c55e31edb2006117e374374cf4f0dcbb0fbae004 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Tue, 25 May 2021 12:42:16 +0200 Subject: [PATCH 0941/2365] adding easyconfigs: Quandl-3.6.1-foss-2020b.eb --- .../q/Quandl/Quandl-3.6.1-foss-2020b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb new file mode 100644 index 0000000000..23278546ce --- /dev/null +++ b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'Quandl' +version = '3.6.1' + +homepage = 'https://pypi.python.org/pypi/Quandl' +description = "A Python library for Quandl’s RESTful API." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('inflection', '0.5.1', { + 'checksums': ['1a29730d366e996aaacffb2f1f1cb9593dc38e2ddd30c91250c6dde09ea9b417'], + }), + ('more-itertools', '8.8.0', { + 'checksums': ['83f0308e05477c68f56ea3a888172c78ed5d5b3c282addb67508e7ba6c8f813a'], + }), + ('pyOpenSSL', '20.0.1', { + 'modulename': 'OpenSSL', + 'checksums': ['4c231c759543ba02560fcd2480c48dcec4dae34c9da7d3747c508227e0624b51'], + }), + ('ndg-httpsclient', '0.5.1', { + 'modulename': 'ndg', + 'source_tmpl': 'ndg_httpsclient-%(version)s.tar.gz', + 'checksums': ['d72faed0376ab039736c2ba12e30695e2788c4aa569c9c3e3d72131de2592210'], + }), + (name, version, { + 'checksums': ['84414e5f8e870a9c8a9392e9dc639d50e839c5f5e07737a09bb57dd8b14b264b'], + }), +] + +moduleclass = 'tools' From 2fd6ead089b86fc546cc2f53ae9b8f70b4f4850a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 May 2021 13:26:30 +0200 Subject: [PATCH 0942/2365] use standard 'postinstallcmds' rather than custom 'ext_postinstallcmds' easyconfig parameter in DROP and CNVkit easyconfigs --- .../easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb | 5 +---- .../easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb | 4 ++-- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb index d6aa968a71..4afe9aa817 100644 --- a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb @@ -32,10 +32,7 @@ exts_list = [ 'checksums': ['b1b803fa18c8a8ca4a8fd2824573914bbff7574e3dc6be770ab68efd00503341'], }), (name, version, { - 'ext_postinstallcmds': [ - 'cd test/', - 'make ', - ], + 'postinstallcmds': ["cd test/ && make"], 'modulename': 'cnvlib', 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/etal/cnvkit/archive/'], diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb index 83694e1330..020b8f5f67 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -26,7 +26,7 @@ dependencies = [ ('Pandoc', '2.13', '', True), ] -# added ext_postinstallcmds to pandoc: import fails if pandoc/definitions dir is not installed +# postinstallcmds for pandoc are required to avoid that import fails because pandoc/definitions dir is not installed exts_list = [ ('wbuild', '1.8.0', { 'checksums': ['3088d3fcbc71106464f20e3546a73df400dc03d17f11e70bdb15d35d7e6c5a7e'], @@ -45,7 +45,7 @@ exts_list = [ 'checksums': ['4a318ad1dcf6e9355b8ae18195c707d26413782b57ac5c740cc696b44350c959'], }), ('pandoc', '1.0.2', { - 'ext_postinstallcmds': [ + 'postinstallcmds': [ 'cp -a pandoc/definitions %(installdir)s/lib/python%(pyshortver)s/site-packages/pandoc/', ], 'source_tmpl': 'v%(version)s.tar.gz', From eb60236706a114a23018a44c2bc1c65aa2de9f8c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 25 May 2021 12:41:18 +0200 Subject: [PATCH 0943/2365] Add patch to fix GCC 10.2.0 rejecting valid code on PPC --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index ead740a862..c145d06599 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -32,7 +32,8 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', - 'GCC-10.2_fix-has-include-Fortran.patch', + 'GCCcore-10.2.0_fix-has-include-Fortran.patch', + 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', ] checksums = [ '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz @@ -44,7 +45,9 @@ checksums = [ 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # nvptx-tools-20180301.tar.gz '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCC-10.2_fix-has-include-Fortran.patch + 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCCcore-10.2.0_fix-has-include-Fortran.patch + # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch + 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', ] builddependencies = [ From dacbe10110aaa7714f09ad343fb7a704f65db0ae Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 25 May 2021 14:18:07 +0200 Subject: [PATCH 0944/2365] transctiptclean and its dependencies --- .../p/pyfasta/pyfasta-0.5.2-foss-2020b.eb | 29 +++++++++++++++ .../TranscriptClean-2.0.2-foss-2020b.eb | 35 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb new file mode 100644 index 0000000000..60fad1ab28 --- /dev/null +++ b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pyfasta' +version = '0.5.2' + +homepage = 'https://pypi.org/project/pyfasta/' +description = """fast, memory-efficient, pythonic (and command-line) access to fasta sequence files""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'] + +use_pip = True + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11') +] +modextrapaths = { + 'PYTHONPATH': ['lib/python3.8/site-packages/'] +} +sanity_check_paths = { + 'files': ['bin/pyfasta'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb b/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb new file mode 100644 index 0000000000..045f172b48 --- /dev/null +++ b/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Denis Kristak (INUITS) + +easyblock = "Tarball" + +name = 'TranscriptClean' +version = '2.0.2' + +homepage = 'https://github.com/mortazavilab/TranscriptClean' +description = """TranscriptClean is a Python program that corrects mismatches, microindels, +and noncanonical splice junctions in long reads that have been mapped to the genome.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +source_urls = ['https://github.com/mortazavilab/TranscriptClean/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['27326c10d04a2e2fef29865fc3f040a8db705ea4a4aeb6cf48a36c102f00381c'] + +dependencies = [ + ('R', '4.0.4'), + ('Python', '3.8.6'), + ('BEDTools', '2.30.0'), + ('SAMtools', '1.12'), + ('pybedtools', '0.8.2'), + ('SciPy-bundle', '2020.11'), + ('pyfasta', '0.5.2'), +] + +sanity_check_commands = ['python %(installdir)s/TranscriptClean.py --help'] + +sanity_check_paths = { + 'files': ['dstruct.py', 'TranscriptClean.py', 'transcript.py'], + 'dirs': [], +} + +moduleclass = 'tools' From e217428b146ea52b688116d5cc923ba394620c95 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Tue, 25 May 2021 14:24:37 +0200 Subject: [PATCH 0945/2365] Added build dependency on 'elfutils' --- easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb index 4577ff337d..6e2b175192 100644 --- a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('CMake', '3.18.4'), ('Perl', '5.32.0'), ('Python', '3.8.6'), + ('elfutils', '0.183'), ('pkg-config', '0.29.2'), ] From ac3fbb33070fd1842c215ebbd7238a620fe3e28b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Tue, 25 May 2021 14:44:56 +0200 Subject: [PATCH 0946/2365] {lib}[GCCcore/10.2.0] Updated 'elfutils' Updated `elfutils` and its dependency `libmicrohttpd` to use `GCCcore/10.2.0` toolchain. --- .../elfutils/elfutils-0.183-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ .../libmicrohttpd-0.9.73-GCCcore-10.2.0.eb | 31 ++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..33fce2dbe9 --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.183' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/0.183/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['c3637c208d309d58714a51e61e63f1958808fead882e9b607506a29e5474f2c5'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.35'), + ('bzip2', '1.0.8'), + ('cURL', '7.72.0'), + ('libarchive', '3.4.3'), + ('libmicrohttpd', '0.9.73'), + ('SQLite', '3.33.0'), + ('XZ', '5.2.5'), + ('zstd', '1.4.5'), +] + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.so'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8665a8d9e2 --- /dev/null +++ b/easybuild/easyconfigs/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libmicrohttpd' +version = '0.9.73' + +homepage = 'https://www.gnu.org/software/libmicrohttpd/' + +description = """ + GNU libmicrohttpd is a small C library that is supposed to make it easy to run + an HTTP server as part of another application. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libmicrohttpd/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a37b2f1b88fd1bfe74109586be463a434d34e773530fc2a74364cfcf734c032e'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('cURL', '7.72.0')] + +sanity_check_paths = { + 'files': ['include/microhttpd.h', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'share/man/man3/%(name)s.3'], + 'dirs': [] +} + +moduleclass = 'lib' From 8bc159b96cc3813e2a065d267b541ba9f50040df Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 25 May 2021 15:01:54 +0200 Subject: [PATCH 0947/2365] fix installation of fmesher within INLA --- .../R-INLA-21.05.02-foss-2020b-R-4.0.4.eb | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb index 2760903f45..c6cab7567a 100644 --- a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb @@ -54,7 +54,7 @@ components = [ }), ('rinla', version, { 'checksums': default_component_specs['checksums'] + [ - 'c88e22739d1238414d10a5473a99dbc8fa6ccf811f2e6dc7701e015025f62f07', + '368bef641bbb55fe198529ee350e603936efebfca7b16f54a6c60573ecef2e9d', ], 'patches': ['R-INLA-%(version)s-foss-2020b-remove-hardcoding.patch'], 'easyblock': 'RPackage', @@ -71,19 +71,18 @@ components = [ }), ] -postinstallcmds = ['ln -s %(installdir)s/bin/inla %(installdir)s/INLA/bin/linux/64bit/inla'] +local_bins = ['inla', 'fmesher'] -modextrapaths = {'R_LIBS_SITE': ''} +postinstallcmds = ['ln -s %%(installdir)s/bin/%s %%(installdir)s/INLA/bin/linux/64bit/%s' % (x,x) for x in local_bins] sanity_check_paths = { - 'files': ['bin/fmesher', 'bin/inla', 'lib/libGMRFLib.a', 'lib/libGMRFLib-geo.a', 'lib/libtaucs.a'], + 'files': ['%s/%s' % (p, x) for p in ['bin', 'INLA/bin/linux/64bit'] for x in local_bins] + + ['lib/libGMRFLib.a', 'lib/libGMRFLib-geo.a', 'lib/libtaucs.a'], 'dirs': ['doc', 'include/GMRFLib'], } -sanity_check_commands = [ - "fmesher -h", - "inla -h", - "Rscript -e 'library(INLA)'", -] +sanity_check_commands = ["Rscript -e 'library(INLA)'"] + ["%s -h" % x for x in local_bins] + +modextrapaths = {'R_LIBS_SITE': ''} moduleclass = 'math' From 2abf717dbf6b19831802da78e704ee48331648b8 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 25 May 2021 15:10:10 +0200 Subject: [PATCH 0948/2365] added download_dep_fail and sanity_pip_check parameters --- easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb index 60fad1ab28..79b24c73ca 100644 --- a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] checksums = ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'] use_pip = True +download_dep_fail = True +sanity_pip_check = True dependencies = [ ('Python', '3.8.6'), From ebacf3535512fa3ac54b10ab32dc7c70566f00d8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 25 May 2021 15:37:42 +0200 Subject: [PATCH 0949/2365] Remove patch --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 5 ++--- .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 3 --- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 02180159e4..1328e5c514 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -39,6 +39,8 @@ dependencies = [ ('libpng', '1.6.37'), ('snappy', '1.1.8'), ('zlib', '1.2.11'), + # Must be here to fix a bug with ld.gold on PPC and last as e.g. Python also loads binutils (the old version) + ('binutils', '2.35.2'), ] exts_default_options = { @@ -151,7 +153,6 @@ exts_list = [ 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', - 'TensorFlow-2.5.0_fix-compilation-on-ppc.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -193,8 +194,6 @@ exts_list = [ '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', - # TensorFlow-2.5.0_fix-compilation-on-ppc.patch - 'e408251d6bd8cbd811e5d1244e211621f17b64d22fd18fd6ec1a59edb8e0460d', ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 049feeb9c2..c08ced19df 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -154,7 +154,6 @@ exts_list = [ 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', - 'TensorFlow-2.5.0_fix-compilation-on-ppc.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -200,8 +199,6 @@ exts_list = [ '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', - # TensorFlow-2.5.0_fix-compilation-on-ppc.patch - 'e408251d6bd8cbd811e5d1244e211621f17b64d22fd18fd6ec1a59edb8e0460d', # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch 'e8159e92e68e88095a553dd4eb1d4354861e35bcdac32f938a055bc1e69dd82e', ], From 1d78845c07a8d7ab6dc18b900cd589d3cb1635d5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 25 May 2021 15:53:27 +0200 Subject: [PATCH 0950/2365] Use keras as the modulename --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 1328e5c514..39a76d38d8 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -143,6 +143,7 @@ exts_list = [ 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], }), ('keras_nightly', '2.5.0.dev2021032900', { + 'modulename': 'keras', 'source_tmpl': SOURCE_WHL, 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], }), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index c08ced19df..b15e08f3b9 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -143,6 +143,7 @@ exts_list = [ 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], }), ('keras_nightly', '2.5.0.dev2021032900', { + 'modulename': 'keras', 'source_tmpl': SOURCE_WHL, 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], }), From f36dbce367c08ebac4ccbca66497ebb8f3ff934b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 25 May 2021 16:03:00 +0200 Subject: [PATCH 0951/2365] Fix GPU patch checksum --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index b15e08f3b9..e80854a3f6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -201,7 +201,7 @@ exts_list = [ # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch - 'e8159e92e68e88095a553dd4eb1d4354861e35bcdac32f938a055bc1e69dd82e', + 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', ], }), ] From 0a18774439ff8eabb82009aa8c1f137f7990d42b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 May 2021 16:38:06 +0200 Subject: [PATCH 0952/2365] fix trivial code style issue --- .../easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb index c6cab7567a..030a7dd0a2 100644 --- a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb @@ -73,7 +73,7 @@ components = [ local_bins = ['inla', 'fmesher'] -postinstallcmds = ['ln -s %%(installdir)s/bin/%s %%(installdir)s/INLA/bin/linux/64bit/%s' % (x,x) for x in local_bins] +postinstallcmds = ['ln -s %%(installdir)s/bin/%s %%(installdir)s/INLA/bin/linux/64bit/%s' % (x, x) for x in local_bins] sanity_check_paths = { 'files': ['%s/%s' % (p, x) for p in ['bin', 'INLA/bin/linux/64bit'] for x in local_bins] + From 7d4d954e2c762d409401884ba83fa054f24ef0ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 May 2021 20:18:55 +0200 Subject: [PATCH 0953/2365] {bio}[GCC/10.2.0] pyspoa v0.0.8, spoa v4.0.7 w/ Python 3.8.6 --- .../p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb | 50 +++++++++++++++++++ .../s/spoa/spoa-4.0.7-GCC-10.2.0.eb | 29 +++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb new file mode 100644 index 0000000000..5de35fb7c3 --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'pyspoa' +version = '0.0.8' + +homepage = 'https://github.com/nanoporetech/pyspoa' +description = "Python bindings to spoa." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [ + { + 'source_urls': ['https://github.com/nanoporetech/pyspoa/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'pyspoa-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/USCiLab/cereal/archive/'], + 'download_filename': '3e4d1b8.tar.gz', + 'filename': 'cereal-20200423.tar.gz', + }, +] +patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] +checksums = [ + 'a1e630ef30a42d8e8c076d914261d0d34060631d64694569d52c1a2be5deada7', # pyspoa-0.0.8.tar.gz + '284cd14c1e60b36c966bcc8ce650d0b798b8a836d6c379e021e0da0dbe6ddf38', # cereal-20200423.tar.gz + 'a98c82ae8346b48952b171675f9df7ab1c95ea5421afcf5bcd778c01c5ee5a52', # pyspoa-0.0.8_use-spoa-dep.patch +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), + ('spoa', '4.0.7'), +] + +download_dep_fail = True + +preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +# strip out cmake requirements, since we provide that as proper dependency +preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " + +use_pip = True + +options = {'modulename': 'spoa'} + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb new file mode 100644 index 0000000000..61912e520f --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '4.0.7' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] +sources = ['spoa-v%(version)s.tar.gz'] +checksums = ['f7a8cd039e4aabea1481e123387fedaa8f87e55418a3649408a615f5c6b1b9a4'] + +builddependencies = [('CMake', '3.18.4')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a', 'lib/pkgconfig/spoa-1.pc'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +moduleclass = 'bio' From 28035821a01a4785526ed9e1333e29d62b9933f6 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Tue, 25 May 2021 20:46:41 +0200 Subject: [PATCH 0954/2365] Drop source_urls --- easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb index 23278546ce..3c6f28fca3 100644 --- a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb +++ b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb @@ -15,8 +15,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('inflection', '0.5.1', { 'checksums': ['1a29730d366e996aaacffb2f1f1cb9593dc38e2ddd30c91250c6dde09ea9b417'], From fed81471bd333f9301e0581f33eaf8ea6a166811 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Wed, 26 May 2021 00:43:56 +0200 Subject: [PATCH 0955/2365] sanity_pip_check --- easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb index 3c6f28fca3..ea0ed5b542 100644 --- a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb +++ b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb @@ -14,6 +14,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ ('inflection', '0.5.1', { From 76aceabb53ec9ed3a3b2946d668ef6891f077a59 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Wed, 26 May 2021 00:48:30 +0200 Subject: [PATCH 0956/2365] adding easyconfigs: XCFun-2.1.1-GCCcore-10.2.0.eb --- .../x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c9423b441d --- /dev/null +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'XCFun' +version = '2.1.1' + +homepage = 'https://xcfun.readthedocs.io' +description = """Arbitrary order exchange-correlation functional library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/dftlibs/xcfun/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8b602df74c7be83d501532565deafd1b7881946d94789122f24c309a669298ab'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] + +separate_build_dir = True +build_type = 'release' + +modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} + +sanity_check_paths = { + 'files': ['lib/libxcfun.%s' % SHLIB_EXT], + 'dirs': ['include/XCFun'] +} + +moduleclass = 'chem' From 4c23d4eddf5fda24ea098cedddaeee98b1ea963e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 26 May 2021 10:18:41 +0200 Subject: [PATCH 0957/2365] updating ECs to pass tests --- .../easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb | 7 ++----- .../t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb | 3 ++- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb index 79b24c73ca..c288ff59f2 100644 --- a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb @@ -8,7 +8,6 @@ description = """fast, memory-efficient, pythonic (and command-line) access to f toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'] @@ -20,12 +19,10 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11') ] -modextrapaths = { - 'PYTHONPATH': ['lib/python3.8/site-packages/'] -} +sanity_check_commands = ['pyfasta extract --help'] sanity_check_paths = { 'files': ['bin/pyfasta'], - 'dirs': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb b/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb index 045f172b48..0774208a6d 100644 --- a/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb @@ -11,12 +11,13 @@ description = """TranscriptClean is a Python program that corrects mismatches, m and noncanonical splice junctions in long reads that have been mapped to the genome.""" toolchain = {'name': 'foss', 'version': '2020b'} + source_urls = ['https://github.com/mortazavilab/TranscriptClean/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['27326c10d04a2e2fef29865fc3f040a8db705ea4a4aeb6cf48a36c102f00381c'] dependencies = [ - ('R', '4.0.4'), + ('R', '4.0.3'), ('Python', '3.8.6'), ('BEDTools', '2.30.0'), ('SAMtools', '1.12'), From eba3509ccc7a0604d3f7884b62e0026810756a9d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 26 May 2021 10:47:30 +0200 Subject: [PATCH 0958/2365] updating ECs to pass tests --- .../t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb b/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb index 0774208a6d..8c99143619 100644 --- a/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb @@ -20,7 +20,7 @@ dependencies = [ ('R', '4.0.3'), ('Python', '3.8.6'), ('BEDTools', '2.30.0'), - ('SAMtools', '1.12'), + ('SAMtools', '1.11'), ('pybedtools', '0.8.2'), ('SciPy-bundle', '2020.11'), ('pyfasta', '0.5.2'), From 42c0bf6103c9d9357da299b24e57652e969ef3d8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Wed, 26 May 2021 12:53:47 +0200 Subject: [PATCH 0959/2365] {devel}[gcccuda/2020b] hipify-clang 4.2.0 `hipify-clang` is a clang-based tool for translating CUDA sources into HIP sources. It translates CUDA source into an abstract syntax tree, which is traversed by transformation matchers. After applying all the matchers, the output HIP source is produced. --- .../hipify-clang-4.2.0-gcccuda-2020b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/c/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb diff --git a/easybuild/easyconfigs/c/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/c/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb new file mode 100644 index 0000000000..661e8fe8d5 --- /dev/null +++ b/easybuild/easyconfigs/c/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'hipify-clang' +version = '4.2.0' + +homepage = 'https://github.com/ROCm-Developer-Tools/HIPIFY' +description = """Hipify-clang is a clang-based tool for translating CUDA + sources into HIP sources. It translates CUDA source into an abstract syntax + tree, which is traversed by transformation matchers. After applying all the + matchers, the output HIP source is produced.""" + +toolchain = {'name': 'gcccuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ROCm-Developer-Tools/HIPIFY/archive/refs/tags/'] +sources = ['rocm-%(version)s.tar.gz'] +checksums = ['afdc82ae00e14e8e742be6cd47d8fb120d18fc52fe96cba8d8ac4c56176a432e'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('zlib', '1.2.11'), +] + +dependencies = [ + # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), + ('Clang', '11.0.1'), + # ('Python', '3.8.6'), +] + +configopts = '-DHIPIFY_CLANG_TESTS=0' +configopts += ' -DCMAKE_INSTALL_PREFIX=%(installdir)s' +configopts += ' -DCMAKE_PREFIX_PATH=$EBROOTCLANG' +# NOTE: The following configuration options are needed if building with tests +# (as activated by 'runtest' below), for these to work the above commented +# dependencies need to be uncommented +# configopts += ' -DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA' +# configopts += ' -DCUDA_DNN_ROOT_DIR=$EBROOTCUDNN' +# configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python' + +# runtest = 'test-hipify' + +# For some reason the executable is not placed in 'bin' +postinstallcmds = [ + 'mv %(installdir)s/%(namelower)s %(installdir)s/bin/.' +] + +sanity_check_commands = [('hipify-clang', '--version')] +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['include'], +} + +moduleclass = 'devel' From 147c4866257c631042304dae0d6e96e303151723 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Wed, 26 May 2021 13:25:41 +0200 Subject: [PATCH 0960/2365] Moved EB to correct directory --- .../{c => h}/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{c => h}/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb (100%) diff --git a/easybuild/easyconfigs/c/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb similarity index 100% rename from easybuild/easyconfigs/c/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb rename to easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb From 69f808fe479fa6e70bfcdaad4d1073eac55f5e89 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Wed, 26 May 2021 13:40:01 +0200 Subject: [PATCH 0961/2365] [skip ci] Updated reasoning behind disabled testing. --- .../h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb index 661e8fe8d5..79440aa7a2 100644 --- a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb @@ -32,7 +32,8 @@ configopts += ' -DCMAKE_INSTALL_PREFIX=%(installdir)s' configopts += ' -DCMAKE_PREFIX_PATH=$EBROOTCLANG' # NOTE: The following configuration options are needed if building with tests # (as activated by 'runtest' below), for these to work the above commented -# dependencies need to be uncommented +# dependencies need to be uncommented. Currently testing is disabled due to a +# lack of 'llvm-lit'. # configopts += ' -DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA' # configopts += ' -DCUDA_DNN_ROOT_DIR=$EBROOTCUDNN' # configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python' From 188426d994a284d43dc3500517c067495b7d6075 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 26 May 2021 15:29:10 +0200 Subject: [PATCH 0962/2365] adding easyconfigs: TALON-5.0-foss-2020b.eb and patches: TALON-5.0_less_strict_deps.patch --- .../t/TALON/TALON-5.0-foss-2020b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb new file mode 100644 index 0000000000..35ec57d755 --- /dev/null +++ b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'TALON' +version = '5.0' + +homepage = 'https://daler.github.io/pybedtools' +description = """TALON is a Python package for identifying and quantifying known and +novel genes/isoforms in long-read transcriptome data sets. TALON is technology-agnostic +in that it works from mapped SAM files, allowing data from different sequencing platforms +(i.e. PacBio and Oxford Nanopore) to be analyzed side by side.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/mortazavilab/%(name)s/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['TALON-%(version)s_less_strict_deps.patch'] +checksums = [ + 'aeb1c1f46a4c757a8bb866b9a4446186f0f280e9391933a040de9dad30453649', # v5.0.tar.gz + '1207b33ba50ba313ae11f421b8b3fbd5f531421b847f68a1b9760b191337f0ed', # TALON-5.0_less_strict_deps.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('pyfaidx', '0.5.9.5'), + ('SciPy-bundle', '2020.11'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.16.0.1'), + ('pybedtools', '0.8.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True +sanity_check_commands = ['talon_label_reads -h'] + +moduleclass = 'bio' From 27277182fcd3bdb596a8fad2635fd9b89ffcbb23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 May 2021 20:24:14 +0200 Subject: [PATCH 0963/2365] add missing M4 build dependency + add 'eu-elfcmp --help' as sanity check command for eu-elfcmp 0.183 --- .../easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb index 33fce2dbe9..f0b29a4ce5 100644 --- a/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb @@ -19,6 +19,7 @@ sources = [SOURCE_TAR_BZ2] checksums = ['c3637c208d309d58714a51e61e63f1958808fead882e9b607506a29e5474f2c5'] builddependencies = [ + ('M4', '1.4.18'), ('pkg-config', '0.29.2'), ] @@ -38,4 +39,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = ["eu-elfcmp --help"] + moduleclass = 'lib' From a9d21306abdba2ee6ddbd3bbc86ccc3e0c3de66c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 27 May 2021 09:44:58 +0200 Subject: [PATCH 0964/2365] Update binutils 2.35 sources to 2.35.2 --- .../b/binutils/binutils-2.35-GCCcore-10.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb index 4f2b121412..2dbe05e03e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb @@ -7,10 +7,14 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] +# Due to a serious bug of the gold linker on PPC it was decided to use the 2.35.2 sources instead of a +# (potentially large) patch. There are also some more or less minor fixes for ARM and (likely) x86 included. +# Adding a new EC for 2.35.2 was rejected as that would require rebuilding all module files for those using +# binutils as a runtime dep. +sources = ["%(name)s-%(version)s.2.tar.gz"] patches = ['binutils-2.34-readd-avx512-vmovd.patch'] checksums = [ - 'a3ac62bae4f339855b5449cfa9b49df90c635adbd67ecb8a0e7f3ae86a058da6', # binutils-2.35.tar.gz + 'f484f61c81aa679df84d358d9818d5bf3e71fd227303f234f72b24420d98d3cd', # binutils-2.35.2.tar.gz '45ecf7f5d198dd446d1a2e2a4d46b2747eb6fb8f2bfa18d7d42769e710e85716', # binutils-2.34-readd-avx512-vmovd.patch ] From ac2d1f4533d90161a3c5a96e0599e4f959e1e06d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 27 May 2021 10:33:15 +0200 Subject: [PATCH 0965/2365] Remove 2nd part of comment --- .../easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb index 2dbe05e03e..40cb8d3080 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb @@ -9,8 +9,6 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] # Due to a serious bug of the gold linker on PPC it was decided to use the 2.35.2 sources instead of a # (potentially large) patch. There are also some more or less minor fixes for ARM and (likely) x86 included. -# Adding a new EC for 2.35.2 was rejected as that would require rebuilding all module files for those using -# binutils as a runtime dep. sources = ["%(name)s-%(version)s.2.tar.gz"] patches = ['binutils-2.34-readd-avx512-vmovd.patch'] checksums = [ From a32701453a302d92deec635e9873a1a14714d1dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 May 2021 11:01:41 +0200 Subject: [PATCH 0966/2365] fix minor vertical spacing code style in pyfasta easyconfig --- easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb index c288ff59f2..184d742345 100644 --- a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb @@ -13,16 +13,18 @@ checksums = ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'] use_pip = True download_dep_fail = True -sanity_pip_check = True dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11') ] -sanity_check_commands = ['pyfasta extract --help'] + sanity_check_paths = { 'files': ['bin/pyfasta'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ['pyfasta extract --help'] + +sanity_pip_check = True moduleclass = 'tools' From fd8f8ce2f2b42fbb51bd92dbb3c7c38ec4141a70 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 27 May 2021 14:57:10 +0100 Subject: [PATCH 0967/2365] adding easyconfigs: OBITools3-3.0.1b8-GCCcore-10.2.0.eb --- .../OBITools3-3.0.1b8-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f63eac41a1 --- /dev/null +++ b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'OBITools3' +version = '3.0.1b8' + +homepage = 'https://pypi.python.org/pypi/%(name)s/' +description = """A package for the management of analyses and data in DNA metabarcoding.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['33e10ffced0ef34829d6929180d5012afd6857ae87de420f65d789ebe2bb7741'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = "sed -i \"s|get_python_lib()|get_python_lib(prefix='%(installdir)s')|g\" setup.py &&" + +fix_python_shebang_for = ['bin/obi'] + +sanity_check_paths = { + 'files': ['bin/obi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "obi --help", + "obi --version", +] + +moduleclass = 'bio' From 039f6ecd466fd13167a82ef8f74f0bc91892b26a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 27 May 2021 15:17:06 +0100 Subject: [PATCH 0968/2365] adding easyconfigs: MbedTLS-2.26.0-GCCcore-10.2.0.eb --- .../MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c8af21ea5c --- /dev/null +++ b/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +# Author: Jasper Grimm + +easyblock = 'ConfigureMake' + +name = 'MbedTLS' +version = '2.26.0' + +homepage = 'tls.mbed.org' +description = "An open source, portable, easy to use, readable and flexible SSL library." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ARMmbed' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['37949e823c7e1f6695fc56858578df355da0770c284b1c1304cfc8b396d539cd'] + +builddependencies = [ + ('binutils', '2.35'), + # Perl, Python only needed for test suite + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +skipsteps = ['configure'] + +buildopts = 'SHARED=ON' + +runtest = 'check' + +installopts = 'DESTDIR=%(installdir)s' + +local_bins = ['bin/%%(namelower)s_%s' % x for x in ['aescrypt2', 'cert_app', 'ecdsa', 'ssl_client2']] +local_libs = ['lib/libmbed%s.%s' % (x, SHLIB_EXT) for x in ['crypto', 'tls', 'x509']] + +sanity_check_paths = { + 'files': local_bins + local_libs, + 'dirs': [], +} +sanity_check_commands = [ + "%(namelower)s_hello", + "%(namelower)s_selftest", +] + +moduleclass = 'lib' From c544d31630a9fce361b6af6cebd514ff7c1cf46b Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 27 May 2021 15:20:11 +0100 Subject: [PATCH 0969/2365] adding easyconfigs: dSFMT-2.2.5-GCCcore-10.2.0.eb, Autoconf-archive-2021.02.19-GCCcore-10.2.0.eb and patches: dSFMT-2.2.5_autotools.patch --- ...oconf-archive-2021.02.19-GCCcore-10.2.0.eb | 53 +++++++++++++++++++ .../d/dSFMT/dSFMT-2.2.5-GCCcore-10.2.0.eb | 38 +++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2021.02.19-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/d/dSFMT/dSFMT-2.2.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2021.02.19-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2021.02.19-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d5997d9581 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2021.02.19-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU Free Documentation License +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf-archive' +version = '2021.02.19' + +homepage = "https://www.gnu.org/software/autoconf-archive" + +description = """ +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf +that have been contributed as free software by friendly supporters of the cause from +all over the Internet. Every single one of those macros can be re-used without +imposing any restrictions whatsoever on the licensing of the generated configure script. +In particular, it is possible to use all those macros in configure scripts that +are meant for non-free software. This policy is unusual for a Free Software Foundation +project. The FSF firmly believes that software ought to be free, and software licenses +like the GPL are specifically designed to ensure that derivative work based on free +software must be free as well. In case of Autoconf, however, an exception has been made, +because Autoconf is at such a pivotal position in the software development tool chain +that the benefits from having this tool available as widely as possible outweigh the +disadvantage that some authors may choose to use it, too, for proprietary software. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e8a6eb9d28ddcba8ffef3fa211653239e9bf239aba6a01a6b7cfc7ceaec69cbd'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('makeinfo', '6.7'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dSFMT/dSFMT-2.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/dSFMT/dSFMT-2.2.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6e45821bd8 --- /dev/null +++ b/easybuild/easyconfigs/d/dSFMT/dSFMT-2.2.5-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'dSFMT' +version = '2.2.5' + +homepage = 'https://github.com/MersenneTwister-Lab/dSFMT' +description = "Double precision SIMD-oriented Fast Mersenne Twister." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'MersenneTwister-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['dSFMT-2.2.5_autotools.patch'] +checksums = [ + 'b7bc498cd140b4808963b1ff9f33b42a491870f54775c1060ecad0e02bcaffb4', # v2.2.5.tar.gz + '1df9824414428cef26b0912bb03585a008ac1055dd526c58f483cd1cc5d11857', # dSFMT-2.2.5_autotools.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('Autoconf-archive', '2021.02.19'), +] + +preconfigopts = "autoreconf -i -f &&" + +local_libs = ['lib%%(name)s%s' % x for x in ['', '-11213', '-1279', '-132049', '-19937', '-216091', + '-2203', '-4253', '-44497', '-521', '-86243']] + +sanity_check_paths = { + 'files': ['include/dSFMT.h'] + ['lib/%s.%s' % (x, SHLIB_EXT) for x in local_libs], + 'dirs': [], +} + +moduleclass = 'lib' From 9343acdac026daf8d88d27014e5501abc540a5e4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 27 May 2021 15:21:45 +0100 Subject: [PATCH 0970/2365] adding easyconfigs: patchelf-0.12-GCCcore-10.2.0.eb --- .../patchelf/patchelf-0.12-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..af356f8b6c --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.12' + +homepage = 'https://github.com/NixOS/patchelf' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3dca33fb862213b3541350e1da262249959595903f559eae0fbc68966e9c3f56'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From 576585635797175b011e40670820709dc418d2b6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 27 May 2021 15:39:43 +0100 Subject: [PATCH 0971/2365] Add binutils, use default source_urls and add download_dep_fail --- .../o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb index f63eac41a1..412efd2982 100644 --- a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb @@ -10,11 +10,13 @@ description = """A package for the management of analyses and data in DNA metaba toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['33e10ffced0ef34829d6929180d5012afd6857ae87de420f65d789ebe2bb7741'] -builddependencies = [('CMake', '3.18.4')] +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] dependencies = [ ('Python', '3.8.6'), @@ -22,6 +24,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True preinstallopts = "sed -i \"s|get_python_lib()|get_python_lib(prefix='%(installdir)s')|g\" setup.py &&" From 414845085baef066edc70518d8c78d130ea68b03 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 27 May 2021 16:24:01 +0100 Subject: [PATCH 0972/2365] update homepage to match docs --- .../easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb index 412efd2982..765db86558 100644 --- a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb @@ -5,7 +5,7 @@ easyblock = 'PythonPackage' name = 'OBITools3' version = '3.0.1b8' -homepage = 'https://pypi.python.org/pypi/%(name)s/' +homepage = 'https://metabarcoding.org/obitools3' description = """A package for the management of analyses and data in DNA metabarcoding.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From 09e4d30cde145730536406944c65cadae9d9714e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 May 2021 22:46:26 +0200 Subject: [PATCH 0973/2365] fix download URL for DB 18.1.40 --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb index 6b601fe0f4..c409d75484 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -10,10 +10,9 @@ description = """Berkeley DB enables the development of custom data management toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -# use Homebrew source mirror to allow auto-downloading source tarball -# (Oracle website - https://www.oracle.com/technetwork/products/berkeleydb/downloads/ - requires reigstration) -source_urls = ['https://bintray.com/homebrew/mirror/download_file?file_path='] -sources = [{'download_filename': 'berkeley-db-%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_fix_doc_install.patch'] checksums = [ '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz From 2b485594085ccbd178e285b5a3282d0729772239 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 28 May 2021 09:26:55 +0200 Subject: [PATCH 0974/2365] Remove binutils --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 39a76d38d8..f1268b2903 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -39,8 +39,6 @@ dependencies = [ ('libpng', '1.6.37'), ('snappy', '1.1.8'), ('zlib', '1.2.11'), - # Must be here to fix a bug with ld.gold on PPC and last as e.g. Python also loads binutils (the old version) - ('binutils', '2.35.2'), ] exts_default_options = { From 7a40ec88cc1b524fea90f48ffffb8cafc39568b5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 28 May 2021 11:19:16 +0200 Subject: [PATCH 0975/2365] Fix test failure in TF 2.4.1 on recent CUDA drivers --- .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index c832a52b75..b949cd6858 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -167,6 +167,7 @@ exts_list = [ 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', 'TensorFlow-2.4.0_fix-absl-on-power.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_fix-min-priority-test.patch', 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -224,6 +225,8 @@ exts_list = [ 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', # TensorFlow-2.4.0_dont-use-var-lock.patch 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_fix-min-priority-test.patch + '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', # TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch 'f384cd97e004673ae530b6e5cc826f8fddb46646991f1a228fc07b2aac87ee80', ], From 77a9c35277548fe1438c278073eb6bdc25486cb0 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 28 May 2021 11:40:29 +0200 Subject: [PATCH 0976/2365] Remove source_urls --- .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index b949cd6858..9a4a9e1ad3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -45,10 +45,8 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d From bd8c01563def6dba3d76330f6dd0762ab674c55f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 28 May 2021 17:15:27 +0200 Subject: [PATCH 0977/2365] fix error in configopts for netCDF and HDF5 and add missing dependencies of ABINIT 9.x --- .../easyconfigs/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb index 943b370cb5..1cf3882b38 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb @@ -21,7 +21,9 @@ builddependencies = [ ] dependencies = [ ('libxc', '4.3.4'), + ('netCDF', '4.7.4'), ('netCDF-Fortran', '4.5.3'), + ('HDF5', '1.10.7'), ('Wannier90', '3.1.0'), ] @@ -38,10 +40,10 @@ configopts += '--with-fft-flavor=dfti ' # libxc support configopts += '--with-libxc=${EBROOTLIBXC} ' -# hdf5/netcdf4. -configopts += 'with_netcdf="${EBROOTNETCDF}" ' -configopts += 'with_netcdf_fortran="${EBROOTNETCDFMINFORTRAN}" ' -configopts += 'with_hdf5="${EBROOTHDF5}" ' +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' # Wannier90 configopts += '--with-wannier90="${EBROOTWANNIER90}" ' From 7ecb1776c3ed602ff63495d87b0befc85e9f4d7a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 28 May 2021 19:02:52 +0200 Subject: [PATCH 0978/2365] Fix buffer overflow in OpenMPI 4.x --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index b4d152df08..6ceb24c25d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -8,7 +8,10 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a'] +patches = ['OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch'] +checksums = [ + '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a' +] builddependencies = [ ('pkg-config', '0.29.2'), From 9876811e9232a9dd31d9e3b6b5840b094610b858 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 28 May 2021 19:15:21 +0200 Subject: [PATCH 0979/2365] Fix checksums --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index 6ceb24c25d..c80283a715 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -10,7 +10,9 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_GZ] patches = ['OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch'] checksums = [ - '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a' + '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a', # openmpi-4.1.0.tar.gz + # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', ] builddependencies = [ From 774a664956abb13992420534c9b77b2f6a076da9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 29 May 2021 15:45:53 +0200 Subject: [PATCH 0980/2365] add symlink for shared libraries in binutils 2.35 easyconfigs using 2.35.2 source tarball --- .../easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb index 40cb8d3080..c3fb942ee7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb @@ -34,4 +34,11 @@ dependencies = [ buildopts = 'MAKEINFO=true' installopts = buildopts +# symlink libbfd-2.35.so to libbfd-2.35.2.so to avoid breaking binaries/libraries that resolved libbfd.so symlink; +# likewise for libopcodes-2.35.so +postinstallcmds = [ + "cd %(installdir)s/lib && ln -s libbfd-%(version)s.2.so libbfd-%(version)s.so", + "cd %(installdir)s/lib && ln -s libopcodes-%(version)s.2.so libopcodes-%(version)s.so", +] + moduleclass = 'tools' From 92a933a5636aa33391b001a6f728b6ac81b83e00 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 29 Jan 2021 16:32:17 +0100 Subject: [PATCH 0981/2365] Add PSolver-1.8.3-foss-2020b and PSolver-1.8.3-intel-2020b. This version has a new dependency on the futile library, so we also include futile-1.8.3-foss-2020b and futile-1.8.3-foss-2020b. --- .../f/futile/futile-1.8.3-foss-2020b.eb | 37 +++++++++++++++++ .../f/futile/futile-1.8.3-intel-2020b.eb | 41 +++++++++++++++++++ .../p/PSolver/PSolver-1.8.3-foss-2020b.eb | 38 +++++++++++++++++ .../p/PSolver/PSolver-1.8.3-intel-2020b.eb | 38 +++++++++++++++++ 4 files changed, 154 insertions(+) create mode 100644 easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb create mode 100644 easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb new file mode 100644 index 0000000000..85a09882d5 --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +sources = ['bigdft-suite-%(version)s.tar.gz'] +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +checksums = ['7ecb968a16e9cba35966f9f4d8acc454'] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCLAGS -fallow-argument-mismatch" ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb new file mode 100644 index 0000000000..92b2ab07c5 --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +patches = ['futile_intel_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '9efc3f94cdb6131b00715afcdeb16c7ed016b8fc69a2c95f4449088bf79f84ba', # futile_intel_bug.patch +] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb new file mode 100644 index 0000000000..586020123e --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True} + +sources = ['bigdft-suite-%(version)s.tar.gz'] +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +checksums = ['7ecb968a16e9cba35966f9f4d8acc454'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb new file mode 100644 index 0000000000..addac3b9e5 --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True} + +sources = ['bigdft-suite-%(version)s.tar.gz'] +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +checksums = ['7ecb968a16e9cba35966f9f4d8acc454'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' From fac1def46e2c6983c999d930cc61e6db81fcc57c Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 14 May 2021 14:48:46 +0200 Subject: [PATCH 0982/2365] Update checksums. --- easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb | 4 ++-- easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb | 4 ++-- easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb index 85a09882d5..6648c32dd2 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb @@ -12,9 +12,9 @@ description = """ toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'usempi': True} -sources = ['bigdft-suite-%(version)s.tar.gz'] source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] -checksums = ['7ecb968a16e9cba35966f9f4d8acc454'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb index 586020123e..34640f7529 100644 --- a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb @@ -11,9 +11,9 @@ description = """ toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'usempi': True, 'opt': True} -sources = ['bigdft-suite-%(version)s.tar.gz'] source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] -checksums = ['7ecb968a16e9cba35966f9f4d8acc454'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] local_cddir = ' cd psolver-%(version_major_minor)s && ' preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb index addac3b9e5..df8ca360b5 100644 --- a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb @@ -11,9 +11,9 @@ description = """ toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'usempi': True, 'opt': True} -sources = ['bigdft-suite-%(version)s.tar.gz'] source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] -checksums = ['7ecb968a16e9cba35966f9f4d8acc454'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] local_cddir = ' cd psolver-%(version_major_minor)s && ' preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir From 869d03d0227d2d7d3daaa027294ebe7df8355d98 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 31 May 2021 08:22:47 +0200 Subject: [PATCH 0983/2365] Add short description and author to futile patch. --- easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb index 92b2ab07c5..318f3bb9b9 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb @@ -17,7 +17,7 @@ sources = ['bigdft-suite-%(version)s.tar.gz'] patches = ['futile_intel_bug.patch'] checksums = [ '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz - '9efc3f94cdb6131b00715afcdeb16c7ed016b8fc69a2c95f4449088bf79f84ba', # futile_intel_bug.patch + 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch ] unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " From 4d387f5473320d4e74895eca98193923cf7b3566 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 31 May 2021 11:54:08 +0200 Subject: [PATCH 0984/2365] Run all tests before failing --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb | 4 +++- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb index 2b9c404e04..785a48ff87 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -240,6 +240,7 @@ patches = [ 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.7.1_fix-err-variable.patch', 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', ] checksums = [ @@ -292,6 +293,7 @@ checksums = [ '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + 'abb79e7ffd10be87adfb62e79131c50079c32470031ac22b12b273cfae85ca4c', # PyTorch-1.7.1_fix-err-variable.patch # PyTorch-1.7.1_run-large-tests-on-GPU.patch '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', ] @@ -312,7 +314,7 @@ excluded_tests = { ] } -runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' sanity_check_commands = ["python -c 'import caffe2.python'"] tests = ['PyTorch-check-cpp-extension.py'] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index d014c83683..c841f62815 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -252,6 +252,7 @@ patches = [ 'PyTorch-1.7.1_complex32.patch', 'PyTorch-1.7.1_bypass-nan-compare.patch', 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.7.1_fix-err-variable.patch', 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', 'PyTorch-1.7.1_relax_precision_in_test_nn.patch', @@ -317,6 +318,7 @@ checksums = [ '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + 'abb79e7ffd10be87adfb62e79131c50079c32470031ac22b12b273cfae85ca4c', # PyTorch-1.7.1_fix-err-variable.patch # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch @@ -339,7 +341,7 @@ excluded_tests = { ] } -runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' sanity_check_commands = ["python -c 'import caffe2.python'"] tests = ['PyTorch-check-cpp-extension.py'] From 38e11a71a5837910611e3b21cbbde05263ea661f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 31 May 2021 12:09:13 +0200 Subject: [PATCH 0985/2365] deleting patchfile, moving tweaks to preinstallopts --- easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb index 35ec57d755..595fe31958 100644 --- a/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'TALON' version = '5.0' -homepage = 'https://daler.github.io/pybedtools' +homepage = 'https://github.com/mortazavilab/TALON' description = """TALON is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets. TALON is technology-agnostic in that it works from mapped SAM files, allowing data from different sequencing platforms @@ -13,10 +13,9 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/mortazavilab/%(name)s/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] -patches = ['TALON-%(version)s_less_strict_deps.patch'] +# patches = ['TALON-%(version)s_less_strict_deps.patch'] checksums = [ 'aeb1c1f46a4c757a8bb866b9a4446186f0f280e9391933a040de9dad30453649', # v5.0.tar.gz - '1207b33ba50ba313ae11f421b8b3fbd5f531421b847f68a1b9760b191337f0ed', # TALON-5.0_less_strict_deps.patch ] dependencies = [ @@ -28,6 +27,9 @@ dependencies = [ ('pybedtools', '0.8.2'), ] +preinstallopts = "sed -i 's/pysam==/pysam>=/g' requirements.txt && " +preinstallopts += "sed -i 's/pysam==/pysam>=/g' setup.py && " + download_dep_fail = True use_pip = True From 8a2c9ee63e4a28b3b0bc60dc1d5db0f5dead75aa Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 31 May 2021 12:10:28 +0200 Subject: [PATCH 0986/2365] Rename rmats-turbo-4.1.1-foss-2020b.eb to rMATS-turbo-4.1.1-foss-2020b.eb renaming --- .../rMATS-turbo-4.1.1-foss-2020b.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/r/rmats-turbo/rMATS-turbo-4.1.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/rmats-turbo/rMATS-turbo-4.1.1-foss-2020b.eb b/easybuild/easyconfigs/r/rmats-turbo/rMATS-turbo-4.1.1-foss-2020b.eb new file mode 100644 index 0000000000..c4ab2d228d --- /dev/null +++ b/easybuild/easyconfigs/r/rmats-turbo/rMATS-turbo-4.1.1-foss-2020b.eb @@ -0,0 +1,68 @@ +easyblock = 'Bundle' + +name = 'rMATS-turbo' +version = '4.1.1' + +homepage = 'https://github.com/Xinglab/rmats-turbo' +description = """rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net).""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), +] +dependencies = [ + ('Python', '3.8.6'), + ('GSL', '2.6'), + ('SAMtools', '1.11'), + ('STAR', '2.7.6a'), + ('BamTools', '2.5.1'), +] + +local_ldflags = " -lm -lgfortran -lgsl -lgslcblas -lgomp -lopenblas $LIBLAPACK " +local_buildopts = ' CC="$CC" CXX="$CXX" FC="$FC" LDFLAGS="%s"' % local_ldflags + +default_component_specs = { + 'sources': ['v%(version)s.tar.gz'], + 'source_urls': ['https://github.com/Xinglab/%(name)s/archive/refs/tags/'], + 'checksums': ['cdfde24b68be0b41b4ca43e5414d3c292deb7efd617d7ee2315e2d6e6bcb1c92'], +} + +components = [ + (name, version, { + 'easyblock': 'MakeCp', + 'start_dir': 'rmats-turbo-%(version)s/rMATS_C', + 'buildopts': "%s" % local_buildopts, + 'files_to_copy': [(['rMATSexe', '../rmats.py'], 'bin')], + }), + ('rmats-turbo-python', version, { + 'easyblock': 'PythonPackage', + 'patches': [('rMATS-turbo-%(version)s_bamtools_as_dependency.patch')], + 'checksums': [ + 'cdfde24b68be0b41b4ca43e5414d3c292deb7efd617d7ee2315e2d6e6bcb1c92', + 'e3b4d6a8d612a909cb9b920a7770406955f093b2788f6d7bf6ccab5527eda86a', + ], + 'start_dir': 'rmats-turbo-%(version)s/rMATS_pipeline', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'options': {'modulename': 'rmatspipeline'}, + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +postinstallcmds = ["chmod a+x %(installdir)s/bin/rmats.py"] + +sanity_check_commands = [ + 'rmats.py --version', +] + +sanity_check_paths = { + 'files': ['bin/rMATSexe', 'bin/rmats.py'], + 'dirs': [], +} + +moduleclass = 'bio' From a896fbdbfd8a7fbf2d2b0b0faa0144a6856cbfe1 Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Mon, 31 May 2021 12:40:35 +0200 Subject: [PATCH 0987/2365] adding easyconfigs: WhatsHap-1.1-foss-2020b.eb --- .../w/WhatsHap/WhatsHap-1.1-foss-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb new file mode 100644 index 0000000000..b569e2b709 --- /dev/null +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'WhatsHap' +version = '1.1' + +homepage = 'https://whatshap.readthedocs.io' +description = """WhatsHap is a software for phasing genomic variants using DNA +sequencing reads, also called read-based phasing or haplotype assembly. It is +especially suitable for long reads, but works also well with short reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Pysam', '0.16.0.1'), + ('networkx', '2.5'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), + ('Yasm', '1.3.0'), +] + +use_pip = True +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('pyfaidx', '0.5.9.5', { + 'checksums': ['9965644c5bd62bedc0ff7f336cbb2baef6406a36b4ec5c786b199872ce46192b'], + }), + ('isal', '0.10.0', { + 'checksums': ['3f89471065c2837d1235877dbdcdbd8b7649068723026b0582010fa106a71ff3'], + }), + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f'], + }), +] + +moduleclass = 'bio' From 8ab4799adc9fa00269bd94aacece49b4846ec868 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 31 May 2021 12:57:58 +0200 Subject: [PATCH 0988/2365] renaming subdir and patchfile --- .../{rmats-turbo => rMATS-turbo}/rMATS-turbo-4.1.1-foss-2020b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/r/{rmats-turbo => rMATS-turbo}/rMATS-turbo-4.1.1-foss-2020b.eb (100%) diff --git a/easybuild/easyconfigs/r/rmats-turbo/rMATS-turbo-4.1.1-foss-2020b.eb b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb similarity index 100% rename from easybuild/easyconfigs/r/rmats-turbo/rMATS-turbo-4.1.1-foss-2020b.eb rename to easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb From 8b5cad05a702aaee35db354c0d5e7fee88c1fa2b Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Mon, 31 May 2021 13:04:01 +0200 Subject: [PATCH 0989/2365] remove source_urls --- easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb index b569e2b709..5ccb28918a 100644 --- a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} +sanity_pip_check = True exts_list = [ ('pyfaidx', '0.5.9.5', { From de1b1148038cfd2979f4399801e549b7d4da5205 Mon Sep 17 00:00:00 2001 From: bennetsw Date: Mon, 31 May 2021 10:41:42 -0400 Subject: [PATCH 0990/2365] adding easyconfigs: bcl2fastq2-2.20.0-GCC-10.2.0.eb and patches: bcl2fastq2-2.20.0-find-boost.patch --- .../bcl2fastq2-2.20.0-GCC-10.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..4a5b394adf --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'bcl2fastq2' +version = '2.20.0' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' +description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by + Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] +sources = [{ + 'filename': '%s-v%s-tar.zip' % (name, version.replace('.', '-')), + 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz +}] + +patches = [ + 'bcl2fastq2-%(version)s-find-boost.patch', #bcl2fastq2-2-20-0-find-boost.patch +] + +checksums = [ + '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3', # bcl2fastq2-v2-20-0-tar.zip + '0155ebd6ec6bd1e6d8361be046e77f469e56594eb397b6b9012aef9c4abbeb70', # bcl2fastq2-2-20-0-find-boost.patch +] + +# CMake, Boost, libxml2 and libxslt are all built and used internally with specific versions +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'src' +configopts = '--force-builddir' + +sanity_check_paths = { + 'files': ['bin/bcl2fastq'], + 'dirs': ['lib'] +} + +moduleclass = 'bio' From 30e7eae6bd669bebfdc7838aaef5fae4167a887e Mon Sep 17 00:00:00 2001 From: bennetsw Date: Mon, 31 May 2021 11:10:56 -0400 Subject: [PATCH 0991/2365] Correcting style --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb index 4a5b394adf..ba89df0415 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -19,7 +19,7 @@ sources = [{ }] patches = [ - 'bcl2fastq2-%(version)s-find-boost.patch', #bcl2fastq2-2-20-0-find-boost.patch + 'bcl2fastq2-%(version)s-find-boost.patch', # bcl2fastq2-2-20-0-find-boost.patch ] checksums = [ From 34d63e0ad4864ca6edbce71b1411314ed2b21f55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 May 2021 18:47:28 +0200 Subject: [PATCH 0992/2365] adding easyconfigs: SeuratData-20210514-foss-2020b-R-4.0.3.eb --- .../SeuratData-20210514-foss-2020b-R-4.0.3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..bc92c7305e --- /dev/null +++ b/easybuild/easyconfigs/s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'SeuratData' +local_commit = 'b59556b' +version = '20210514' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/satijalab/seurat-data' +description = """SeuratData is a mechanism for distributing datasets in the form of Seurat objects using R's internal +package and data management systems.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/satijalab', + 'repo_name': 'seurat-data', + 'commit': local_commit, + }, +}] +checksums = [None] + +dependencies = [('R', '4.0.3')] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From d970d0d4fd4cf1259ed2050007094c52e8d8b6c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 May 2021 18:47:57 +0200 Subject: [PATCH 0993/2365] adding easyconfigs: SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb --- ...ratWrappers-20210528-foss-2020b-R-4.0.3.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..badc4022cc --- /dev/null +++ b/easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'SeuratWrappers' +local_commit = '7b9818d' +version = '20210528' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/satijalab/seurat-wrappers' +description = "SeuratWrappers is a collection of community-provided methods and extensions for Seurat" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/satijalab', + 'repo_name': 'seurat-wrappers', + 'commit': local_commit, + }, +}] +checksums = [None] + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), + ('Seurat', '4.0.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From c2a38fa44a37ecd6a11bbecc21b4afa0a7b91744 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 1 Jun 2021 15:57:10 +0100 Subject: [PATCH 0994/2365] adding easyconfigs: AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb, EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb, libharu-2.3.0-GCCcore-10.2.0.eb, RAxML-8.2.12-GCC-10.2.0-pthreads-avx2.eb --- ...90730-gompi-2020b-Java-13-pthreads-avx2.eb | 51 +++++++++++++++ .../EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb | 64 +++++++++++++++++++ .../l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb | 50 +++++++++++++++ .../RAxML-8.2.12-GCC-10.2.0-pthreads-avx2.eb | 29 +++++++++ 4 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb create mode 100644 easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-GCC-10.2.0-pthreads-avx2.eb diff --git a/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb b/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb new file mode 100644 index 0000000000..c9a3002ee8 --- /dev/null +++ b/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb @@ -0,0 +1,51 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'Tarball' + +name = 'AMPHORA2' +version = '20190730' +local_commit = '9fb9ce8' +local_raxmlsuffix = '-pthreads-avx2' +local_javasuffix = '-Java-%(javaver)s' +versionsuffix = local_javasuffix + local_raxmlsuffix + +homepage = 'https://github.com/wu-lab-uva/AMPHORA2' +description = "An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences." + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'wu-lab-uva' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +checksums = ['2d361fcc2b800c3daaf25692988af6105669cba2ff513aba82f36089beb2839f'] + +dependencies = [ + ('Perl', '5.32.0'), + ('Java', '13', '', True), + ('BioPerl', '1.7.8'), + ('HMMER', '3.3.2'), + ('EMBOSS', '6.6.0', local_javasuffix), + ('RAxML', '8.2.12', local_raxmlsuffix), +] + +local_scripts = ['%s.pl' % x for x in ['MarkerAlignTrim', 'MarkerScanner', 'Phylotyping']] +fix_perl_shebang_for = ['Scripts/*.pl'] + +# Exit with code 0 when running -Help +preinstall_cmd = "sed -i 's|die $usage if $help|if ($help) {print $usage; exit 0}|g' Scripts/*.pl && " +# Fix RAxML binary name +preinstall_cmd += "sed -i 's|raxmlHPC-PTHREADS|raxmlHPC%s|g' Scripts/Phylotyping.pl" % local_raxmlsuffix.upper() + +sanity_check_paths = { + 'files': ['Scripts/%s' % x for x in local_scripts], + 'dirs': [], +} + +sanity_check_commands = ["%s -Help" % x for x in local_scripts] + +modextrapaths = { + 'AMPHORA2_home': '', + 'PATH': 'Scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb new file mode 100644 index 0000000000..eaf6f22dc1 --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb @@ -0,0 +1,64 @@ +# authors: Kenneth Hoste (Ghent University) +# George Tsouloupas +# Fotis Georgatos +# +# This work implements a part of the HPCBIOS project and is a component +# of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute +# +# Updated: Pavel Grochal (INUITS) +# +easyblock = 'ConfigureMake' + +name = 'EMBOSS' +version = '6.6.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://emboss.sourceforge.net/' +description = """EMBOSS is 'The European Molecular Biology Open Software Suite' +. EMBOSS is a free Open Source software analysis package specially developed + for the needs of the molecular biology (e.g. EMBnet) user community.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'kimrutherford' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_disable-embossupdate.patch'] +checksums = [ + ( + '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', + '85f53a19125735e4a49fc25620d507fd86bf189e49096578924fe04893f2f7a9', + ), + # EMBOSS-6.6.0.tar.gz + '7e0a7deffd76f60093be9c5253605f2d6d2e3b0c2d3c9365035cc6bda43eb46c', # EMBOSS-6.6.0_disable-embossupdate.patch +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('X11', '20201008'), + ('libharu', '2.3.0'), + ('Java', '13', '', True), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', + 'epcre', 'eplplot', 'ezlib', 'nucleus']] + + ['share/EMBOSS/jemboss/lib/jemboss.jar'], + 'dirs': [], +} +sanity_check_commands = [ + 'embossdata -h' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..507b4b404b --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Modified for foss-2016b by: +# Adam Huffman +# The Francis Crick Institute +# +# Updated: Pavel Grochal (INUITS) +# + +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'https://github.com/libharu/libharu/' +description = """libHaru is a free, cross platform, open source library for +generating PDF files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# 'https://github.com/libharu/libharu/archive/' +source_urls = [GITHUB_SOURCE] +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] + +dependencies = [('libpng', '1.6.37')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-GCC-10.2.0-pthreads-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-GCC-10.2.0-pthreads-avx2.eb new file mode 100644 index 0000000000..0d508c3044 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-GCC-10.2.0-pthreads-avx2.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.12' +versionsuffix = '-pthreads-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105'] + +buildopts = '-f Makefile.AVX2.PTHREADS.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-PTHREADS-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-PTHREADS-AVX2 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +sanity_check_commands = ["raxmlHPC -%s" % x for x in ['h', 'v']] + +moduleclass = 'bio' From 1881a54463647ac9aac7e62e32e9fdf2a376dbb4 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Tue, 1 Jun 2021 18:01:12 +0200 Subject: [PATCH 0995/2365] Drop pyopqnssl version for compatibility --- easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb index ea0ed5b542..fad68609dd 100644 --- a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb +++ b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb @@ -23,9 +23,9 @@ exts_list = [ ('more-itertools', '8.8.0', { 'checksums': ['83f0308e05477c68f56ea3a888172c78ed5d5b3c282addb67508e7ba6c8f813a'], }), - ('pyOpenSSL', '20.0.1', { + ('pyOpenSSL', '19.1.0', { 'modulename': 'OpenSSL', - 'checksums': ['4c231c759543ba02560fcd2480c48dcec4dae34c9da7d3747c508227e0624b51'], + 'checksums': ['9a24494b2602aaf402be5c9e30a0b82d4a5c67528fe8fb475e3f3bc00dd69507'], }), ('ndg-httpsclient', '0.5.1', { 'modulename': 'ndg', From bce4e1fcb81033e62b25c107c0afd7f0a8d44516 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Jun 2021 18:01:36 +0200 Subject: [PATCH 0996/2365] add lslx, regsem, semPLS extensions to R v4.0.3 and v4.0.4 --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 15 +++++++++++ .../easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 25 +++++++++++++++---- .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 15 +++++++++++ .../easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 25 +++++++++++++++---- 4 files changed, 70 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index c349c0338d..f4c74e7d9b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2831,6 +2831,21 @@ exts_list = [ 'sources': ['%(name)s_%(version)s.tar.gz'], 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], }), + ('lslx', '0.6.10', { + 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.6.2', { + 'checksums': ['b65201c730e10b0a80d1dd788e0c370372a1f22f314f2e49ce4dc63cb3ffd992'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index fbed579c88..6b48ef208c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2836,6 +2836,26 @@ exts_list = [ ('image.binarization', '0.1.1', { 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.10', { + 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.6.2', { + 'checksums': ['b65201c730e10b0a80d1dd788e0c370372a1f22f314f2e49ce4dc63cb3ffd992'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], @@ -2843,11 +2863,6 @@ exts_list = [ ('RViennaCL', '1.7.1.8', { 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], }), - ('lassosum', '0.4.5', { - 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], - 'sources': ['%(name)s_%(version)s.tar.gz'], - 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 4f78e77a11..4d3fed4c0c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2866,6 +2866,21 @@ exts_list = [ 'sources': ['%(name)s_%(version)s.tar.gz'], 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], }), + ('lslx', '0.6.10', { + 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.6.2', { + 'checksums': ['b65201c730e10b0a80d1dd788e0c370372a1f22f314f2e49ce4dc63cb3ffd992'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 5a91968ee9..8eac804505 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2866,6 +2866,26 @@ exts_list = [ ('image.binarization', '0.1.1', { 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.10', { + 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.6.2', { + 'checksums': ['b65201c730e10b0a80d1dd788e0c370372a1f22f314f2e49ce4dc63cb3ffd992'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], @@ -2873,11 +2893,6 @@ exts_list = [ ('RViennaCL', '1.7.1.8', { 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], }), - ('lassosum', '0.4.5', { - 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], - 'sources': ['%(name)s_%(version)s.tar.gz'], - 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], - }), ] moduleclass = 'lang' From 25d56648518022ea36f74fe514d99b72b6903b3a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Wed, 2 Jun 2021 07:10:43 +0200 Subject: [PATCH 0997/2365] Add 'elfutils' as build dependency --- easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb index ef7462a07f..037c1ef7f8 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb @@ -57,6 +57,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.18.4'), ('Python', '3.8.6'), + ('elfutils', '0.183'), ] assertions = True From f25cb10e889c8e10cd345ff7ea2adc7437925189 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Jun 2021 11:53:33 +0200 Subject: [PATCH 0998/2365] {geo}[foss/2020b] microctools v0.1.0-20201209, rgdal v1.5-23 w/ R v4.0.4 --- ...tools-0.1.0-20201209-foss-2020b-R-4.0.4.eb | 27 ++++++++++++++++ .../rgdal/rgdal-1.5-23-foss-2020b-R-4.0.4.eb | 32 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb create mode 100644 easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2020b-R-4.0.4.eb diff --git a/easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..e61fdd21ea --- /dev/null +++ b/easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'microctools' +local_commit = 'f642925' +version = '0.1.0-20201209' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/ilyamaclean/microctools' +description = "Various worker functions for microclimc package" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/ilyamaclean/microctools/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit,'filename': SOURCE_TAR_GZ}] +checksums = ['8b6c0b784301bb61f0a67f6abb118fc49a15841902015833efc32373cfe3f515'] + +dependencies = [ + ('R', '4.0.4'), + ('rgdal', '1.5-23', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..c0c6e75fd5 --- /dev/null +++ b/easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2020b-R-4.0.4.eb @@ -0,0 +1,32 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'RPackage' + +name = 'rgdal' +version = '1.5-23' +versionsuffix = '-R-%(rver)s' + +homepage = "https://rgdal.r-forge.r-project.org/" +description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and + access to projection/transformation operations from the 'PROJ.4' library.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['9ca5744b946e7a3c4ca26598612bf54e550d3a0c5811d56e22c30b73f83ccb6e'] + +dependencies = [ + ('R', '4.0.4'), + ('GDAL', '3.2.1'), +] + +sanity_check_paths = { + 'files': ['rgdal/R/rgdal'], + 'dirs': [], +} + +moduleclass = 'geo' From b776a065c7e0a806a72e4f72399019f0c32fedf6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Jun 2021 13:05:29 +0200 Subject: [PATCH 0999/2365] add space to fix trivial style issue --- .../microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb index e61fdd21ea..205c6e8881 100644 --- a/easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb @@ -11,7 +11,7 @@ description = "Various worker functions for microclimc package" toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/ilyamaclean/microctools/archive'] -sources = [{'download_filename': '%s.tar.gz' % local_commit,'filename': SOURCE_TAR_GZ}] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['8b6c0b784301bb61f0a67f6abb118fc49a15841902015833efc32373cfe3f515'] dependencies = [ From 9ff0771fea63d9ef16372a3aa6f49bc265b8e477 Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Wed, 2 Jun 2021 22:50:28 +0200 Subject: [PATCH 1000/2365] missing cmake option to actually use external CLHEP --- easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb index 1227d2ac3a..61156a0a8f 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb @@ -20,7 +20,7 @@ dependencies = [ ('CLHEP', '2.4.4.0'), ] -configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include -DCLHEP_ROOT_DIR=$EBROOTCLHEP" configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' From 0f7ac704ce133bbb5277385eef778806fe9278ab Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Wed, 2 Jun 2021 23:02:34 +0200 Subject: [PATCH 1001/2365] move config option to avoid too long line --- easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb index 61156a0a8f..b8b3910444 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb @@ -20,7 +20,7 @@ dependencies = [ ('CLHEP', '2.4.4.0'), ] -configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include -DCLHEP_ROOT_DIR=$EBROOTCLHEP" -configopts += " -DGEANT4_INSTALL_DATA=OFF" +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += " -DCLHEP_ROOT_DIR=$EBROOTCLHEP -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' From d1c20f5caea5c79b967796a82599137fb896f10a Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Wed, 2 Jun 2021 23:26:05 +0200 Subject: [PATCH 1002/2365] add sanity checks and pyfaidx as dep --- .../w/WhatsHap/WhatsHap-1.1-foss-2020b.eb | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb index 5ccb28918a..1cdcd817b6 100644 --- a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb @@ -19,15 +19,13 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('Biopython', '1.78'), ('Yasm', '1.3.0'), + ('pyfaidx', '0.5.9.5'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('pyfaidx', '0.5.9.5', { - 'checksums': ['9965644c5bd62bedc0ff7f336cbb2baef6406a36b4ec5c786b199872ce46192b'], - }), ('isal', '0.10.0', { 'checksums': ['3f89471065c2837d1235877dbdcdbd8b7649068723026b0582010fa106a71ff3'], }), @@ -40,4 +38,14 @@ exts_list = [ }), ] + +sanity_check_paths = { + 'files': ['bin/whatshap'], + 'dirs': ['bin', 'lib'], +} + +sanity_check_commands = [ + 'whatshap --help', +] + moduleclass = 'bio' From 1ba0595e5f372604ac17136a2ce6d71a5205f2fd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Jun 2021 01:08:21 +0200 Subject: [PATCH 1003/2365] use CMakeMake with bcl2fastq2-2.20.0-GCC-10.2.0.eb --- .../bcl2fastq2-2.20.0-GCC-10.2.0.eb | 39 ++++++++++++++----- 1 file changed, 29 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb index ba89df0415..cf80489b22 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -1,6 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'bcl2fastq2' version = '2.20.0' @@ -10,34 +8,55 @@ description = """bcl2fastq Conversion Software both demultiplexes data and conve Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'cstd': 'c++11'} source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] sources = [{ 'filename': '%s-v%s-tar.zip' % (name, version.replace('.', '-')), 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz }] - patches = [ - 'bcl2fastq2-%(version)s-find-boost.patch', # bcl2fastq2-2-20-0-find-boost.patch + 'bcl2fastq2-%(version)s-fix-cmake-target-libs.patch', + # bcl2fastq2 v2.20.0 is not compatible with recent Boost versions, use bundled Boost + 'bcl2fastq2-%(version)s-find-boost.patch', ] - checksums = [ '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3', # bcl2fastq2-v2-20-0-tar.zip - '0155ebd6ec6bd1e6d8361be046e77f469e56594eb397b6b9012aef9c4abbeb70', # bcl2fastq2-2-20-0-find-boost.patch + '7908c268c213a6cfeafe05afcd5d3b34098241b6ab0a62c11ea47664cd0a63c5', # bcl2fastq2-2.20.0-fix-cmake-target-libs.patch + '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1', # bcl2fastq2-2.20.0-find-boost.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), ] -# CMake, Boost, libxml2 and libxslt are all built and used internally with specific versions dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), ('zlib', '1.2.11'), ] start_dir = 'src' -configopts = '--force-builddir' + +# check versions of libxml2 and libxslt from EB +local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' +local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +preconfigopts = local_sed_libver % {'l':'LIBXML2', 'f': local_cmakelists} +preconfigopts += local_sed_libver % {'l':'LIBXSLT', 'f': local_cmakelists} + +# remove hardcoded compilation flags +local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' +preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx + +configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' +configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' +configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' sanity_check_paths = { 'files': ['bin/bcl2fastq'], 'dirs': ['lib'] } +sanity_check_commands = ["bcl2fastq --help"] + moduleclass = 'bio' From 4bcdbb8bc5567cb61bb671abb6126aafe500b775 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Thu, 3 Jun 2021 11:03:09 +0100 Subject: [PATCH 1004/2365] Update R-4.0.4-foss-2020b.eb Corrected checksum for extension mvabund 4.1.9. --- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 4d3fed4c0c..0e94f20f2e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2151,7 +2151,7 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + 'checksums': ['fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30'], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], From 947f754809c6fb473025537cb8a56d468a0e5ef8 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Thu, 3 Jun 2021 11:05:37 +0100 Subject: [PATCH 1005/2365] Update R-4.0.4-fosscuda-2020b.eb Corrected checksum for extension mvabund 4.1.9. --- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 8eac804505..8a47161e25 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2155,7 +2155,7 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + 'checksums': ['fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30'], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], From 47338620c149fb7530b9a579e69faea9567612b3 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 3 Jun 2021 15:07:41 +0200 Subject: [PATCH 1006/2365] VMD: fixes for noticed issues --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb | 4 ++-- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb index 10015c6588..e2b6645847 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -36,8 +36,8 @@ checksums = [ 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch - '5afd42629fa7a1a9835e6479caca30995ea284a62e54b0c75a9dbfbaef98418c', # VMD-1.9.4_configure.patch - '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4_extra_colors.patch + 'dc9fc419e2e938f42d2e4784b0c9c7429317893f08d3ed170f949c3ee3aec062', # VMD-1.9.4a51_configure.patch + '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4a51_extra_colors.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb index c5061caf58..854dade5cb 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -36,8 +36,8 @@ checksums = [ 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch - '5afd42629fa7a1a9835e6479caca30995ea284a62e54b0c75a9dbfbaef98418c', # VMD-1.9.4_configure.patch - '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4_extra_colors.patch + 'dc9fc419e2e938f42d2e4784b0c9c7429317893f08d3ed170f949c3ee3aec062', # VMD-1.9.4a51_configure.patch + '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4a51_extra_colors.patch ] dependencies = [ From 71a71cf8b60ce0b9f4fc9d0f769adad52477fbff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Jun 2021 19:50:30 +0200 Subject: [PATCH 1007/2365] adding easyconfigs: ont-fast5-api-3.3.0-foss-2020b.eb --- .../ont-fast5-api-3.3.0-foss-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb new file mode 100644 index 0000000000..a8d05c6400 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '3.3.0' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + (name, version, { + 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From f3ab59f8d88504dd48157b04b104416c61193f8a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Jun 2021 23:18:27 +0200 Subject: [PATCH 1008/2365] retain old cheksum of mvabund in R-4.0.4-fosscuda-2020b.eb --- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 8a47161e25..f0b431cd09 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2155,7 +2155,8 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30'], + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], From 54569b14f109efe86d59f76ce4648a46ad17d5cd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Jun 2021 23:26:32 +0200 Subject: [PATCH 1009/2365] retain old cheksum of mvabund in R-4.0.4-foss-2020b.eb --- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 0e94f20f2e..1d52f7bc27 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2151,7 +2151,8 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30'], + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], From 12d73037379b06567901fd983797133391121f53 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Jun 2021 00:06:21 +0200 Subject: [PATCH 1010/2365] disable debuginfod from elfutils --- .../easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb index f0b29a4ce5..e51ac2c864 100644 --- a/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb @@ -26,14 +26,13 @@ builddependencies = [ dependencies = [ ('binutils', '2.35'), ('bzip2', '1.0.8'), - ('cURL', '7.72.0'), ('libarchive', '3.4.3'), - ('libmicrohttpd', '0.9.73'), - ('SQLite', '3.33.0'), ('XZ', '5.2.5'), ('zstd', '1.4.5'), ] +configopts = "--disable-debuginfod --disable-libdebuginfod" + sanity_check_paths = { 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.so'], 'dirs': [] From 4beecc84176f3fe0413a8e2937aeb73573282683 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Jun 2021 00:31:42 +0200 Subject: [PATCH 1011/2365] fix formatting of bcl2fastq2-2.20.0-GCC-10.2.0.eb --- .../b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb index cf80489b22..8e067a6bd0 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -41,8 +41,8 @@ start_dir = 'src' # check versions of libxml2 and libxslt from EB local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' -preconfigopts = local_sed_libver % {'l':'LIBXML2', 'f': local_cmakelists} -preconfigopts += local_sed_libver % {'l':'LIBXSLT', 'f': local_cmakelists} +preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} +preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} # remove hardcoded compilation flags local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' @@ -54,7 +54,7 @@ configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' sanity_check_paths = { 'files': ['bin/bcl2fastq'], - 'dirs': ['lib'] + 'dirs': ['lib'], } sanity_check_commands = ["bcl2fastq --help"] From 16bf021ff468b07d841fc55ae3c02e57210d4d4b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Jun 2021 01:02:54 +0200 Subject: [PATCH 1012/2365] fix homepage of MbedTLS-2.26.0-GCCcore-10.2.0.eb --- .../easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb index c8af21ea5c..8f51ba4fe1 100644 --- a/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb @@ -5,7 +5,7 @@ easyblock = 'ConfigureMake' name = 'MbedTLS' version = '2.26.0' -homepage = 'tls.mbed.org' +homepage = 'https://tls.mbed.org/' description = "An open source, portable, easy to use, readable and flexible SSL library." toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From d1a28e34a2666dd84361b3e13ab231de231d59b9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 4 Jun 2021 11:11:37 +0100 Subject: [PATCH 1013/2365] Add GxEScanR extension --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 ++ .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 30 ++++++++----------- 2 files changed, 16 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index f4c74e7d9b..9bb63be795 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2846,6 +2846,9 @@ exts_list = [ ('semPLS', '1.0-10', { 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 1d52f7bc27..a357afaff0 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -116,13 +116,13 @@ exts_list = [ ('geometry', '0.4.5', { 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], }), - ('bit', '4.0.4', { + ('bit', version, { 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], }), ('filehash', '2.4-2', { 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], }), - ('ff', '4.0.4', { + ('ff', version, { 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], }), ('bnlearn', '4.6.1', { @@ -1728,7 +1728,7 @@ exts_list = [ 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], 'checksums': [ 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz - '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch ], }), ('diveRsity', '1.9.90', { @@ -2151,8 +2151,7 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', - 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], + 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], @@ -2213,13 +2212,12 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.1', { 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], @@ -2333,8 +2331,7 @@ exts_list = [ 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], }), ('rda', '1.0.2-2.1', { - 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', - 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], }), ('sampling', '2.9', { 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], @@ -2433,9 +2430,9 @@ exts_list = [ 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], }), ('V8', '3.4.0', { - 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], - 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], }), ('rstan', '2.21.2', { 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], @@ -2687,13 +2684,9 @@ exts_list = [ 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), ('gWidgets2tcltk', '1.0-6', { - 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... 'modulename': False, + 'preinstallopts': "xvfb-run ", + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], }), ('mgsub', '1.7.2', { 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], @@ -2882,6 +2875,9 @@ exts_list = [ ('semPLS', '1.0-10', { 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), ] moduleclass = 'lang' From e5c0d0baf32a8f7cac7f91b7118437de1984bf9e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 4 Jun 2021 19:40:36 +0800 Subject: [PATCH 1014/2365] remove misleading comment from Python >= 3.7 easyconfigs, libffi is now also required for python itself (no longer bundled) --- easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 74d7a4c702..602f3f5c32 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('SQLite', '3.33.0'), ('XZ', '5.2.5'), ('GMP', '6.2.0'), # required for pycrypto - ('libffi', '3.3'), # required for cryptography + ('libffi', '3.3'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) From bb507637829b4a3c38384163f814cab0d4fb759f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Jun 2021 17:28:14 +0200 Subject: [PATCH 1015/2365] adding easyconfigs: harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb --- ...rmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/h/harmony/harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/h/harmony/harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/h/harmony/harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..4bb2570376 --- /dev/null +++ b/easybuild/easyconfigs/h/harmony/harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'harmony' +local_commit = '2586afd' +# see DESCRIPTION to determine version, +# but also take date of last commit into account (since version isn't always bumped) +version = '0.1.0-20210528' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://portals.broadinstitute.org/harmony' +description = "Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/immunogenomics/harmony/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['55c4aaa3cef0c06216a2a51946fb4ed7b189967e34c88bb0dfa53c4d52135d2f'] + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'data' From 67cd5b3e7e58d6c32a96bb045bd7522c291a5168 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Jun 2021 18:21:48 +0200 Subject: [PATCH 1016/2365] also install scripts with RegTools 0.4.2 + add missing dependencies and bump toolchain to foss --- .../r/RegTools/RegTools-0.4.2-foss-2020b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/r/RegTools/RegTools-0.4.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/RegTools/RegTools-0.4.2-foss-2020b.eb b/easybuild/easyconfigs/r/RegTools/RegTools-0.4.2-foss-2020b.eb new file mode 100644 index 0000000000..3e59121909 --- /dev/null +++ b/easybuild/easyconfigs/r/RegTools/RegTools-0.4.2-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'RegTools' +version = '0.4.2' + +homepage = 'https://regtools.readthedocs.org' +description = """RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a +regulatory and splicing context.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/griffithlab/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['47b52015c4d36d064f1ebf36c8481f6119b9e993df3c078d1e2925c45d2e72d0'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +# required by included scripts +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), # required by create_IGVsessions.py script + ('R', '4.0.3'), +] + +# 'make install' is not supported... +install_cmd = "mkdir %(installdir)s/bin && cp -a regtools %(installdir)s/bin/ && " +install_cmd += "cp -a %(builddir)s/regtools-%(version)s/scripts %(installdir)s/" + +sanity_check_paths = { + 'files': ['bin/regtools'], + 'dirs': ['scripts'], +} + +sanity_check_commands = ["regtools --help"] + +moduleclass = 'bio' From 61396eb4bbe63cb3fe3ffa6bf55a0238b24cdd0f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 5 Jun 2021 16:32:54 +0200 Subject: [PATCH 1017/2365] add patch to fix installation of HDF 4.2.15 on aarch64 --- easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb index 6a9f6d507b..bdb2cb878e 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459'] +patches = ['HDF-4.2.15_fix-aarch64.patch'] +checksums = [ + 'dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459', # hdf-4.2.15.tar.gz + '1b4341e309cccefc6ea4310c8f8b08cc3dfe1fa9609b7fa7aee80e4dac598473', # HDF-4.2.15_fix-aarch64.patch +] builddependencies = [ ('binutils', '2.35'), From 484d2b10855be05bd71c3e29ef181bba8fcdd39d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 5 Jun 2021 19:53:08 +0200 Subject: [PATCH 1018/2365] use Python 2 as build dependency for MbedTLS --- .../easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb index 8f51ba4fe1..8632f3021f 100644 --- a/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb @@ -17,8 +17,8 @@ checksums = ['37949e823c7e1f6695fc56858578df355da0770c284b1c1304cfc8b396d539cd'] builddependencies = [ ('binutils', '2.35'), - # Perl, Python only needed for test suite - ('Python', '3.8.6'), + # Perl, Python only needed for test suite (python2 required) + ('Python', '2.7.18'), ('Perl', '5.32.0'), ] From f77a1328b5c93bc4d3e8bd73b6ac64d5f2710874 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 5 Jun 2021 21:32:57 +0200 Subject: [PATCH 1019/2365] undo unintented changes to R-4.0.4-foss-2020b.eb --- .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 25 ++++++++++++------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index a357afaff0..af2ecce031 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -116,13 +116,13 @@ exts_list = [ ('geometry', '0.4.5', { 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], }), - ('bit', version, { + ('bit', '4.0.4', { 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], }), ('filehash', '2.4-2', { 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], }), - ('ff', version, { + ('ff', '4.0.4', { 'checksums': ['22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5'], }), ('bnlearn', '4.6.1', { @@ -2151,7 +2151,8 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], @@ -2212,12 +2213,13 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.1', { 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], @@ -2331,7 +2333,8 @@ exts_list = [ 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.9', { 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], @@ -2430,9 +2433,9 @@ exts_list = [ 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], }), ('V8', '3.4.0', { - 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', - 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', }), ('rstan', '2.21.2', { 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], @@ -2684,9 +2687,13 @@ exts_list = [ 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), ('gWidgets2tcltk', '1.0-6', { - 'modulename': False, - 'preinstallopts': "xvfb-run ", 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, }), ('mgsub', '1.7.2', { 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], From 3b73cd935180dfcd98f4ed0ebd070e3be31ac53a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 5 Jun 2021 21:40:33 +0200 Subject: [PATCH 1020/2365] stick to Python 3 as build dep for MbedTLS, make sure that Makefile uses 'python' rather than 'python2' --- .../easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb index 8632f3021f..aa73c698f4 100644 --- a/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb @@ -17,14 +17,14 @@ checksums = ['37949e823c7e1f6695fc56858578df355da0770c284b1c1304cfc8b396d539cd'] builddependencies = [ ('binutils', '2.35'), - # Perl, Python only needed for test suite (python2 required) - ('Python', '2.7.18'), + # Perl, Python only needed for test suite + ('Python', '3.8.6'), ('Perl', '5.32.0'), ] skipsteps = ['configure'] -buildopts = 'SHARED=ON' +buildopts = 'SHARED=ON PYTHON=python' runtest = 'check' From df95cb9ab6f1f80971eda308e0cee7831e2f298e Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 6 Jun 2021 14:42:16 +0100 Subject: [PATCH 1021/2365] run the CSB tests --- easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb index c3feca2d8a..7ca1ed8855 100644 --- a/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb @@ -33,7 +33,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -sanity_check_commands = ['csb-%s -h' % x for x in [ +sanity_check_commands = ['csb-test'] + ['csb-%s -h' % x for x in [ 'bfit', 'bfite', 'buildhmm', 'csfrag', 'embd', 'hhfrag', 'hhsearch', 'precision', 'promix', 'test']] From 2c76f5fad39ebc12e7d536b3be2e972ed875673f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 6 Jun 2021 14:48:37 +0100 Subject: [PATCH 1022/2365] A successful run of the CSB tests returns error code --- easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb index 7ca1ed8855..c3feca2d8a 100644 --- a/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb @@ -33,7 +33,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -sanity_check_commands = ['csb-test'] + ['csb-%s -h' % x for x in [ +sanity_check_commands = ['csb-%s -h' % x for x in [ 'bfit', 'bfite', 'buildhmm', 'csfrag', 'embd', 'hhfrag', 'hhsearch', 'precision', 'promix', 'test']] From 4d934fc12b5f5f42fbc8e088ffab7fe239ed6251 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Jun 2021 14:39:32 +0200 Subject: [PATCH 1023/2365] add commented out post-install commands to download antiSMASH databases --- .../a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb index 57fe702e6c..a0c8a90bc5 100644 --- a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -46,8 +46,6 @@ components = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('helperlibs', '0.2.1', { 'checksums': ['4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732'], @@ -72,12 +70,25 @@ exts_list = [ 'a6fae892e46fd945701dda4640d07467e2d0ab37913d29da403127833bc77291', # 5-2-0.tar.gz '4ca5d671085761c5f86719603fa3bbd0e82b7b52deefe8cac6eb4a3973825f16', # antiSMASH-5.2.0_Biopython-1.78.patch ], + # use http mirrors for ftp URLs + 'preinstallopts': "sed -i 's/ftp:/http:/g' antismash/download_databases.py && ", + # run additional commands to download databases and check prerequisites, + # which creates some missing .pkl files (which requires the databases); + # this is not done by default because the resulting installation is pretty big (~18GB) + # 'postinstallcmds': [ + # "download-antismash-databases", + # # check prerequisites, which also creates some missing .pkl files in the installation... + # "antismash --check-prereqs", + # ], }), ] sanity_check_paths = { 'files': ['bin/antismash', 'bin/meme'], - 'dirs': [], + 'dirs': [ + # antismash/databases subdirectory is only populated when postinstallcmds above are commented out + # 'lib/python%(pyshortver)s/site-packages/antismash/databases', + ], } sanity_check_commands = [ From fa304ce4d2db58af06fc1a99037e9fbef1297948 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Jun 2021 17:01:03 +0200 Subject: [PATCH 1024/2365] adding easyconfigs: minimap2-2.20-GCCcore-10.2.0.eb --- .../minimap2/minimap2-2.20-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5cff5bf900 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.20' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['f9eff90a7f14f999df93dff6ed4e3428277edbbd6bda6bdb1800e8d57c9135e3'] + +builddependencies = [('binutils', '2.35')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' From 6ff87a5e2e9d94ba3ed9ea5c3830242a9b5e2d64 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Jun 2021 08:52:37 +0200 Subject: [PATCH 1025/2365] Add patch for cuda prios --- .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index e80854a3f6..3f0b630f48 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -152,6 +152,7 @@ exts_list = [ 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.4.0_add-ldl.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_fix-min-priority-test.patch', 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', @@ -194,6 +195,8 @@ exts_list = [ '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch # TensorFlow-2.4.0_dont-use-var-lock.patch 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_fix-min-priority-test.patch + '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', # TensorFlow-2.5.0_add-default-shell-env.patch '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', # TensorFlow-2.5.0_add-protobuf-deps.patch From 7813ca3749033d6b05aa3e272a480b67978a32e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Tue, 8 Jun 2021 10:27:52 +0200 Subject: [PATCH 1026/2365] Removed PIC setting --- .../h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb index 79440aa7a2..eb31446fcf 100644 --- a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb @@ -10,7 +10,6 @@ description = """Hipify-clang is a clang-based tool for translating CUDA matchers, the output HIP source is produced.""" toolchain = {'name': 'gcccuda', 'version': '2020b'} -toolchainopts = {'pic': True} source_urls = ['https://github.com/ROCm-Developer-Tools/HIPIFY/archive/refs/tags/'] sources = ['rocm-%(version)s.tar.gz'] From bb790d9b04ebc6405024229177551a44d92d543b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Jun 2021 11:01:02 +0200 Subject: [PATCH 1027/2365] adding easyconfigs: NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb and patches: NCCL-2.8.3_fix-isend-irecv.patch --- .../NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb new file mode 100644 index 0000000000..49428f98e6 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -0,0 +1,30 @@ +name = 'NCCL' +version = '2.8.3' +local_gcc_ver = '10.2.0' +local_cuda_version = '11.1.1' +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': local_gcc_ver} + +builddependencies = [('GCC', local_gcc_ver, '', True)] +dependencies = [('CUDAcore', local_cuda_version, '', True)] + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +patches = ['NCCL-2.8.3_fix-isend-irecv.patch'] +checksums = [ + '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6', # v2.8.3-1.tar.gz + '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92', # NCCL-2.8.3_fix-isend-irecv.patch +] + +sanity_check_paths = { + 'files': ['include/nccl.h', 'lib/libnccl.%s' % SHLIB_EXT, 'lib/libnccl_static.a', 'lib/pkgconfig/nccl.pc'], + 'dirs': [], +} + +moduleclass = 'lib' From e78def52ebbb58e41716721cda4ecde346a89120 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Jun 2021 14:14:40 +0200 Subject: [PATCH 1028/2365] Remove sanity check --- .../n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb index 49428f98e6..cbf8532c70 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -22,9 +22,4 @@ checksums = [ '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92', # NCCL-2.8.3_fix-isend-irecv.patch ] -sanity_check_paths = { - 'files': ['include/nccl.h', 'lib/libnccl.%s' % SHLIB_EXT, 'lib/libnccl_static.a', 'lib/pkgconfig/nccl.pc'], - 'dirs': [], -} - moduleclass = 'lib' From 254e03f6d0e2539bd5e3692273082f16de3c56d1 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 8 Jun 2021 14:46:46 +0200 Subject: [PATCH 1029/2365] R-4.0.5: adds patch from #12583 --- .../easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 7 ++++- .../easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 26 +++++++++++++++++++ 2 files changed, 32 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 7d1c7c7892..a57bd0cfba 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2845,7 +2845,12 @@ exts_list = [ 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], }), ('DMCfun', '1.3.0', { - 'checksums': ['2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7'], + 'patches': ['DMCfun-1.3.0_fix-parallel-detect.patch'], + 'checksums': [ + '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz + # DMCfun-1.3.0_fix-parallel-detect.patch + '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', + ], }), ] diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 3616a01a5e..7b025f6a92 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2837,6 +2837,32 @@ exts_list = [ ('rnetcarto', '0.2.4', { 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], }), + ('DEoptim', '2.2-5', { + 'checksums': ['ae12dedcd4a43994e811e7285f8c12bfdb688e7c99d65515cf7e8cb6db13955a'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2013.9-1', { + 'checksums': ['1a1a399682a06a5fea3934985ebb1334005676c6a2a22d06f3c91c3923432908'], + }), + ('Rvmmin', '2018-4.17', { + 'checksums': ['d53ba7ab06596a47990caf101a50935b2b34402f9dd8414f098a873026ff1f56'], + }), + ('Rcgmin', '2013-2.21', { + 'checksums': ['a824a09c32d7565a3e30607c71333506d5b7197478fbe8b43f8a77dad6c12f0a'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '1.3.0', { + 'patches': ['DMCfun-1.3.0_fix-parallel-detect.patch'], + 'checksums': [ + '2ca5e633c1af56d7f13a811a72e33853026ad4b6ca34290d017c8bb66443d2e7', # DMCfun_1.3.0.tar.gz + # DMCfun-1.3.0_fix-parallel-detect.patch + '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', + ], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From a1a752625c4704a593b3023c813a2e49a34989c0 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 8 Jun 2021 18:07:30 +0200 Subject: [PATCH 1030/2365] R-4.0.5: alternative checksum for mvabund --- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index a57bd0cfba..83657b8665 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2160,7 +2160,8 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 7b025f6a92..545eb8a4f7 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2170,7 +2170,8 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], From d9388f345e7cb49825182f6d31475a5436d4a9e0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 8 Jun 2021 17:59:08 +0100 Subject: [PATCH 1031/2365] adding easyconfigs: BBMap-38.90-GCC-9.3.0.eb, BBMap-38.90-GCC-10.2.0.eb --- .../b/BBMap/BBMap-38.90-GCC-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb new file mode 100644 index 0000000000..94e6c8540f --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '38.90' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1'] + +dependencies = [('Java', '11', '', True)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +moduleclass = 'bio' From 3d554625e13a0ebac0481dd607b8eeae2c2f0ec5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?P=C3=A4r=20Axel=20Leonard=20Ros=C3=A9n?= Date: Tue, 8 Jun 2021 21:36:35 +0200 Subject: [PATCH 1032/2365] Add preinstallopts for minimap2 build if aarch64 --- easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb index fbfc9e5978..6ab5c77652 100644 --- a/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb @@ -18,6 +18,9 @@ dependencies = [('Python', '3.8.6')] download_dep_fail = True use_pip = True +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + sanity_check_paths = { 'files': ['bin/flye'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From ee3a1eae28371cdc00e03e6b7a58da291a51251b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Wed, 9 Jun 2021 07:30:11 +0200 Subject: [PATCH 1033/2365] Removed unnecessary build commands --- .../h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb index eb31446fcf..90ce08e94f 100644 --- a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb @@ -21,14 +21,12 @@ builddependencies = [ ] dependencies = [ - # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), ('Clang', '11.0.1'), + # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), # ('Python', '3.8.6'), ] configopts = '-DHIPIFY_CLANG_TESTS=0' -configopts += ' -DCMAKE_INSTALL_PREFIX=%(installdir)s' -configopts += ' -DCMAKE_PREFIX_PATH=$EBROOTCLANG' # NOTE: The following configuration options are needed if building with tests # (as activated by 'runtest' below), for these to work the above commented # dependencies need to be uncommented. Currently testing is disabled due to a From da0a6d86651aa11e062ac3fbba1db6b59418de64 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 9 Jun 2021 08:39:35 +0200 Subject: [PATCH 1034/2365] Workaround failures on recent x86 archs --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 4 ++++ .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 5 +++++ 2 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index f1268b2903..b94130e744 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -8,6 +8,10 @@ description = "An open-source software library for Machine Intelligence" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True} +if ARCH == 'x86_64': + # required workaround for failing tests on Intel Skylake and Cascade Lake, + # see https://github.com/tensorflow/tensorflow/issues/49944 + toolchainopts['extra_cxxflags'] = '-mno-avx512f' builddependencies = [ ('Bazel', '3.7.2'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 3f0b630f48..29aeba8a34 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -8,6 +8,11 @@ description = "An open-source software library for Machine Intelligence" toolchain = {'name': 'fosscuda', 'version': '2020b'} toolchainopts = {'pic': True} +if ARCH == 'x86_64': + # required workaround for failing tests on Intel Skylake and Cascade Lake, + # see https://github.com/tensorflow/tensorflow/issues/49944 + toolchainopts['extra_cxxflags'] = '-mno-avx512f' + builddependencies = [ ('Bazel', '3.7.2'), From 44d3bf88019896e411f4c48460d081048ca53987 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 09:44:24 +0200 Subject: [PATCH 1035/2365] bonito and its deps --- .../b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb | 129 ++++++++++++++++++ .../GenomeWorks-2021.02.2-fosscuda-2020b.eb | 118 ++++++++++++++++ .../p/parasail/parasail-2.4.3-GCC-10.2.0.eb | 1 - .../p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb | 13 +- .../python-parasail-1.2.4-fosscuda-2020b.eb | 5 +- .../s/spoa/spoa-4.0.7-GCC-10.2.0.eb | 3 +- 6 files changed, 253 insertions(+), 16 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..15b503ae26 --- /dev/null +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb @@ -0,0 +1,129 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'Bonito' +version = '0.4.0' + +homepage = 'https://github.com/nanoporetech/bonito' +description = "Convolution Basecaller for Oxford Nanopore Reads" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('h5py', '3.1.0'), + ('Mako', '1.1.3'), + ('PyYAML', '5.3.1'), + ('python-parasail', '1.2.4'), + ('tqdm', '4.56.2'), + ('apex', '20210420'), + ('minimap2', '2.18'), + ('CuPy', '8.5.0'), + ('GenomeWorks', '2021.02.2'), + ('pyspoa', '0.0.8'), +] + +use_pip = True + +local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2//g' requirements.txt && " +# CuPy is provided as proper dependency, installed from source +local_bonito_preinstallopts += "sed -i 's/cupy-cuda102//g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && " +local_bonito_preinstallopts += "export PATH=%(installdir)s/bin/:$PATH && " + +exts_list = [ + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('alembic', '1.6.4', { + 'checksums': ['becb572c6701c90ca249f97fc1ae231468cc9516df367a350901eeb9310a8d43'], + }), + ('cmd2', '1.5.0', { + 'checksums': ['701a8c9975c4abc45e5d13906ab149f959f812869106347323a3f89ac0e82a62'], + }), + ('prettytable', '2.1.0', { + 'checksums': ['5882ed9092b391bb8f6e91f59bcdbd748924ff556bb7c634089d5519be87baa0'], + }), + ('cliff', '3.7.0', { + 'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ", + 'checksums': ['389c81960de13f05daf1cbd546f33199e86c518ba4266c79ec7a153a280980ea'], + }), + ('colorlog', '5.0.1', { + 'checksums': ['f17c013a06962b02f4449ee07cfdbe6b287df29efc2c9a1515b4a376f4e588ea'], + }), + ('greenlet', '1.1.0', { + 'checksums': ['c87df8ae3f01ffb4483c796fe1b15232ce2b219f0b18126948616224d3f658ee'], + }), + ('SQLAlchemy', '1.4.15', { + 'checksums': ['0ff100c75cd175f35f4d24375a0b3d82461f5b1af5fc8d112ef0e5ceea8049e6'], + }), + ('cmaes', '0.8.2', { + 'checksums': ['1c04ba23ded925ef13b96f42cfbd667a905ea5b80754c750e6448b9fcda96a5d'], + }), + ('optuna', '2.7.0', { + 'checksums': ['eb1595108ec444e840deb0037351074144fecb7a4eff6870fc11569ab782cfc6'], + }), + ('colorama', '0.4.4', { + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('importlib_metadata', '4.0.1', { + 'checksums': ['8c501196e49fb9df5df43833bdb1e4328f64847763ec8a50703148b73784d581'], + }), + ('stevedore', '3.3.0', { + 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], + }), + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '3.3.0', { + 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], + }), + ('fast-ctc-decode', '0.3.0', { + 'source_tmpl': 'fast_ctc_decode-%(version)s-cp38-cp38-manylinux2010_x86_64.whl', + 'unpack_sources': False, + 'checksums': ['623d83f8de5e02199a09bfe0160a1e477f0db8d4ab612b26a7e42c2a335b378c'], + }), + ('mappy', '2.18', { + 'checksums': ['18fffdb4b831cc3f5399b919b0942c640bf9a943ca22102ac446f53af3b905a8'], + }), + ('seqdist', '0.0.3', { + 'preinstallopts': "sed -i 's/cupy-cuda102//g' settings.ini && sed -i 's/[<>=]=[0-9].*//g' settings.ini && ", + 'checksums': ['bdbbea6ebba1c6dd6698d46e23ba7858f93a7cdf0c7cbc2ea66660291acb044f'], + }), + ('crf-beam', '0.0.1a0', { + 'modulename': 'kbeam', + 'sources': ['crf_beam-%(version)s-cp38-cp38-manylinux1_x86_64.whl'], + 'unpack_sources': False, + 'checksums': ['0cba80ff4d7f90595f498921cf904736e3bce558dba80de5611874d89e72312e'], + }), + ('networkx', '2.5.1', { + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'preinstallopts': local_bonito_preinstallopts, + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bonito'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bonito --help", + "bonito convert --help", + "bonito download --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..e1bc29d6ac --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -0,0 +1,118 @@ +# author: Denis Kristak (INUITS) +easyblock = 'CMakePythonPackage' + +name = 'GenomeWorks' +version = '2021.02.2' +local_git_commit = '691380d1122a9ad86f91b3038c8b6625d137b6ed' + +homepage = 'https://github.com/clara-parabricks/GenomeWorks' +description = "SDK for GPU accelerated genome assembly and analysis" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +sources = [ + { + 'source_urls': ['https://github.com/clara-parabricks/GenomeWorks/archive/'], + 'filename': 'v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'filename': 'benchmark-20190513.tar.gz', + 'download_filename': '090faecb454fbd6e6e17a75ef8146acb037118d4.tar.gz', + }, + { + 'source_urls': ['https://github.com/NVIDIA/cub/archive'], + 'filename': 'cub-20201123.tar.gz', + 'download_filename': '618a46c27764f0e0b86fb3643a572ed039180ad8.tar.gz', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'filename': 'googletest-20190424.tar.gz', + 'download_filename': '84d986531e8df9fb6ea4a7bae8fb130c05b3782c.tar.gz', + }, + { + 'source_urls': ['https://github.com/samtools/htslib/archive'], + 'filename': 'htslib-20200806.tar.gz', + 'download_filename': 'a79009b38ce83e39bcbc8f54c00cf203621aa5bb.tar.gz', + }, + { + 'source_urls': ['https://github.com/cartoonist/kseqpp/archive'], + 'filename': 'kseqpp-20181009.tar.gz', + 'download_filename': 'c7add979ac77ec8ada07b25aab7dcf0c5e87f90e.tar.gz', + }, + { + 'source_urls': ['https://github.com/NVIDIA/libcudacxx/archive'], + 'filename': 'libcudacxx-20201003.tar.gz', + 'download_filename': 'd0bafdb9fdde2ee99932d42f1deec74d53e19514.tar.gz', + }, + { + 'source_urls': ['https://github.com/rvaser/spoa/archive'], + 'filename': 'spoa-20190416.tar.gz', + 'download_filename': '0b9e56da3241d6a887d64adcfd1ebfae29810c04.tar.gz', + }, +] + +builddependencies = [('CMake', '3.18.4')] +dependencies = [ + ('Python', '3.8.6'), + ('Autoconf', '2.69'), + ('matplotlib', '3.3.3'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), + ('tqdm', '4.56.2'), +] +local_vendor_dir = '%(builddir)s/GenomeWorks-*/3rdparty/' +# benchmark +preconfigopts = "mv %%(builddir)s/benchmark-*/* %s/benchmark/ && " % local_vendor_dir +# cub +preconfigopts += "mv %%(builddir)s/cub-*/* %s/cub/ && " % local_vendor_dir +# googletest +preconfigopts += "mv %%(builddir)s/googletest-*/* %s/googletest/ && " % local_vendor_dir +# htslib +preconfigopts += "mv %%(builddir)s/htslib-*/* %s/htslib/ && " % local_vendor_dir +# kseqpp +preconfigopts += "mv %%(builddir)s/kseqpp-*/* %s/kseqpp/ && " % local_vendor_dir +# libcudacxx +preconfigopts += "mv %%(builddir)s/libcudacxx-*/* %s/libcudacxx/ && " % local_vendor_dir +# spoa +preconfigopts += "mv %%(builddir)s/spoa-*/* %s/spoa/ && " % local_vendor_dir + +# add missing include to a file +preconfigopts += "sed -i'' 's/#include /#include \\n#include /g'" +preconfigopts += " %(builddir)s/GenomeWorks-*/3rdparty/spoa/src/alignment_engine.cpp && """ + +configopts = "-Dgw_cuda_gen_all_arch=OFF" + +skipsteps = ['test'] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': ['https://github.com/clara-parabricks/GenomeWorks/archive/'], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('genomeworks', '%s' % version, { + 'sources': ['v%(version)s.tar.gz'], + 'patches': ['GenomeWorks-2021-02-2_dep_versions_n_file_extension.patch'], + 'start_dir': 'pygenomeworks', + 'preinstallopts': """export GW_INSTALL_DIR=%(installdir)s && + export GW_VERSION=%(version)s && + export GW_ROOT_DIR=%(builddir)s/GenomeWorks-%(version)s && + """, + 'postinstallcmds': [""" + sed -i'' 's/==/>=/g' %(builddir)s/GenomeWorks-%(version)s/pygenomeworks/requirements.txt + """], + }), + ('sortedcollections', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcollections/'], + }), + ('pytest', '6.2.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb index 9ad845641f..52f6deb0a0 100644 --- a/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb @@ -14,7 +14,6 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} github_account = 'jeffdaily' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['6f0cddcaaf7c00573e62a3b081a09380cb022b2ed6a3a138108f8823775ca026'] builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb index 5de35fb7c3..3d8c51604a 100644 --- a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb @@ -21,25 +21,18 @@ sources = [ }, ] patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] -checksums = [ - 'a1e630ef30a42d8e8c076d914261d0d34060631d64694569d52c1a2be5deada7', # pyspoa-0.0.8.tar.gz - '284cd14c1e60b36c966bcc8ce650d0b798b8a836d6c379e021e0da0dbe6ddf38', # cereal-20200423.tar.gz - 'a98c82ae8346b48952b171675f9df7ab1c95ea5421afcf5bcd778c01c5ee5a52', # pyspoa-0.0.8_use-spoa-dep.patch -] - -builddependencies = [('CMake', '3.18.4')] dependencies = [ ('Python', '3.8.6'), ('pybind11', '2.6.0'), ('spoa', '4.0.7'), + ('CMake', '3.18.4'), ] download_dep_fail = True preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " -# strip out cmake requirements, since we provide that as proper dependency -preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " +preinstallopts += """sed -i "s/, 'cmake==3.18.4'//g" %(builddir)s/pyspoa*/setup.py && """ use_pip = True @@ -47,4 +40,6 @@ options = {'modulename': 'spoa'} sanity_pip_check = True +sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb index 0f02c50779..5224c3f2d7 100644 --- a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb @@ -10,14 +10,11 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] sources = ['parasail-%(version)s.tar.gz'] -checksums = ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'] -builddependencies = [ - ('parasail', '2.4.3'), -] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), + ('parasail', '2.4.3'), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb index 61912e520f..01ed022662 100644 --- a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb @@ -12,9 +12,8 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] sources = ['spoa-v%(version)s.tar.gz'] -checksums = ['f7a8cd039e4aabea1481e123387fedaa8f87e55418a3649408a615f5c6b1b9a4'] -builddependencies = [('CMake', '3.18.4')] +dependencies = [('CMake', '3.18.4')] configopts = "-Dspoa_build_executable=ON" From 23630adbb616e146c5a17b22770e8689c1c7b174 Mon Sep 17 00:00:00 2001 From: Martin Lueders Date: Wed, 9 Jun 2021 09:55:00 +0200 Subject: [PATCH 1036/2365] easyconfigs for libmbd added --- .../l/libmbd/libmbd-0.10.4-foss-2020b.eb | 45 +++++++++++++++++++ .../l/libmbd/libmbd-0.10.4-intel-2020b.eb | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb new file mode 100644 index 0000000000..057ee5f7d9 --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.10.4' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] + +builddependencies = [ + ('CMake', '3.18.4') +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.so'] + + ['lib64/libmbd.so'], + 'dirs': ['include', 'lib/cmake/mbd'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb new file mode 100644 index 0000000000..2785d0ed46 --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.10.4' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] + +builddependencies = [ + ('CMake', '3.18.4') +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.so'] + + ['lib64/libmbd.so'], + 'dirs': ['include', 'lib/cmake/mbd'], +} + +moduleclass = 'chem' From 160b833f76110bcd5f8b182a8928dab7ef076e3d Mon Sep 17 00:00:00 2001 From: Martin Lueders Date: Wed, 9 Jun 2021 10:25:16 +0200 Subject: [PATCH 1037/2365] fixed line length issue --- .../l/libmbd/libmbd-0.10.4-foss-2020b.eb | 15 ++++++++++----- .../l/libmbd/libmbd-0.10.4-intel-2020b.eb | 15 ++++++++++----- 2 files changed, 20 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb index 057ee5f7d9..149f34fc77 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -7,11 +7,16 @@ homepage = 'https://libmbd.github.io/index.html' description = """ Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. - -The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. """ toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb index 2785d0ed46..32d0079345 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -7,11 +7,16 @@ homepage = 'https://libmbd.github.io/index.html' description = """ Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. - -The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. """ toolchain = {'name': 'intel', 'version': '2020b'} From 611edfac532da8615af4d7fb67942c4dda75080a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 10:40:43 +0200 Subject: [PATCH 1038/2365] checksums --- .../b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb | 4 ++- .../GenomeWorks-2021.02.2-fosscuda-2020b.eb | 29 +++++++++++++++---- .../p/parasail/parasail-2.4.3-GCC-10.2.0.eb | 1 + .../p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb | 5 ++++ .../s/spoa/spoa-4.0.7-GCC-10.2.0.eb | 1 + 5 files changed, 33 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb index 15b503ae26..d56602a794 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb @@ -106,10 +106,12 @@ exts_list = [ 'checksums': ['0cba80ff4d7f90595f498921cf904736e3bce558dba80de5611874d89e72312e'], }), ('networkx', '2.5.1', { + 'checksums': ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'], }), ('ont-bonito', version, { 'modulename': 'bonito', - 'preinstallopts': local_bonito_preinstallopts, + 'preinstallopts': "sed -i 's/[><=]=.*//g' requirements.txt && sed -i 's/genomeworks-cuda-10-2//g' requirements.txt && sed -i 's/cupy-cuda102//g' requirements.txt && sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && export PATH=%(installdir)s/bin/:$PATH && ", + 'checksums': ['429310d56e2d7dabd91a9a9c972504a0aa2b6d6469563b14d4aae30adfe9a87e'], }), ] diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index e1bc29d6ac..65b231aca7 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -52,6 +52,16 @@ sources = [ 'download_filename': '0b9e56da3241d6a887d64adcfd1ebfae29810c04.tar.gz', }, ] +checksums = [ + 'f036f066b3ae22e603786f79d374cde28942c22064a169f123fb085fd6b4ccaf', # v2021.02.2.tar.gz + 'f68aec93154d010324c05bcd8c5cc53468b87af88d87acb5ddcfaa1bba044837', # benchmark-20190513.tar.gz + '7831843b8ab5f9d9dfbcea3b9ad2632a229c6d1aa9a5a335b8d8b813707dd9ec', # cub-20201123.tar.gz + '6fcf88c123bdee5cbef5f1d3b2b34fa6f20cb3168bf05a2adbe20428cae3fe0e', # googletest-20190424.tar.gz + '28455110611f6330b5d6b49ff5c3c1c824a7727944c66c8c6f0e9ce1209740ea', # htslib-20200806.tar.gz + 'ae64499023d4705f42e79a966f175c31a46a794a1dd6fe9c03dd1827efe4a953', # kseqpp-20181009.tar.gz + '0427eaf2c5deabdeeb7f1a894fd362823e32450d6c2c79fe20e64a8898968ef9', # libcudacxx-20201003.tar.gz + '9608c0d31dc158aaab8916b8977962f88e42d2341f979d517daac03db525ea70', # spoa-20190416.tar.gz +] builddependencies = [('CMake', '3.18.4')] dependencies = [ @@ -95,23 +105,30 @@ exts_default_options = { } exts_list = [ - ('genomeworks', '%s' % version, { - 'sources': ['v%(version)s.tar.gz'], + ('genomeworks', version, { 'patches': ['GenomeWorks-2021-02-2_dep_versions_n_file_extension.patch'], - 'start_dir': 'pygenomeworks', + 'postinstallcmds': [""" + sed -i'' 's/==/>=/g' %(builddir)s/GenomeWorks-%(version)s/pygenomeworks/requirements.txt + """], 'preinstallopts': """export GW_INSTALL_DIR=%(installdir)s && export GW_VERSION=%(version)s && export GW_ROOT_DIR=%(builddir)s/GenomeWorks-%(version)s && """, - 'postinstallcmds': [""" - sed -i'' 's/==/>=/g' %(builddir)s/GenomeWorks-%(version)s/pygenomeworks/requirements.txt - """], + 'sources': ['v%(version)s.tar.gz'], + 'start_dir': 'pygenomeworks', + 'checksums': [ + 'f036f066b3ae22e603786f79d374cde28942c22064a169f123fb085fd6b4ccaf', # v2021.02.2.tar.gz + # GenomeWorks-2021-02-2_dep_versions_n_file_extension.patch + '3e33e4ecc03aa43699748a623a331ed9be45a9e8a9c519c0fca6deff17144baf', + ], }), ('sortedcollections', '2.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcollections/'], + 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], }), ('pytest', '6.2.4', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + 'checksums': ['50bcad0a0b9c5a72c8e4e7c9855a3ad496ca6a881a3641b4260605450772c54b'], }), ] diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb index 52f6deb0a0..9ad845641f 100644 --- a/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.2.0.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} github_account = 'jeffdaily' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['6f0cddcaaf7c00573e62a3b081a09380cb022b2ed6a3a138108f8823775ca026'] builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb index 3d8c51604a..decf52d2f3 100644 --- a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb @@ -21,6 +21,11 @@ sources = [ }, ] patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] +checksums = [ + 'a1e630ef30a42d8e8c076d914261d0d34060631d64694569d52c1a2be5deada7', # pyspoa-0.0.8.tar.gz + '284cd14c1e60b36c966bcc8ce650d0b798b8a836d6c379e021e0da0dbe6ddf38', # cereal-20200423.tar.gz + '504f6df0c8789093ff91eed0340c2ad9532700ed03cd2ca202d10c434bca34b2', # pyspoa-0.0.8_use-spoa-dep.patch +] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb index 01ed022662..f061b069e1 100644 --- a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb @@ -12,6 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] sources = ['spoa-v%(version)s.tar.gz'] +checksums = ['f7a8cd039e4aabea1481e123387fedaa8f87e55418a3649408a615f5c6b1b9a4'] dependencies = [('CMake', '3.18.4')] From 7b80ee8d231557c27749c85493df515c26b39a56 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 10:50:48 +0200 Subject: [PATCH 1039/2365] checksums --- .../p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb index 5224c3f2d7..2ac61b6c7d 100644 --- a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] sources = ['parasail-%(version)s.tar.gz'] +checksums = ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'] dependencies = [ ('Python', '3.8.6'), From fdca6f7b73074884a9e0a89bd2ca77c0683209a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Wed, 9 Jun 2021 10:58:58 +0200 Subject: [PATCH 1040/2365] Added comments to patch file and renamed --- .../easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb index 6e2b175192..d922959587 100644 --- a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb @@ -16,10 +16,12 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/ROCm-Developer-Tools/aomp/releases/download/rel_%(version)s/'] sources = ['aomp-%(version)s.tar.gz'] -patches = ['build_aomp-%(version)s.patch'] +patches = ['AOMP-%(version)s_remove_hardcoded_paths.patch'] checksums = [ - '0256a84aefcbf7c49112f068321b84e0620f4c43a9d490c64d820e40658e0d67', # aomp-13.0-2.tar.gz - '1deca48ec55e74b091731e48ce54097b88620062ed0cb05de1dc9d56c2016a21', # build_aomp-13.0-2.patch + # aomp-13.0-2.tar.gz: + '0256a84aefcbf7c49112f068321b84e0620f4c43a9d490c64d820e40658e0d67', + # AOMP-13.0-2_remove_hardcoded_paths.patch: + 'ec41ffcec63d079b6a73c93bea29e0b8d77ca7b059725aa1d47c334f7e476ff0', ] builddependencies = [ From bfaa8ccac51f861207b302440d8d627a716ff945 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Wed, 9 Jun 2021 11:09:28 +0200 Subject: [PATCH 1041/2365] Remove sanity check from easyconfig --- easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb index d922959587..008bcc0a9d 100644 --- a/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb @@ -39,9 +39,4 @@ dependencies = [ ('numactl', '2.0.13'), ] -sanity_check_paths = { - 'files': ['bin/clang', 'bin/ld.lld', 'include/omp.h'], - 'dirs': ['amdgcn', 'bin', 'include', 'lib'], -} - moduleclass = 'compiler' From 69f840a6bc91068e5ee20d839d57d1ac9871446c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Wed, 9 Jun 2021 11:12:41 +0200 Subject: [PATCH 1042/2365] Do not explicitly disable testing --- .../h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb index 90ce08e94f..d06d9b20df 100644 --- a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb @@ -26,11 +26,11 @@ dependencies = [ # ('Python', '3.8.6'), ] -configopts = '-DHIPIFY_CLANG_TESTS=0' # NOTE: The following configuration options are needed if building with tests # (as activated by 'runtest' below), for these to work the above commented # dependencies need to be uncommented. Currently testing is disabled due to a # lack of 'llvm-lit'. +# configopts = '-DHIPIFY_CLANG_TESTS=1' # configopts += ' -DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA' # configopts += ' -DCUDA_DNN_ROOT_DIR=$EBROOTCUDNN' # configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python' From 2014c71c47f2f79db3919e6d32d91988c03757d5 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 11:33:06 +0200 Subject: [PATCH 1043/2365] checks --- easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb index d56602a794..795fc117a2 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb @@ -110,7 +110,7 @@ exts_list = [ }), ('ont-bonito', version, { 'modulename': 'bonito', - 'preinstallopts': "sed -i 's/[><=]=.*//g' requirements.txt && sed -i 's/genomeworks-cuda-10-2//g' requirements.txt && sed -i 's/cupy-cuda102//g' requirements.txt && sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && export PATH=%(installdir)s/bin/:$PATH && ", + 'preinstallopts': local_bonito_preinstallopts, 'checksums': ['429310d56e2d7dabd91a9a9c972504a0aa2b6d6469563b14d4aae30adfe9a87e'], }), ] From caf1dd5464d25456e20fe4dadc5b535de98352a8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 9 Jun 2021 12:17:45 +0200 Subject: [PATCH 1044/2365] Fix ARM compilation --- .../TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 31 +++++++------- .../TensorFlow-2.5.0-fosscuda-2020b.eb | 41 ++++++++++--------- 2 files changed, 39 insertions(+), 33 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index b94130e744..62efc7ee14 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -150,15 +150,30 @@ exts_list = [ 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], }), (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'patches': [ 'TensorFlow-2.4.0_add-ldl.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + ], + 'checksums': [ + '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', 'test_targets': [ @@ -186,18 +201,6 @@ exts_list = [ 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", 'with_xla': True, - 'checksums': [ - '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch - # TensorFlow-2.4.0_dont-use-var-lock.patch - 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', - # TensorFlow-2.5.0_add-default-shell-env.patch - '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', - # TensorFlow-2.5.0_add-protobuf-deps.patch - '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', - # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch - '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', - ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 29aeba8a34..b9f42c51b5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -153,6 +153,8 @@ exts_list = [ 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], }), (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'patches': [ 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.4.0_add-ldl.patch', @@ -161,10 +163,28 @@ exts_list = [ 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'checksums': [ + '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_fix-min-priority-test.patch + '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch + 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', + ], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' @@ -194,23 +214,6 @@ exts_list = [ 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", 'with_xla': True, - 'checksums': [ - '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz - '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch - # TensorFlow-2.4.0_dont-use-var-lock.patch - 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', - # TensorFlow-2.4.1_fix-min-priority-test.patch - '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', - # TensorFlow-2.5.0_add-default-shell-env.patch - '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', - # TensorFlow-2.5.0_add-protobuf-deps.patch - '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', - # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch - '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', - # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch - 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', - ], }), ] From b5c6f40c2780ef17657481254e1944bbb7aaba4a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 9 Jun 2021 14:02:55 +0200 Subject: [PATCH 1045/2365] Fix ICE in GCC 10.2.0 on ARM --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index c145d06599..33e8317d38 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -33,6 +33,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-10.2.0_fix-has-include-Fortran.patch', + 'GCCcore-10.2.0_fix-ice-on-arm.patch', 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', ] checksums = [ @@ -46,6 +47,7 @@ checksums = [ '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCCcore-10.2.0_fix-has-include-Fortran.patch + '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278', # GCCcore-10.2.0_fix-ice-on-arm.patch # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', ] From 77841707d007d7cb1c72da9df0bf0d1be3ef17cd Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 9 Jun 2021 15:27:39 +0200 Subject: [PATCH 1046/2365] Delete python-parasail-1.2.4-fosscuda-2020b.eb making new pr for this --- .../python-parasail-1.2.4-fosscuda-2020b.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb deleted file mode 100644 index 2ac61b6c7d..0000000000 --- a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'python-parasail' -version = '1.2.4' - -homepage = 'https://github.com/jeffdaily/parasail-python' -description = "Python Bindings for the Parasail C Library" - -toolchain = {'name': 'fosscuda', 'version': '2020b'} - -source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] -sources = ['parasail-%(version)s.tar.gz'] -checksums = ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'] - -dependencies = [ - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('parasail', '2.4.3'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -# make sure setup.py finds the parasail library -preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT - -options = {'modulename': 'parasail'} - -moduleclass = 'bio' From f5326687fbf552ea99225c14f94fe6f4671459f1 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 9 Jun 2021 15:29:57 +0200 Subject: [PATCH 1047/2365] Update spoa-4.0.7-GCC-10.2.0.eb cmake in builddependencies --- easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb index f061b069e1..61912e520f 100644 --- a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.2.0.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] sources = ['spoa-v%(version)s.tar.gz'] checksums = ['f7a8cd039e4aabea1481e123387fedaa8f87e55418a3649408a615f5c6b1b9a4'] -dependencies = [('CMake', '3.18.4')] +builddependencies = [('CMake', '3.18.4')] configopts = "-Dspoa_build_executable=ON" From 2811f05a0997dac425edff9115056f90b77fbaee Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 9 Jun 2021 15:32:10 +0200 Subject: [PATCH 1048/2365] Update pyspoa-0.0.8-GCC-10.2.0.eb cmake as builddependencies --- easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb index decf52d2f3..7711d23ebd 100644 --- a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb @@ -27,11 +27,12 @@ checksums = [ '504f6df0c8789093ff91eed0340c2ad9532700ed03cd2ca202d10c434bca34b2', # pyspoa-0.0.8_use-spoa-dep.patch ] +builddependencies = [('CMake', '3.18.4')] + dependencies = [ ('Python', '3.8.6'), ('pybind11', '2.6.0'), ('spoa', '4.0.7'), - ('CMake', '3.18.4'), ] download_dep_fail = True From 965119c6e4c61c662ff0f3c02c7af3e404ccbb7a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 15:37:18 +0200 Subject: [PATCH 1049/2365] returning python-parasail back to how it was --- .../python-parasail-1.2.4-fosscuda-2020b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..b222262157 --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.2.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'] + +builddependencies = [ + ('parasail', '2.4.3'), +] +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' \ No newline at end of file From bc5f93666d534b1344d1cfa8b5544b20a583ee0f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 15:38:16 +0200 Subject: [PATCH 1050/2365] returning python-parasail back to how it was --- .../p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb index b222262157..0f02c50779 100644 --- a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb @@ -29,4 +29,4 @@ preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail. options = {'modulename': 'parasail'} -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 8848ee90ed445092afa590ddece2060460f7e933 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 15:43:17 +0200 Subject: [PATCH 1051/2365] returning patch back to how it was --- easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb index 7711d23ebd..5438826450 100644 --- a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb @@ -33,6 +33,7 @@ dependencies = [ ('Python', '3.8.6'), ('pybind11', '2.6.0'), ('spoa', '4.0.7'), + # ('CMake', '3.18.4'), ] download_dep_fail = True From 10fae35009159e5d375b9180931069f92e74b4df Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 15:47:15 +0200 Subject: [PATCH 1052/2365] returning patch back to how it was --- easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb index 5438826450..b027af4877 100644 --- a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb @@ -24,7 +24,7 @@ patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] checksums = [ 'a1e630ef30a42d8e8c076d914261d0d34060631d64694569d52c1a2be5deada7', # pyspoa-0.0.8.tar.gz '284cd14c1e60b36c966bcc8ce650d0b798b8a836d6c379e021e0da0dbe6ddf38', # cereal-20200423.tar.gz - '504f6df0c8789093ff91eed0340c2ad9532700ed03cd2ca202d10c434bca34b2', # pyspoa-0.0.8_use-spoa-dep.patch + 'a98c82ae8346b48952b171675f9df7ab1c95ea5421afcf5bcd778c01c5ee5a52', # pyspoa-0.0.8_use-spoa-dep.patch ] builddependencies = [('CMake', '3.18.4')] @@ -33,13 +33,12 @@ dependencies = [ ('Python', '3.8.6'), ('pybind11', '2.6.0'), ('spoa', '4.0.7'), - # ('CMake', '3.18.4'), ] download_dep_fail = True preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " -preinstallopts += """sed -i "s/, 'cmake==3.18.4'//g" %(builddir)s/pyspoa*/setup.py && """ +preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " use_pip = True From 9b2241181584e6c75b16c9156e8b9f15bc5b41d3 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 15:48:52 +0200 Subject: [PATCH 1053/2365] returning patch back to how it was --- easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb index b027af4877..6e7e7a5935 100644 --- a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb @@ -38,6 +38,7 @@ dependencies = [ download_dep_fail = True preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +# strip out cmake requirements, since we provide that as proper dependency preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " use_pip = True From c920fcef9e9ccc5d858603e8d4e9090b594d9d49 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 16:21:40 +0200 Subject: [PATCH 1054/2365] tweaks --- .../GenomeWorks-2021.02.2-fosscuda-2020b.eb | 32 +++++++++---------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 65b231aca7..5cb1aaa540 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -92,8 +92,14 @@ preconfigopts += "mv %%(builddir)s/spoa-*/* %s/spoa/ && " % local_vendor_dir preconfigopts += "sed -i'' 's/#include /#include \\n#include /g'" preconfigopts += " %(builddir)s/GenomeWorks-*/3rdparty/spoa/src/alignment_engine.cpp && """ -configopts = "-Dgw_cuda_gen_all_arch=OFF" +preconfigopts += "sed -i 's/==/>=/g' %(builddir)s/GenomeWorks-%(version)s/pygenomeworks/requirements.txt && " +preconfigopts += "sed -i 's/~=/>=/g' %(builddir)s/GenomeWorks-%(version)s/pygenomeworks/requirements.txt && " +# instruction from GenomeWorks' readme +configopts = "-Dgw_cuda_gen_all_arch=OFF " +configopts += " --enable-shared " + +# no test targets skipsteps = ['test'] exts_defaultclass = 'PythonPackage' @@ -104,16 +110,18 @@ exts_default_options = { 'use_pip': True, } +local_genomeworks_preinstallopts = "export GW_INSTALL_DIR=%(installdir)s && " +local_genomeworks_preinstallopts += "export GW_VERSION=%(version)s && " +local_genomeworks_preinstallopts += "export GW_ROOT_DIR=%(builddir)s/GenomeWorks-%(version)s && " + exts_list = [ + ('sortedcollections', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcollections/'], + 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], + }), ('genomeworks', version, { 'patches': ['GenomeWorks-2021-02-2_dep_versions_n_file_extension.patch'], - 'postinstallcmds': [""" - sed -i'' 's/==/>=/g' %(builddir)s/GenomeWorks-%(version)s/pygenomeworks/requirements.txt - """], - 'preinstallopts': """export GW_INSTALL_DIR=%(installdir)s && - export GW_VERSION=%(version)s && - export GW_ROOT_DIR=%(builddir)s/GenomeWorks-%(version)s && - """, + 'preinstallopts': "export GW_INSTALL_DIR=%(installdir)s && export GW_VERSION=%(version)s && export GW_ROOT_DIR=%(builddir)s/GenomeWorks-%(version)s && ", 'sources': ['v%(version)s.tar.gz'], 'start_dir': 'pygenomeworks', 'checksums': [ @@ -122,14 +130,6 @@ exts_list = [ '3e33e4ecc03aa43699748a623a331ed9be45a9e8a9c519c0fca6deff17144baf', ], }), - ('sortedcollections', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcollections/'], - 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], - }), - ('pytest', '6.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], - 'checksums': ['50bcad0a0b9c5a72c8e4e7c9855a3ad496ca6a881a3641b4260605450772c54b'], - }), ] moduleclass = 'bio' From 26f0ba237442b9b8e3bf18aff7a6ff284b2a2b39 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 17:03:20 +0200 Subject: [PATCH 1055/2365] tweaks --- .../g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 5cb1aaa540..621024a487 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -97,7 +97,7 @@ preconfigopts += "sed -i 's/~=/>=/g' %(builddir)s/GenomeWorks-%(version)s/pygeno # instruction from GenomeWorks' readme configopts = "-Dgw_cuda_gen_all_arch=OFF " -configopts += " --enable-shared " +configopts += " -DBUILD_SHARED_LIBS=true " # no test targets skipsteps = ['test'] @@ -127,7 +127,7 @@ exts_list = [ 'checksums': [ 'f036f066b3ae22e603786f79d374cde28942c22064a169f123fb085fd6b4ccaf', # v2021.02.2.tar.gz # GenomeWorks-2021-02-2_dep_versions_n_file_extension.patch - '3e33e4ecc03aa43699748a623a331ed9be45a9e8a9c519c0fca6deff17144baf', + '2ce8691bcf09f2c1863078094e0322d54e5974d244ba1ae9d791a61a8d46fafc', ], }), ] From 6a8f11ef12d94350a4c1f5e4a4a94d590942a08f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Jun 2021 18:01:53 +0200 Subject: [PATCH 1056/2365] tweaks --- .../g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 621024a487..3c9410af05 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -127,7 +127,7 @@ exts_list = [ 'checksums': [ 'f036f066b3ae22e603786f79d374cde28942c22064a169f123fb085fd6b4ccaf', # v2021.02.2.tar.gz # GenomeWorks-2021-02-2_dep_versions_n_file_extension.patch - '2ce8691bcf09f2c1863078094e0322d54e5974d244ba1ae9d791a61a8d46fafc', + 'a39c4e594eee0cf99c9b36195c09d44fc8ea022423e729a431d74f6c47c3e84d', ], }), ] From 8753a73f1b7544da62da19d30f812b31c7392793 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Jun 2021 18:43:20 +0200 Subject: [PATCH 1057/2365] clean up GenomeWorks easyconfig by using git_config to download sources, install shared libraries, remove patch, enhance sanity check --- .../GenomeWorks-2021.02.2-fosscuda-2020b.eb | 124 ++++++------------ 1 file changed, 41 insertions(+), 83 deletions(-) diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 3c9410af05..d90652ad6f 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakePythonPackage' name = 'GenomeWorks' version = '2021.02.2' -local_git_commit = '691380d1122a9ad86f91b3038c8b6625d137b6ed' +local_commit = '691380d' # corresponds to 2021.02.2 tag homepage = 'https://github.com/clara-parabricks/GenomeWorks' description = "SDK for GPU accelerated genome assembly and analysis" @@ -11,59 +11,20 @@ description = "SDK for GPU accelerated genome assembly and analysis" toolchain = {'name': 'fosscuda', 'version': '2020b'} toolchainopts = {'pic': True} -sources = [ - { - 'source_urls': ['https://github.com/clara-parabricks/GenomeWorks/archive/'], - 'filename': 'v%(version)s.tar.gz', +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/clara-parabricks', + 'repo_name': name, + 'commit': local_commit, + 'recursive': True, }, - { - 'source_urls': ['https://github.com/google/benchmark/archive'], - 'filename': 'benchmark-20190513.tar.gz', - 'download_filename': '090faecb454fbd6e6e17a75ef8146acb037118d4.tar.gz', - }, - { - 'source_urls': ['https://github.com/NVIDIA/cub/archive'], - 'filename': 'cub-20201123.tar.gz', - 'download_filename': '618a46c27764f0e0b86fb3643a572ed039180ad8.tar.gz', - }, - { - 'source_urls': ['https://github.com/google/googletest/archive'], - 'filename': 'googletest-20190424.tar.gz', - 'download_filename': '84d986531e8df9fb6ea4a7bae8fb130c05b3782c.tar.gz', - }, - { - 'source_urls': ['https://github.com/samtools/htslib/archive'], - 'filename': 'htslib-20200806.tar.gz', - 'download_filename': 'a79009b38ce83e39bcbc8f54c00cf203621aa5bb.tar.gz', - }, - { - 'source_urls': ['https://github.com/cartoonist/kseqpp/archive'], - 'filename': 'kseqpp-20181009.tar.gz', - 'download_filename': 'c7add979ac77ec8ada07b25aab7dcf0c5e87f90e.tar.gz', - }, - { - 'source_urls': ['https://github.com/NVIDIA/libcudacxx/archive'], - 'filename': 'libcudacxx-20201003.tar.gz', - 'download_filename': 'd0bafdb9fdde2ee99932d42f1deec74d53e19514.tar.gz', - }, - { - 'source_urls': ['https://github.com/rvaser/spoa/archive'], - 'filename': 'spoa-20190416.tar.gz', - 'download_filename': '0b9e56da3241d6a887d64adcfd1ebfae29810c04.tar.gz', - }, -] -checksums = [ - 'f036f066b3ae22e603786f79d374cde28942c22064a169f123fb085fd6b4ccaf', # v2021.02.2.tar.gz - 'f68aec93154d010324c05bcd8c5cc53468b87af88d87acb5ddcfaa1bba044837', # benchmark-20190513.tar.gz - '7831843b8ab5f9d9dfbcea3b9ad2632a229c6d1aa9a5a335b8d8b813707dd9ec', # cub-20201123.tar.gz - '6fcf88c123bdee5cbef5f1d3b2b34fa6f20cb3168bf05a2adbe20428cae3fe0e', # googletest-20190424.tar.gz - '28455110611f6330b5d6b49ff5c3c1c824a7727944c66c8c6f0e9ce1209740ea', # htslib-20200806.tar.gz - 'ae64499023d4705f42e79a966f175c31a46a794a1dd6fe9c03dd1827efe4a953', # kseqpp-20181009.tar.gz - '0427eaf2c5deabdeeb7f1a894fd362823e32450d6c2c79fe20e64a8898968ef9', # libcudacxx-20201003.tar.gz - '9608c0d31dc158aaab8916b8977962f88e42d2341f979d517daac03db525ea70', # spoa-20190416.tar.gz -] +}] +# no checksum for source tarball because it's created locally via 'git clone' +checksums = [None] builddependencies = [('CMake', '3.18.4')] + dependencies = [ ('Python', '3.8.6'), ('Autoconf', '2.69'), @@ -72,32 +33,17 @@ dependencies = [ ('networkx', '2.5'), ('tqdm', '4.56.2'), ] -local_vendor_dir = '%(builddir)s/GenomeWorks-*/3rdparty/' -# benchmark -preconfigopts = "mv %%(builddir)s/benchmark-*/* %s/benchmark/ && " % local_vendor_dir -# cub -preconfigopts += "mv %%(builddir)s/cub-*/* %s/cub/ && " % local_vendor_dir -# googletest -preconfigopts += "mv %%(builddir)s/googletest-*/* %s/googletest/ && " % local_vendor_dir -# htslib -preconfigopts += "mv %%(builddir)s/htslib-*/* %s/htslib/ && " % local_vendor_dir -# kseqpp -preconfigopts += "mv %%(builddir)s/kseqpp-*/* %s/kseqpp/ && " % local_vendor_dir -# libcudacxx -preconfigopts += "mv %%(builddir)s/libcudacxx-*/* %s/libcudacxx/ && " % local_vendor_dir -# spoa -preconfigopts += "mv %%(builddir)s/spoa-*/* %s/spoa/ && " % local_vendor_dir # add missing include to a file -preconfigopts += "sed -i'' 's/#include /#include \\n#include /g'" -preconfigopts += " %(builddir)s/GenomeWorks-*/3rdparty/spoa/src/alignment_engine.cpp && """ +preconfigopts = "sed -i'' 's/#include /#include \\n#include /g'" +preconfigopts += " %(builddir)s/GenomeWorks/3rdparty/spoa/src/alignment_engine.cpp && """ -preconfigopts += "sed -i 's/==/>=/g' %(builddir)s/GenomeWorks-%(version)s/pygenomeworks/requirements.txt && " -preconfigopts += "sed -i 's/~=/>=/g' %(builddir)s/GenomeWorks-%(version)s/pygenomeworks/requirements.txt && " +preconfigopts += "sed -i 's/==/>=/g' %(builddir)s/GenomeWorks/pygenomeworks/requirements.txt && " +preconfigopts += "sed -i 's/~=/>=/g' %(builddir)s/GenomeWorks/pygenomeworks/requirements.txt && " # instruction from GenomeWorks' readme configopts = "-Dgw_cuda_gen_all_arch=OFF " -configopts += " -DBUILD_SHARED_LIBS=true " +configopts += " -Dgw_build_shared=ON " # no test targets skipsteps = ['test'] @@ -105,31 +51,43 @@ skipsteps = ['test'] exts_defaultclass = 'PythonPackage' exts_default_options = { - 'source_urls': ['https://github.com/clara-parabricks/GenomeWorks/archive/'], 'download_dep_fail': True, 'use_pip': True, + 'sanity_pip_check': True, } -local_genomeworks_preinstallopts = "export GW_INSTALL_DIR=%(installdir)s && " +local_genomeworks_preinstallopts = "sed -i 's/[=~]=/>=/g' requirements.txt && " +local_genomeworks_preinstallopts += "export GW_INSTALL_DIR=%(installdir)s && " local_genomeworks_preinstallopts += "export GW_VERSION=%(version)s && " -local_genomeworks_preinstallopts += "export GW_ROOT_DIR=%(builddir)s/GenomeWorks-%(version)s && " +local_genomeworks_preinstallopts += "export GW_ROOT_DIR=%(builddir)s/GenomeWorks && " exts_list = [ ('sortedcollections', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcollections/'], 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], }), ('genomeworks', version, { - 'patches': ['GenomeWorks-2021-02-2_dep_versions_n_file_extension.patch'], - 'preinstallopts': "export GW_INSTALL_DIR=%(installdir)s && export GW_VERSION=%(version)s && export GW_ROOT_DIR=%(builddir)s/GenomeWorks-%(version)s && ", - 'sources': ['v%(version)s.tar.gz'], + 'sources': ['GenomeWorks-%(version)s.tar.gz'], + # no checksum for source tarball because it's created locally via 'git clone' + 'checksums': [None], 'start_dir': 'pygenomeworks', - 'checksums': [ - 'f036f066b3ae22e603786f79d374cde28942c22064a169f123fb085fd6b4ccaf', # v2021.02.2.tar.gz - # GenomeWorks-2021-02-2_dep_versions_n_file_extension.patch - 'a39c4e594eee0cf99c9b36195c09d44fc8ea022423e729a431d74f6c47c3e84d', - ], + 'preinstallopts': local_genomeworks_preinstallopts, }), ] +sanity_check_paths = { + 'files': ['bin/cudamapper', 'bin/cudapoa', 'bin/genome_simulator', + 'lib/libgwbase.%s' % SHLIB_EXT, 'lib/libgwio.%s' % SHLIB_EXT], + 'dirs': ['benchmarks', 'docs', 'include/claraparabricks/genomeworks', + 'lib/python%(pyshortver)s/site-packages', 'samples', 'tests'], +} + +sanity_check_commands = [ + "cudamapper --help", + "cudapoa --help", + "genome_simulator --help", + "python -c 'import genomeworks'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'bio' From ca009962a2486c681c806b61cb774b370738a72a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Jun 2021 19:16:53 +0200 Subject: [PATCH 1058/2365] add ont-fast5-api as proper dependency for Bonito 0.4.0 + fix sed commands to tweak requirements.txt --- .../b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb | 15 +++---- .../ont-fast5-api-3.3.0-fosscuda-2020b.eb | 43 +++++++++++++++++++ 2 files changed, 48 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb index 795fc117a2..59554e81a1 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb @@ -23,14 +23,16 @@ dependencies = [ ('CuPy', '8.5.0'), ('GenomeWorks', '2021.02.2'), ('pyspoa', '0.0.8'), + ('ont-fast5-api', '3.3.0'), ] use_pip = True +# strip out too strict version requirements for dependencies local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && " -local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2//g' requirements.txt && " -# CuPy is provided as proper dependency, installed from source -local_bonito_preinstallopts += "sed -i 's/cupy-cuda102//g' requirements.txt && " +# fix requirements for stuff we include as a proper dependency +local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2/genomeworks/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/cupy-cuda102/cupy/g' requirements.txt && " local_bonito_preinstallopts += "sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && " local_bonito_preinstallopts += "sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && " local_bonito_preinstallopts += "export PATH=%(installdir)s/bin/:$PATH && " @@ -80,13 +82,6 @@ exts_list = [ ('stevedore', '3.3.0', { 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], }), - ('progressbar33', '2.4', { - 'modulename': 'progressbar', - 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], - }), - ('ont-fast5-api', '3.3.0', { - 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], - }), ('fast-ctc-decode', '0.3.0', { 'source_tmpl': 'fast_ctc_decode-%(version)s-cp38-cp38-manylinux2010_x86_64.whl', 'unpack_sources': False, diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..b4a6b8321b --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '3.3.0' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + (name, version, { + 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 95f993a4007a13dc9cb5eecc998cf6dae63fb9da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Jun 2021 19:54:12 +0200 Subject: [PATCH 1059/2365] add missing source URL for sortedcollections in GenomeWorks easyconfig --- .../g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index d90652ad6f..101b0be39c 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -63,6 +63,7 @@ local_genomeworks_preinstallopts += "export GW_ROOT_DIR=%(builddir)s/GenomeWorks exts_list = [ ('sortedcollections', '2.1.0', { + 'source_urls': [PYPI_SOURCE], 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], }), ('genomeworks', version, { From fff3d8c91f3cf8fca9460c956dc0772fddc9cba2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 10 Jun 2021 01:58:04 +0200 Subject: [PATCH 1060/2365] fix Compress:Zlib version mismatch in Perl-5.32.0-GCCcore-10.2.0.eb --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 76d0b56cf8..515872cd4a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -1761,10 +1761,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], }), - ('IO::Compress::Bzip2', '2.096', { + ('IO::Compress::Bzip2', '2.093', { 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], - 'checksums': ['9d219fd5df4b490b5d2f847921e3cb1c3392758fa0bae9b05a8992b3620ba572'], + 'checksums': ['5f8f5d06913f16c16759cc4e06749692208b8947910ffedd2c00a74ed0d60ba2'], }), ('JSON::XS', '4.03', { 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', From 5382790093973aad46ed064964bf9895573e48cd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 10 Jun 2021 01:59:04 +0200 Subject: [PATCH 1061/2365] remove extension Compress::Raw::Zlib from VEP-103.1-GCC-10.2.0.eb --- easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb index 25ee10d70c..b53ccb6277 100644 --- a/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/VEP/VEP-103.1-GCC-10.2.0.eb @@ -31,12 +31,6 @@ exts_list = [ 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], }), - ('Compress::Raw::Zlib', '2.101', { - # Perl v5.32.0 already provides this extension, but VEP needs a more recent version - 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], - 'checksums': ['9d1b9515e8277c1b007e33fad1fd0f18717d56bf647e3794d61289c45b1aabb2'], - }), ] moduleclass = 'bio' From d44cd93a1d7d0e0da125a9f81656fdd7f351e41c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Jun 2021 09:03:51 +0200 Subject: [PATCH 1062/2365] use patch for OpenMM 7.5.0 to ensure that correct nvcc command is used + minor style fixes --- .../o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb index 420b7a7e03..1032553184 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb @@ -16,8 +16,10 @@ toolchainopts = {'opt': True} source_urls = ['https://github.com/openmm/openmm/archive/'] sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_path_to_nvcc.patch'] checksums = [ '516748b4f1ae936c4d70cc6401174fc9384244c65cd3aef27bc2c53eac6d6de5', # 7.5.0.tar.gz + '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch ] builddependencies = [ @@ -34,10 +36,11 @@ dependencies = [ ] # Flags for CUDA-enabled build -configopts = "-DOPENMM_BUILD_CUDA_LIB=ON -DCUDA_CUDA_LIBRARY=$EBROOTCUDACORE/lib64/stubs/libcuda.so" +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON -DCUDA_CUDA_LIBRARY=$EBROOTCUDACORE/lib64/stubs/libcuda.%s" % SHLIB_EXT pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" -runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)\'" """ +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' @@ -57,8 +60,5 @@ modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', } -modextravars = { - 'OPENMM_CUDA_COMPILER': 'nvcc', -} moduleclass = 'bio' From 1a0dd8a95b229f0b641d297ad180f74b7e9b785b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 May 2021 13:11:07 +0200 Subject: [PATCH 1063/2365] adding easyconfigs: PyTorch-1.8.1-fosscuda-2020b.eb --- .../p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..4a7d0a5701 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -0,0 +1,87 @@ +name = 'PyTorch' +version = '1.8.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', + 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', + 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + # PyTorch-1.7.0_increase-distributed-test-timeout.patch + '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch + # PyTorch-1.8.0_correct-skip-tests-decorators.patch + '4b2fe7616217dd6fd12d667cb1439dde58f84bf234fbf3e6026c4665fc697a2e', + '018d0abbba60c23d01d96273d8ba4f79f2710ff59018729bdb3081b8965b99ec', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + + +excluded_tests = { + '': [ + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! + # https://github.com/pytorch/pytorch/issues/43209 + 'test_quantization', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From 3389c8f274f287da1aaa237cdd67d054d57ab94c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 May 2021 14:02:58 +0200 Subject: [PATCH 1064/2365] Add patch file and add to foss version --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index f8827697e0..28c99595ab 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -23,6 +23,7 @@ patches = [ 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', + 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -35,6 +36,7 @@ checksums = [ 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch # PyTorch-1.8.0_correct-skip-tests-decorators.patch '4b2fe7616217dd6fd12d667cb1439dde58f84bf234fbf3e6026c4665fc697a2e', + '018d0abbba60c23d01d96273d8ba4f79f2710ff59018729bdb3081b8965b99ec', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] From 9646f89846dd045f547d6a30ec43cbf65802f040 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 6 May 2021 18:17:22 +0200 Subject: [PATCH 1065/2365] Patch some bugs --- .../p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 4 ++++ .../p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 24 +++++++++++++++---- 2 files changed, 24 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index 28c99595ab..cab88ce695 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -63,6 +63,10 @@ dependencies = [ ] excluded_tests = { + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/57617 + 'test_autograd', + ], '': [ # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index 4a7d0a5701..76730fd240 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -19,10 +19,14 @@ sources = [{ patches = [ 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', - 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', - 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', + 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', + 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_honor_shared_cupti-setting.patch', 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', ] checksums = [ @@ -30,12 +34,19 @@ checksums = [ # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.0_increase-distributed-test-timeout.patch '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', - '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch + '18ecad081a8c940add64040ad9698d3273366acf738a8a44eab1c793d3f49950', # PyTorch-1.8.0_correct-skip-tests-decorators.patch '4b2fe7616217dd6fd12d667cb1439dde58f84bf234fbf3e6026c4665fc697a2e', + 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.8.1_honor_shared_cupti-setting.patch + '86f2b27dc221fef327e4db5037868dc3da41e039fdf78fc77ccd22bf1d62f218', '018d0abbba60c23d01d96273d8ba4f79f2710ff59018729bdb3081b8965b99ec', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch ] @@ -68,8 +79,13 @@ dependencies = [ # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] +custom_opts = ["USE_CUPTI_SO=1"] excluded_tests = { + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/57617 + 'test_autograd', + ], '': [ # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', From 5645c8f188caf9913dab00ad9e273652423362b6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 6 May 2021 18:31:40 +0200 Subject: [PATCH 1066/2365] Add patch --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index 76730fd240..f6e03193cc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -46,7 +46,7 @@ checksums = [ 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.8.1_honor_shared_cupti-setting.patch - '86f2b27dc221fef327e4db5037868dc3da41e039fdf78fc77ccd22bf1d62f218', + 'a6459fe544f9e2b61ab09ba54e8db5b294176ffdbf41c99e0d0b678e1e617b8f', '018d0abbba60c23d01d96273d8ba4f79f2710ff59018729bdb3081b8965b99ec', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch ] From 650d7146f5c6cabcdd1ecdfe0eaaf7c3369e161f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 10 May 2021 12:11:45 +0200 Subject: [PATCH 1067/2365] Update skip-MKL-test patch to work for CUDA --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index cab88ce695..ff44cacf2b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -35,7 +35,7 @@ checksums = [ '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch # PyTorch-1.8.0_correct-skip-tests-decorators.patch - '4b2fe7616217dd6fd12d667cb1439dde58f84bf234fbf3e6026c4665fc697a2e', + 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', '018d0abbba60c23d01d96273d8ba4f79f2710ff59018729bdb3081b8965b99ec', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index f6e03193cc..137e3d7ae8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -42,7 +42,7 @@ checksums = [ # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch '18ecad081a8c940add64040ad9698d3273366acf738a8a44eab1c793d3f49950', # PyTorch-1.8.0_correct-skip-tests-decorators.patch - '4b2fe7616217dd6fd12d667cb1439dde58f84bf234fbf3e6026c4665fc697a2e', + 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.8.1_honor_shared_cupti-setting.patch From 9d029ae430d8371d26229d9721bfa82c5c4ec310 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 11 May 2021 16:49:01 +0200 Subject: [PATCH 1068/2365] Add alias patch --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 5 +++++ .../easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 4 ++++ 2 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index ff44cacf2b..ca0647dae3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -21,6 +21,7 @@ patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', @@ -33,6 +34,8 @@ checksums = [ # PyTorch-1.7.0_increase-distributed-test-timeout.patch '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch # PyTorch-1.8.0_correct-skip-tests-decorators.patch 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', @@ -73,6 +76,8 @@ excluded_tests = { # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! # https://github.com/pytorch/pytorch/issues/43209 'test_quantization', + # Flaky test: test_bottleneck_cpu_only + 'test_utils', ] } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index 137e3d7ae8..6ea4596210 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -23,11 +23,13 @@ patches = [ 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_honor_shared_cupti-setting.patch', 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', + 'PyTorch-1.8.1_skip-nccl-error-tests.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -41,6 +43,8 @@ checksums = [ 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch '18ecad081a8c940add64040ad9698d3273366acf738a8a44eab1c793d3f49950', + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', # PyTorch-1.8.0_correct-skip-tests-decorators.patch 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch From 80108d35a694501296f2c81e40fd0973a8821b39 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 18 May 2021 10:40:41 +0200 Subject: [PATCH 1069/2365] Add new patch for PPC and checksums --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 4 ++++ 2 files changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index ca0647dae3..60ce9e2c5f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', + 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', ] checksums = [ @@ -39,6 +40,8 @@ checksums = [ 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch # PyTorch-1.8.0_correct-skip-tests-decorators.patch 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', + # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch + 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', '018d0abbba60c23d01d96273d8ba4f79f2710ff59018729bdb3081b8965b99ec', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index 6ea4596210..6d41901599 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -28,6 +28,7 @@ patches = [ 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_honor_shared_cupti-setting.patch', + 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', 'PyTorch-1.8.1_skip-nccl-error-tests.patch', ] @@ -51,7 +52,10 @@ checksums = [ '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.8.1_honor_shared_cupti-setting.patch 'a6459fe544f9e2b61ab09ba54e8db5b294176ffdbf41c99e0d0b678e1e617b8f', + # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch + 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', '018d0abbba60c23d01d96273d8ba4f79f2710ff59018729bdb3081b8965b99ec', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch + 'a1167a68a4f983af99da386e0cf9c6f2cb9bf94566bad5a9824112c275753f51', # PyTorch-1.8.1_skip-nccl-error-tests.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] From 381090cd6734fafe3a72472c593715f8202a3cdd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 18 May 2021 16:09:55 +0200 Subject: [PATCH 1070/2365] Add patch for adding missing skip on PPC --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index 60ce9e2c5f..3c335e19b0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', ] @@ -40,6 +41,8 @@ checksums = [ 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch # PyTorch-1.8.0_correct-skip-tests-decorators.patch 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', '018d0abbba60c23d01d96273d8ba4f79f2710ff59018729bdb3081b8965b99ec', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index 6d41901599..b773e54917 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -27,6 +27,7 @@ patches = [ 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', 'PyTorch-1.8.1_honor_shared_cupti-setting.patch', 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', @@ -50,6 +51,8 @@ checksums = [ 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', # PyTorch-1.8.1_honor_shared_cupti-setting.patch 'a6459fe544f9e2b61ab09ba54e8db5b294176ffdbf41c99e0d0b678e1e617b8f', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch From ee8f7198218af862aac7fbf5ded43c1952ff9d3a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 19 May 2021 15:23:13 +0200 Subject: [PATCH 1071/2365] Skip more failing NCCL tests --- .../easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 7 ++++++- .../easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 6 ++++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index 3c335e19b0..c45ae4ea0b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -24,6 +24,8 @@ patches = [ 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', + 'PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', @@ -41,11 +43,14 @@ checksums = [ 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch # PyTorch-1.8.0_correct-skip-tests-decorators.patch 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', + # PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch + 'a5bc86837c59a36d59311be9cbd0c6d86ea6be235c2a7ffb400b89c758b28490', + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', - '018d0abbba60c23d01d96273d8ba4f79f2710ff59018729bdb3081b8965b99ec', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch + '079386b25265a8b7c7f5256492b78c1b4065277e4bd2591be57cfc407ecbbb94', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index b773e54917..e68598e2bd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -27,6 +27,7 @@ patches = [ 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', 'PyTorch-1.8.1_honor_shared_cupti-setting.patch', 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', @@ -51,14 +52,15 @@ checksums = [ 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', # PyTorch-1.8.1_honor_shared_cupti-setting.patch 'a6459fe544f9e2b61ab09ba54e8db5b294176ffdbf41c99e0d0b678e1e617b8f', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', - '018d0abbba60c23d01d96273d8ba4f79f2710ff59018729bdb3081b8965b99ec', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch - 'a1167a68a4f983af99da386e0cf9c6f2cb9bf94566bad5a9824112c275753f51', # PyTorch-1.8.1_skip-nccl-error-tests.patch + '079386b25265a8b7c7f5256492b78c1b4065277e4bd2591be57cfc407ecbbb94', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch + '1542fb4c1a3b08dac3ba69e83a038a108e2ad3dd2141e321bbfb610ad9e12336', # PyTorch-1.8.1_skip-nccl-error-tests.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] From 2669d86431392aa991e3f91f83d8edb6f60a1fa9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 21 May 2021 09:07:35 +0200 Subject: [PATCH 1072/2365] Add cuda ipc patch and fix checksum --- .../easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index e68598e2bd..b81a1db6f8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', @@ -48,6 +49,8 @@ checksums = [ '18ecad081a8c940add64040ad9698d3273366acf738a8a44eab1c793d3f49950', # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch + '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', # PyTorch-1.8.0_correct-skip-tests-decorators.patch 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch From 19d04313b9797e8abc778f76c44dd368a433a778 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 3 Jun 2021 19:22:58 +0200 Subject: [PATCH 1073/2365] Fix VSX functions on PPC --- .../p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 14 ++++++-------- .../p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 12 ++++++------ 2 files changed, 12 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index c45ae4ea0b..86354148bc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -19,7 +19,6 @@ sources = [{ patches = [ 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', - 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', @@ -27,16 +26,15 @@ patches = [ 'PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch', 'PyTorch-1.8.1_fix-arange-on-VSX.patch', 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_fix-vsx-vector-functions.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', - 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch - # PyTorch-1.7.0_increase-distributed-test-timeout.patch - '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', @@ -48,9 +46,11 @@ checksums = [ 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + 'a8fcb63cf963dc743e8b0a96b966f18d8edde6a4e76365d6de56aa2c71ce6d3f', # PyTorch-1.8.1_fix-vsx-vector-functions.patch + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + '44eb81c2458524824ce726774c4753b772f0ac1c8b425548aab597961ea5a0c3', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', - '079386b25265a8b7c7f5256492b78c1b4065277e4bd2591be57cfc407ecbbb94', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -87,12 +87,10 @@ excluded_tests = { # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! # https://github.com/pytorch/pytorch/issues/43209 'test_quantization', - # Flaky test: test_bottleneck_cpu_only - 'test_utils', ] } -runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' sanity_check_commands = ["python -c 'import caffe2.python'"] tests = ['PyTorch-check-cpp-extension.py'] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index b81a1db6f8..fd237f9215 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -20,7 +20,6 @@ patches = [ 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', - 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', @@ -30,9 +29,10 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_fix-arange-on-VSX.patch', 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_fix-vsx-vector-functions.patch', 'PyTorch-1.8.1_honor_shared_cupti-setting.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', - 'PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch', 'PyTorch-1.8.1_skip-nccl-error-tests.patch', ] checksums = [ @@ -41,8 +41,6 @@ checksums = [ 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - # PyTorch-1.7.0_increase-distributed-test-timeout.patch - '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch @@ -58,11 +56,13 @@ checksums = [ 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + 'a8fcb63cf963dc743e8b0a96b966f18d8edde6a4e76365d6de56aa2c71ce6d3f', # PyTorch-1.8.1_fix-vsx-vector-functions.patch # PyTorch-1.8.1_honor_shared_cupti-setting.patch 'a6459fe544f9e2b61ab09ba54e8db5b294176ffdbf41c99e0d0b678e1e617b8f', + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + '44eb81c2458524824ce726774c4753b772f0ac1c8b425548aab597961ea5a0c3', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', - '079386b25265a8b7c7f5256492b78c1b4065277e4bd2591be57cfc407ecbbb94', # PyTorch-1.8.1_skip-NaN-tests-on-PPC.patch '1542fb4c1a3b08dac3ba69e83a038a108e2ad3dd2141e321bbfb610ad9e12336', # PyTorch-1.8.1_skip-nccl-error-tests.patch ] @@ -111,7 +111,7 @@ excluded_tests = { ] } -runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' sanity_check_commands = ["python -c 'import caffe2.python'"] tests = ['PyTorch-check-cpp-extension.py'] From a6571809efa4e057b4d8feb1b96eb8a6a389f765 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Jun 2021 18:53:29 +0200 Subject: [PATCH 1074/2365] Fix or skip failing tests --- .../p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 2 +- .../p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 14 +++++++++++--- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index 86354148bc..1d96d37ea3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -48,7 +48,7 @@ checksums = [ '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', 'a8fcb63cf963dc743e8b0a96b966f18d8edde6a4e76365d6de56aa2c71ce6d3f', # PyTorch-1.8.1_fix-vsx-vector-functions.patch # PyTorch-1.8.1_increase-distributed-test-timeout.patch - '44eb81c2458524824ce726774c4753b772f0ac1c8b425548aab597961ea5a0c3', + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index fd237f9215..b7c08cd300 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -29,10 +29,13 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_fix-arange-on-VSX.patch', 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_fix-testnn-on-A100.patch', 'PyTorch-1.8.1_fix-vsx-vector-functions.patch', 'PyTorch-1.8.1_honor_shared_cupti-setting.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch', 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', + 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', 'PyTorch-1.8.1_skip-nccl-error-tests.patch', ] checksums = [ @@ -56,14 +59,19 @@ checksums = [ 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + '241561a0497dd27adffd71b8b0815be1fe924800f4ee336d95e0cc3881fac98b', # PyTorch-1.8.1_fix-testnn-on-A100.patch 'a8fcb63cf963dc743e8b0a96b966f18d8edde6a4e76365d6de56aa2c71ce6d3f', # PyTorch-1.8.1_fix-vsx-vector-functions.patch # PyTorch-1.8.1_honor_shared_cupti-setting.patch 'a6459fe544f9e2b61ab09ba54e8db5b294176ffdbf41c99e0d0b678e1e617b8f', # PyTorch-1.8.1_increase-distributed-test-timeout.patch - '44eb81c2458524824ce726774c4753b772f0ac1c8b425548aab597961ea5a0c3', + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + # PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch + 'c3488fa24405eac6e2e36fbdf94e877bd39fd177e92fb3a0b6bbd5c8b7ddc7bc', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', - '1542fb4c1a3b08dac3ba69e83a038a108e2ad3dd2141e321bbfb610ad9e12336', # PyTorch-1.8.1_skip-nccl-error-tests.patch + # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch + '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', + '33704164ad2da7426a6c21482389826345b92690d37cbf938896eef421a62575', # PyTorch-1.8.1_skip-nccl-error-tests.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -89,7 +97,7 @@ dependencies = [ ('Pillow', '8.0.1'), ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), ('magma', '2.5.4'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) From 662c46ffe9a8269827daa8095e212bf75e3b95a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Jun 2021 11:52:15 +0200 Subject: [PATCH 1075/2365] don't link to CUDA stub library in OpenMM easyconfig --- easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb index 1032553184..37bbd7f044 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb @@ -36,7 +36,7 @@ dependencies = [ ] # Flags for CUDA-enabled build -configopts = "-DOPENMM_BUILD_CUDA_LIB=ON -DCUDA_CUDA_LIBRARY=$EBROOTCUDACORE/lib64/stubs/libcuda.%s" % SHLIB_EXT +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" From b281dce12035f72d7ec7e9da726b1e56ae5b5ad5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 10 Jun 2021 11:31:09 +0100 Subject: [PATCH 1076/2365] adding easyconfigs: RepeatMasker-4.1.2-p1-foss-2020b.eb, RMBlast-2.11.0-gompi-2020b.eb --- .../r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb | 63 +++++++++++++++++++ .../RepeatMasker-4.1.2-p1-foss-2020b.eb | 53 ++++++++++++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb new file mode 100644 index 0000000000..3521576a22 --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb @@ -0,0 +1,63 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.11.0' + +homepage = 'http://www.repeatmasker.org/RMBlast.html' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary + difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' + for use with RepeatMasker and RepeatModeler.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +# RMBlast is distributed as a patch that applies on top of BLAST+ +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [('http://www.repeatmasker.org/isb-%(version)s+-%(namelower)s.patch.gz', 2)] +checksums = [ + 'd88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954', # ncbi-blast-2.11.0+-src.tar.gz + '0fc27781c2ea2f17645247e2f3775b5d18c56f0b62761a865347be745ea4f6be', # isb-2.11.0+-rmblast.patch.gz +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE', '8.44'), + ('Boost', '1.74.0'), + ('GMP', '6.2.0'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), +] + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +prebuildopts = "sed -i 's/LIBS =/LIBS = $(BLAST_THIRD_PARTY_LIBS)/' src/app/rmblastn/Makefile.rmblastn.app && " + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb new file mode 100644 index 0000000000..db71491833 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.2-p1' + +homepage = 'http://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['http://www.repeatmasker.org/%(name)s'] +sources = [ + SOURCE_TAR_GZ, + # optional but recommended: RepBase RepeatMasker Edition + # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php + # { + # 'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz', + # 'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1", + # }, +] +checksums = [ + '4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96', # RepeatMasker-4.1.2-p1.tar.gz + # 'd7fa3bcd55703da14aa456fdc25c0487f171ad34ddfef886f847552993b32d34', # RepBaseRepeatMaskerEdition-20181026.tar.gz +] + +dependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0'), + ('TRF', '4.09.1'), + ('h5py', '3.1.0'), + # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match + ('HMMER', '3.3.2'), + ('RMBlast', '2.11.0'), +] + +local_default_search_engine = 'RMBlast' + +preinstall_cmd = './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +preinstall_cmd += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +preinstall_cmd += '-default_search_engine %s' % local_default_search_engine.lower() +# preinstall_cmd += '-libdir="RepeatMasker/Libraries" + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From f735b77ab906d0dfe85206659c2085609710b94c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 10 Jun 2021 12:04:47 +0100 Subject: [PATCH 1077/2365] Use https in homepage, source_urls --- easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb | 4 ++-- .../r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb index 3521576a22..857bf922ee 100644 --- a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'RMBlast' version = '2.11.0' -homepage = 'http://www.repeatmasker.org/RMBlast.html' +homepage = 'https://www.repeatmasker.org/RMBlast.html' description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler.""" @@ -26,7 +26,7 @@ toolchainopts = {'usempi': True} # RMBlast is distributed as a patch that applies on top of BLAST+ source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] sources = ['ncbi-blast-%(version)s+-src.tar.gz'] -patches = [('http://www.repeatmasker.org/isb-%(version)s+-%(namelower)s.patch.gz', 2)] +patches = [('https://www.repeatmasker.org/isb-%(version)s+-%(namelower)s.patch.gz', 2)] checksums = [ 'd88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954', # ncbi-blast-2.11.0+-src.tar.gz '0fc27781c2ea2f17645247e2f3775b5d18c56f0b62761a865347be745ea4f6be', # isb-2.11.0+-rmblast.patch.gz diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb index db71491833..726cafbe03 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb @@ -3,13 +3,13 @@ easyblock = 'Tarball' name = 'RepeatMasker' version = '4.1.2-p1' -homepage = 'http://www.repeatmasker.org/' +homepage = 'https://www.repeatmasker.org/' description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.""" toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = ['http://www.repeatmasker.org/%(name)s'] +source_urls = ['https://www.repeatmasker.org/%(name)s'] sources = [ SOURCE_TAR_GZ, # optional but recommended: RepBase RepeatMasker Edition From 8790f9f05e43041b6a92807024f8ef08b2b95026 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 10 Jun 2021 13:25:18 +0200 Subject: [PATCH 1078/2365] Use new easyblock for torchvision ECs --- .../torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb | 8 -------- 1 file changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb index bbec243ce6..8d0b69baaf 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'torchvision' version = '0.8.2' local_pytorch_version = '1.7.1' @@ -22,13 +20,7 @@ dependencies = [ ('PyTorch', local_pytorch_version), ] -use_pip = True -download_dep_fail = True - # Defaults. Can be changed with --cuda-compute-capabilities cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] -preinstallopts = 'export TORCH_CUDA_ARCH_LIST="%(cuda_cc_semicolon_sep)s" && ' - -sanity_pip_check = True moduleclass = 'vis' From 51db93239d9e8139de7c8afee1dcadd27760bebe Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 10 Jun 2021 15:01:26 +0200 Subject: [PATCH 1079/2365] Use updated NCCL --- easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb | 8 ++++---- .../Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb | 2 +- .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 +- .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 4 ++-- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb index e7d275c6ef..498590b96e 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb @@ -7,15 +7,15 @@ homepage = 'https://cupy.dev' description = "CuPy is an open-source array library accelerated with NVIDIA CUDA." toolchain = {'name': 'fosscuda', 'version': '2020b'} -# setup.py requirement Cython>=0.29.22. Build fails with 0.29.21 +# setup.py requirement Cython>=0.29.22. Build fails with 0.29.21 # after patching setup.py builddependencies = [('Cython', '0.29.22')] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), - ('NCCL', '2.8.3', '-CUDA-11.1.1', True), - ('cuTENSOR', '1.2.2.5', '-CUDA-11.1.1', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('cuTENSOR', '1.2.2.5', '-CUDA-%(cudaver)s', True), ] use_pip = True diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb index fe80381811..7335bc5ac2 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb @@ -17,7 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), ('PyYAML', '5.3.1'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('PyTorch', local_pt_version), ] diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index f0a678a0df..e2f3288212 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('Mako', '1.1.3'), - ('NCCL', '2.8.3', '-CUDA-11.1.1', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] build_type = 'Release' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index c841f62815..12289d484d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('Pillow', '8.0.1'), ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), ('magma', '2.5.4'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 9a4a9e1ad3..c86bf99f9f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -18,8 +18,8 @@ builddependencies = [ ('pkgconfig', '1.5.1', '-python'), # For h5py ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), - ('NCCL', '2.8.3', '-CUDA-11.1.1', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.6'), # Next 2 are for h5py ('SciPy-bundle', '2020.11'), From 6a420f5083ef651352a59b1195e77709ad7fe366 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 10 Jun 2021 14:18:14 +0100 Subject: [PATCH 1080/2365] adding easyconfigs: GenomeTools-1.6.1-GCC-10.2.0.eb and patches: GenomeTools-1.6.1_fix-GCC-10.patch --- .../GenomeTools-1.6.1-GCC-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..cc36082f36 --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'GenomeTools' +version = '1.6.1' + +homepage = 'http://genometools.org' +description = "A comprehensive software library for efficient processing of structured genome annotations." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'genometools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.6.1_fix-GCC-10.patch'] +checksums = ['528ca143a7f1d42af8614d60ea1e5518012913a23526d82e434f0dad2e2d863f'] + +# GenomeTools-1.6.1 has the following libraries bundled with it: +# bzip2-1.0.6, cgilua-5.1.3, expat-2.0.1, lpeg-0.10.2, lua-5.1.5, luafilesystem-1.5.0, md5-1.2, +# samtools-0.1.18, sqlite-3.8.7.1, tre-0.8.0, zlib-1.2.8 +# +# Bundled libraries can be globally disabled with the option useshared=yes +# However, it is preferable to use the bundled libraries due to the very old versions of some of them + +dependencies = [('Pango', '1.47.0')] + +skipsteps = ['configure'] + +buildopts = 'useshared=no errorcheck=no cairo=yes threads=yes' +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/gt', 'bin/genometools-config', 'lib/libgenometools.a', 'lib/libgenometools.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'bio' From b901222942ef390fe84311e491aa60aaae850fdf Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 10 Jun 2021 14:59:49 +0100 Subject: [PATCH 1081/2365] Add missing patch checksum --- .../g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb index cc36082f36..26842544fe 100644 --- a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb @@ -12,7 +12,10 @@ github_account = 'genometools' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-1.6.1_fix-GCC-10.patch'] -checksums = ['528ca143a7f1d42af8614d60ea1e5518012913a23526d82e434f0dad2e2d863f'] +checksums = [ + '528ca143a7f1d42af8614d60ea1e5518012913a23526d82e434f0dad2e2d863f', # v1.6.1.tar.gz + '743c5f8e9b0b98efb30f0ea2c405022c4f1bac00743de60774fc16e2a4706135', # GenomeTools-1.6.1_fix-GCC-10.patch +] # GenomeTools-1.6.1 has the following libraries bundled with it: # bzip2-1.0.6, cgilua-5.1.3, expat-2.0.1, lpeg-0.10.2, lua-5.1.5, luafilesystem-1.5.0, md5-1.2, From fd6c8e7343fa39669a6d166015b1d825f63f2fd4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Jun 2021 08:47:14 +0200 Subject: [PATCH 1082/2365] use https in OpenMM homepage --- easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb | 2 +- easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb index 04383ac6bc..fb7a82f563 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'OpenMM' version = '7.5.0' -homepage = 'http://openmm.org' +homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb index 37bbd7f044..a7be917c4f 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'OpenMM' version = '7.5.0' -homepage = 'http://openmm.org' +homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb index 07e2f42038..0620868684 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'OpenMM' version = '7.5.0' -homepage = 'http://openmm.org' +homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." toolchain = {'name': 'intel', 'version': '2020b'} From 8ebd0de26420473b8d41072b55542548eb6caa1f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 11 Jun 2021 11:06:07 +0200 Subject: [PATCH 1083/2365] Fix astor dependency --- .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index c86bf99f9f..7693cdd06a 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -129,6 +129,9 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['5b7b7bf2debe19a8794adacc43e8ba6459daa4efaf54d3302623994a359b17f0'], }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), From 51019c34f784de0ffb0a11d4fda1ecc787433d04 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 11 Jun 2021 11:14:12 +0200 Subject: [PATCH 1084/2365] Add astor to TensorFlow 2020b dependencies --- .../TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 3 + .../TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 210 +++++++++++++++++ .../TensorFlow-2.5.0-fosscuda-2020b.eb | 223 ++++++++++++++++++ 3 files changed, 436 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index 1e90ae6d02..046646cc3c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -129,6 +129,9 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['5b7b7bf2debe19a8794adacc43e8ba6459daa4efaf54d3302623994a359b17f0'], }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb new file mode 100644 index 0000000000..45abd15fe0 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -0,0 +1,210 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.5.0' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} +if ARCH == 'x86_64': + # required workaround for failing tests on Intel Skylake and Cascade Lake, + # see https://github.com/tensorflow/tensorflow/issues/49944 + toolchainopts['extra_cxxflags'] = '-mno-avx512f' + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('Python', '3.8.6'), + ('h5py', '3.1.0'), + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +exts_default_options = { + 'sanity_pip_check': True, +} +use_pip = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('google-auth', '1.30.0', { + 'modulename': 'google.auth', + 'checksums': ['9ad25fba07f46a628ad4d0ca09f38dcb262830df2ac95b217f9b0129c9e42206'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.4', { + 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], + }), + ('Werkzeug', '2.0.0', { + 'checksums': ['3389bbfe6d40c6dd25e6d3f974155163c8b3de5bbda6a89342d4ab93fae80ba0'], + }), + ('absl-py', '0.12.0', { + 'modulename': 'absl', + 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.34.1', { + 'modulename': 'grpc', + 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], + }), + ('tensorboard_plugin_wit', '1.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard_plugin_profile', '2.4.0', { + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + ('keras_nightly', '2.5.0.dev2021032900', { + 'modulename': 'keras', + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-default-shell-env.patch', + 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + ], + 'checksums': [ + '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..bd50b65e32 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -0,0 +1,223 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.5.0' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} +if ARCH == 'x86_64': + # required workaround for failing tests on Intel Skylake and Cascade Lake, + # see https://github.com/tensorflow/tensorflow/issues/49944 + toolchainopts['extra_cxxflags'] = '-mno-avx512f' + + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('Python', '3.8.6'), + ('h5py', '3.1.0'), + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +exts_default_options = { + 'sanity_pip_check': True, +} +use_pip = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('google-auth', '1.30.0', { + 'modulename': 'google.auth', + 'checksums': ['9ad25fba07f46a628ad4d0ca09f38dcb262830df2ac95b217f9b0129c9e42206'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.4', { + 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], + }), + ('Werkzeug', '2.0.0', { + 'checksums': ['3389bbfe6d40c6dd25e6d3f974155163c8b3de5bbda6a89342d4ab93fae80ba0'], + }), + ('absl-py', '0.12.0', { + 'modulename': 'absl', + 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.34.1', { + 'modulename': 'grpc', + 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], + }), + ('tensorboard_plugin_wit', '1.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard_plugin_profile', '2.4.0', { + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + ('keras_nightly', '2.5.0.dev2021032900', { + 'modulename': 'keras', + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_fix-min-priority-test.patch', + 'TensorFlow-2.5.0_add-default-shell-env.patch', + 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', + ], + 'checksums': [ + '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_fix-min-priority-test.patch + '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch + 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' From a258adc987e7db54e0ea0b46d535df25e0ee06dc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 11 Jun 2021 11:16:31 +0200 Subject: [PATCH 1085/2365] Add astor to dependencies --- .../t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 3 +++ .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 7 +++++-- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 62efc7ee14..45abd15fe0 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -122,6 +122,9 @@ exts_list = [ 'source_tmpl': SOURCE_WHL, 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), ('gast', '0.4.0', { 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], }), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index b9f42c51b5..bd50b65e32 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -23,8 +23,8 @@ builddependencies = [ ('pkgconfig', '1.5.1', '-python'), # For h5py ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), - ('NCCL', '2.8.3', '-CUDA-11.1.1', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.6'), ('h5py', '3.1.0'), ('cURL', '7.72.0'), @@ -125,6 +125,9 @@ exts_list = [ 'source_tmpl': SOURCE_WHL, 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), ('gast', '0.4.0', { 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], }), From ef03a51ff996e433ca898cb7bbd54c921cd39936 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 11 Jun 2021 12:16:04 +0200 Subject: [PATCH 1086/2365] Cleanupt --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 4 +--- .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 45abd15fe0..62e87e01cd 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -45,9 +45,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index bd50b65e32..f6ad95836c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -48,9 +48,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: From c34ad7ab8cc127b5ea462fa2e9846bb964a7ccc1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 11 Jun 2021 12:16:46 +0200 Subject: [PATCH 1087/2365] Remove TF 2.5 --- .../TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 5 +- .../TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 4 +- .../TensorFlow-2.5.0-fosscuda-2020b.eb | 223 ------------------ 3 files changed, 3 insertions(+), 229 deletions(-) delete mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index 046646cc3c..b3b7e48529 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -43,11 +43,10 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True + # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d exts_list = [ diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 45abd15fe0..62e87e01cd 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -45,9 +45,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb deleted file mode 100644 index bd50b65e32..0000000000 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ /dev/null @@ -1,223 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'TensorFlow' -version = '2.5.0' - -homepage = 'https://www.tensorflow.org/' -description = "An open-source software library for Machine Intelligence" - -toolchain = {'name': 'fosscuda', 'version': '2020b'} -toolchainopts = {'pic': True} -if ARCH == 'x86_64': - # required workaround for failing tests on Intel Skylake and Cascade Lake, - # see https://github.com/tensorflow/tensorflow/issues/49944 - toolchainopts['extra_cxxflags'] = '-mno-avx512f' - - -builddependencies = [ - ('Bazel', '3.7.2'), - ('protobuf', '3.14.0'), - # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 - ('git', '2.28.0', '-nodocs'), - ('pybind11', '2.6.0'), - ('pkgconfig', '1.5.1', '-python'), # For h5py -] -dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), - ('Python', '3.8.6'), - ('h5py', '3.1.0'), - ('cURL', '7.72.0'), - ('double-conversion', '3.1.5'), - ('flatbuffers', '1.12.0'), - ('giflib', '5.2.1'), - ('hwloc', '2.2.0'), - ('ICU', '67.1'), - ('JsonCpp', '1.9.4'), - ('libjpeg-turbo', '2.0.5'), - ('LMDB', '0.9.24'), - ('NASM', '2.15.05'), - ('nsync', '1.24.0'), - ('SQLite', '3.33.0'), - ('PCRE', '8.44'), - ('protobuf-python', '3.14.0'), - ('flatbuffers-python', '1.12'), - ('typing-extensions', '3.7.4.3'), - ('libpng', '1.6.37'), - ('snappy', '1.1.8'), - ('zlib', '1.2.11'), -] - -exts_default_options = { - 'sanity_pip_check': True, -} -use_pip = True - -# Dependencies created and updated using findPythonDeps.sh: -# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d -exts_list = [ - ('Markdown', '3.3.4', { - 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], - }), - ('pyasn1-modules', '0.2.8', { - 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], - }), - ('rsa', '4.7.2', { - 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], - }), - ('cachetools', '4.2.2', { - 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], - }), - ('google-auth', '1.30.0', { - 'modulename': 'google.auth', - 'checksums': ['9ad25fba07f46a628ad4d0ca09f38dcb262830df2ac95b217f9b0129c9e42206'], - }), - ('oauthlib', '3.1.0', { - 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], - }), - ('requests-oauthlib', '1.3.0', { - 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], - }), - ('google-auth-oauthlib', '0.4.4', { - 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], - }), - ('Werkzeug', '2.0.0', { - 'checksums': ['3389bbfe6d40c6dd25e6d3f974155163c8b3de5bbda6a89342d4ab93fae80ba0'], - }), - ('absl-py', '0.12.0', { - 'modulename': 'absl', - 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], - }), - ('astunparse', '1.6.3', { - 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], - }), - ('grpcio', '1.34.1', { - 'modulename': 'grpc', - 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], - }), - ('gviz-api', '1.9.0', { - 'source_tmpl': 'gviz_api-%(version)s.tar.gz', - 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], - }), - ('tensorboard_data_server', '0.6.1', { - 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now - 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], - }), - ('tensorboard', version, { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], - }), - ('tensorboard_plugin_wit', '1.8.0', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], - }), - ('tensorboard_plugin_profile', '2.4.0', { - 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], - }), - ('google-pasta', '0.2.0', { - 'modulename': 'pasta', - 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], - }), - ('termcolor', '1.1.0', { - 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], - }), - ('tensorflow_estimator', version, { - 'source_tmpl': SOURCE_WHL, - 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], - }), - ('astor', '0.8.1', { - 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], - }), - ('gast', '0.4.0', { - 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], - }), - ('opt_einsum', '3.3.0', { - 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('Keras_Preprocessing', '1.1.2', { - 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], - }), - ('dill', '0.3.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], - }), - ('tblib', '1.7.0', { - 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], - }), - ('portpicker', '1.3.1', { - 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], - }), - ('keras_nightly', '2.5.0.dev2021032900', { - 'modulename': 'keras', - 'source_tmpl': SOURCE_WHL, - 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], - }), - (name, version, { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], - 'patches': [ - 'TensorFlow-2.1.0_fix-cuda-build.patch', - 'TensorFlow-2.4.0_add-ldl.patch', - 'TensorFlow-2.4.0_dont-use-var-lock.patch', - 'TensorFlow-2.4.1_fix-min-priority-test.patch', - 'TensorFlow-2.5.0_add-default-shell-env.patch', - 'TensorFlow-2.5.0_add-protobuf-deps.patch', - 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', - 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', - 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', - ], - 'checksums': [ - '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz - '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch - # TensorFlow-2.4.0_dont-use-var-lock.patch - 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', - # TensorFlow-2.4.1_fix-min-priority-test.patch - '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', - # TensorFlow-2.5.0_add-default-shell-env.patch - '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', - # TensorFlow-2.5.0_add-protobuf-deps.patch - '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', - # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch - '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', - # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', - # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch - 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', - ], - 'test_script': 'TensorFlow-2.x_mnist-test.py', - 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', - 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' - '-benchmark-test,-v1only'), - 'test_targets': [ - '//tensorflow/core/...', - '-//tensorflow/core:example_java_proto', - '-//tensorflow/core/example:example_protos_closure', - '//tensorflow/cc/...', - '//tensorflow/c/...', - '//tensorflow/python/...', - # Fails on some nodes but C API isn't installed anyway - '-//tensorflow/c/eager:c_api_test_gpu', - '-//tensorflow/c/eager:c_api_distributed_test', - '-//tensorflow/c/eager:c_api_distributed_test_gpu', - # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 - '-//tensorflow/c/eager:c_api_cluster_test_gpu', - '-//tensorflow/c/eager:c_api_remote_function_test_gpu', - '-//tensorflow/c/eager:c_api_remote_test_gpu', - # Fails to open its own test.xml(?) - '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', - # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 - '-//tensorflow/core/common_runtime:mkl_layout_pass_test', - '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', - ], - 'testopts': "--test_timeout=3600 --test_size_filters=small", - 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + - "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", - 'with_xla': True, - }), -] - -moduleclass = 'lib' From 139cd61170a36137db6b7b25b9eda953f66d3fe9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 11 Jun 2021 12:18:04 +0200 Subject: [PATCH 1088/2365] Remove TF 2.5 --- .../TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 208 ------------------ 1 file changed, 208 deletions(-) delete mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb deleted file mode 100644 index 62e87e01cd..0000000000 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ /dev/null @@ -1,208 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'TensorFlow' -version = '2.5.0' - -homepage = 'https://www.tensorflow.org/' -description = "An open-source software library for Machine Intelligence" - -toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'pic': True} -if ARCH == 'x86_64': - # required workaround for failing tests on Intel Skylake and Cascade Lake, - # see https://github.com/tensorflow/tensorflow/issues/49944 - toolchainopts['extra_cxxflags'] = '-mno-avx512f' - -builddependencies = [ - ('Bazel', '3.7.2'), - ('protobuf', '3.14.0'), - # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 - ('git', '2.28.0', '-nodocs'), - ('pybind11', '2.6.0'), - ('pkgconfig', '1.5.1', '-python'), # For h5py -] -dependencies = [ - ('Python', '3.8.6'), - ('h5py', '3.1.0'), - ('cURL', '7.72.0'), - ('double-conversion', '3.1.5'), - ('flatbuffers', '1.12.0'), - ('giflib', '5.2.1'), - ('hwloc', '2.2.0'), - ('ICU', '67.1'), - ('JsonCpp', '1.9.4'), - ('libjpeg-turbo', '2.0.5'), - ('LMDB', '0.9.24'), - ('NASM', '2.15.05'), - ('nsync', '1.24.0'), - ('SQLite', '3.33.0'), - ('PCRE', '8.44'), - ('protobuf-python', '3.14.0'), - ('flatbuffers-python', '1.12'), - ('typing-extensions', '3.7.4.3'), - ('libpng', '1.6.37'), - ('snappy', '1.1.8'), - ('zlib', '1.2.11'), -] - -sanity_pip_check = True -use_pip = True - -# Dependencies created and updated using findPythonDeps.sh: -# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d -exts_list = [ - ('Markdown', '3.3.4', { - 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], - }), - ('pyasn1-modules', '0.2.8', { - 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], - }), - ('rsa', '4.7.2', { - 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], - }), - ('cachetools', '4.2.2', { - 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], - }), - ('google-auth', '1.30.0', { - 'modulename': 'google.auth', - 'checksums': ['9ad25fba07f46a628ad4d0ca09f38dcb262830df2ac95b217f9b0129c9e42206'], - }), - ('oauthlib', '3.1.0', { - 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], - }), - ('requests-oauthlib', '1.3.0', { - 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], - }), - ('google-auth-oauthlib', '0.4.4', { - 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], - }), - ('Werkzeug', '2.0.0', { - 'checksums': ['3389bbfe6d40c6dd25e6d3f974155163c8b3de5bbda6a89342d4ab93fae80ba0'], - }), - ('absl-py', '0.12.0', { - 'modulename': 'absl', - 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], - }), - ('astunparse', '1.6.3', { - 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], - }), - ('grpcio', '1.34.1', { - 'modulename': 'grpc', - 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], - }), - ('gviz-api', '1.9.0', { - 'source_tmpl': 'gviz_api-%(version)s.tar.gz', - 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], - }), - ('tensorboard_data_server', '0.6.1', { - 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now - 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], - }), - ('tensorboard', version, { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], - }), - ('tensorboard_plugin_wit', '1.8.0', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], - }), - ('tensorboard_plugin_profile', '2.4.0', { - 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], - }), - ('google-pasta', '0.2.0', { - 'modulename': 'pasta', - 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], - }), - ('termcolor', '1.1.0', { - 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], - }), - ('tensorflow_estimator', version, { - 'source_tmpl': SOURCE_WHL, - 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], - }), - ('astor', '0.8.1', { - 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], - }), - ('gast', '0.4.0', { - 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], - }), - ('opt_einsum', '3.3.0', { - 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('Keras_Preprocessing', '1.1.2', { - 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], - }), - ('dill', '0.3.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], - }), - ('tblib', '1.7.0', { - 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], - }), - ('portpicker', '1.3.1', { - 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], - }), - ('keras_nightly', '2.5.0.dev2021032900', { - 'modulename': 'keras', - 'source_tmpl': SOURCE_WHL, - 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], - }), - (name, version, { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], - 'patches': [ - 'TensorFlow-2.4.0_add-ldl.patch', - 'TensorFlow-2.4.0_dont-use-var-lock.patch', - 'TensorFlow-2.5.0_add-default-shell-env.patch', - 'TensorFlow-2.5.0_add-protobuf-deps.patch', - 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', - 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', - ], - 'checksums': [ - '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch - # TensorFlow-2.4.0_dont-use-var-lock.patch - 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', - # TensorFlow-2.5.0_add-default-shell-env.patch - '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', - # TensorFlow-2.5.0_add-protobuf-deps.patch - '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', - # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch - '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', - # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', - ], - 'test_script': 'TensorFlow-2.x_mnist-test.py', - 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', - 'test_targets': [ - '//tensorflow/core/...', - '-//tensorflow/core:example_java_proto', - '-//tensorflow/core/example:example_protos_closure', - '//tensorflow/cc/...', - '//tensorflow/c/...', - '//tensorflow/python/...', - # Fails on some nodes but C API isn't installed anyway - '-//tensorflow/c/eager:c_api_test_gpu', - '-//tensorflow/c/eager:c_api_distributed_test', - '-//tensorflow/c/eager:c_api_distributed_test_gpu', - # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 - '-//tensorflow/c/eager:c_api_cluster_test_gpu', - '-//tensorflow/c/eager:c_api_remote_function_test_gpu', - '-//tensorflow/c/eager:c_api_remote_test_gpu', - # Fails to open its own test.xml(?) - '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', - # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 - '-//tensorflow/core/common_runtime:mkl_layout_pass_test', - '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', - ], - 'testopts': "--test_timeout=3600 --test_size_filters=small", - 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + - "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", - 'with_xla': True, - }), -] - -moduleclass = 'lib' From 490918e5a756b367c60984ea0a899e436e0e69d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Jun 2021 13:11:58 +0200 Subject: [PATCH 1089/2365] {lang}[foss/2020b,fosscuda/2020b] numba v0.53.1 w/ Python 3.8.6 on top of LLLVM 11.0.0 --- .../n/numba/numba-0.53.1-foss-2020b.eb | 51 +++++++++++++++++++ .../n/numba/numba-0.53.1-fosscuda-2020b.eb | 51 +++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb new file mode 100644 index 0000000000..bd578f812f --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.53.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('LLVM', '11.0.0'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + +exts_list = [ + ('llvmlite', '0.36.0', { + 'patches': ['llvmlite-0.36.0_fix-LLVM-11.patch'], + 'preinstallopts': local_llvmlite_preinstallopts, + 'checksums': [ + '765128fdf5f149ed0b889ffbe2b05eb1717f8e20a5c87fa2b4018fbcce0fcfc9', # llvmlite-0.36.0.tar.gz + '17ebf3e8eaea2dd820bf4e089983d5743656613eb6313c1ffed30c58e8d66be4', # llvmlite-0.36.0_fix-LLVM-11.patch + ], + }), + (name, version, { + 'checksums': ['9cd4e5216acdc66c4e9dab2dfd22ddb5bef151185c070d4a3cd8e78638aff5b0'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..c8466673ed --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.53.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('LLVM', '11.0.0'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + +exts_list = [ + ('llvmlite', '0.36.0', { + 'patches': ['llvmlite-0.36.0_fix-LLVM-11.patch'], + 'preinstallopts': local_llvmlite_preinstallopts, + 'checksums': [ + '765128fdf5f149ed0b889ffbe2b05eb1717f8e20a5c87fa2b4018fbcce0fcfc9', # llvmlite-0.36.0.tar.gz + '17ebf3e8eaea2dd820bf4e089983d5743656613eb6313c1ffed30c58e8d66be4', # llvmlite-0.36.0_fix-LLVM-11.patch + ], + }), + (name, version, { + 'checksums': ['9cd4e5216acdc66c4e9dab2dfd22ddb5bef151185c070d4a3cd8e78638aff5b0'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' From d37fdf5b2f42351d2064ee1f6f132ade3ca56e05 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 11 Jun 2021 14:27:03 +0100 Subject: [PATCH 1090/2365] adding easyconfigs: RECON-1.08-GCC-10.2.0.eb --- .../r/RECON/RECON-1.08-GCC-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-10.2.0.eb new file mode 100644 index 0000000000..cc485eefd2 --- /dev/null +++ b/easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'RECON' +version = '1.08' + +homepage = 'https://www.repeatmasker.org/RepeatModeler/' +description = """Patched version of RECON to be used with RepeatModeler.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.repeatmasker.org/RepeatModeler/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8'] + +dependencies = [('Perl', '5.32.0')] + +start_dir = 'src' + +buildopts = 'CC="$CC"' + +local_bins = ['edgeredef', 'eledef', 'eleredef', 'famdef', 'imagespread'] +local_scripts = ['scripts/%s' % x for x in ['MSPCollect.pl', 'recon.pl']] + +files_to_copy = [ + (['src/%s' % x for x in local_bins], 'bin'), + 'scripts', 'COPYRIGHT', 'LICENSE', '00README', +] + +postinstallcmds = ["sed -i 's|$path = \"\"|$path = \"%(installdir)s/bin\"|g' %(installdir)s/scripts/recon.pl"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + local_scripts, + 'dirs': [], +} + +sanity_check_commands = [("recon.pl 2>&1 | grep 'usage: recon seq_name_list_file MSP_file integer'", '')] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From a5ea33578ef43e20a8abdb45ca653d7e12df2391 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 11 Jun 2021 14:27:36 +0100 Subject: [PATCH 1091/2365] adding easyconfigs: RepeatScout-1.0.6-GCC-10.2.0.eb --- .../RepeatScout-1.0.6-GCC-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb new file mode 100644 index 0000000000..5bfb6c8830 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'RepeatScout' +version = '1.0.6' + +homepage = 'http://www.repeatmasker.org/' +description = """De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and + tested with our multiple sequence version of RepeatScout ( 1.0.6 )""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://www.repeatmasker.org'] +sources = ['RepeatScout-%(version)s.tar.gz'] +checksums = ['31a44cf648d78356aec585ee5d3baf936d01eaba43aed382d9ac2d764e55b716'] + +dependencies = [ + ('Perl', '5.32.0'), + ('TRF', '4.09.1'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i -e 's|mkdir|mkdir -p|g' -e 's|VERSION = .*|VERSION = %(version)s|g' Makefile &&" + +installopts = 'INSTDIR="%(installdir)s"' + +sanity_check_paths = { + 'files': [name, 'build_lmer_table', 'README'], + 'dirs': [], +} + +sanity_check_commands = [("RepeatScout 2>&1 | grep 'Usage:\nRepeatScout'", '')] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 213af96755f41989a843605ca85964f9bc6a7170 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 11 Jun 2021 14:28:28 +0100 Subject: [PATCH 1092/2365] adding easyconfigs: LTR_retriever-2.9.0-foss-2020b.eb, NINJA-0.97-cluster_only-GCC-10.2.0.eb --- .../LTR_retriever-2.9.0-foss-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2020b.eb b/easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2020b.eb new file mode 100644 index 0000000000..35d99a92ae --- /dev/null +++ b/easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2020b.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'Tarball' + +name = 'LTR_retriever' +version = '2.9.0' + +homepage = 'https://github.com/oushujun/LTR_retriever' +description = """LTR_retriever is a highly accurate and sensitive program for + identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also + included in this package. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'oushujun' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e2d94f6179c33990a77fa9fdcefb842c8481b4c30833c9c12cbbe54cb3fdda73'] + +dependencies = [ + ('Perl', '5.32.0'), + ('BLAST+', '2.11.0'), + ('RepeatMasker', '4.1.2-p1'), + ('HMMER', '3.3.2'), + ('CD-HIT', '4.8.1'), + ('TRF', '4.09.1'), +] + +sanity_check_paths = { + 'files': ['LTR_retriever'], + 'dirs': ['bin', 'database'], +} + +sanity_check_commands = [("%(name)s -h 2>&1 | grep 'Usage: LTR_retriever'", '')] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 650f1037886ea513729573dc08da9065b58e4056 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 11 Jun 2021 14:29:18 +0100 Subject: [PATCH 1093/2365] adding easyconfigs: RepeatModeler-2.0.2a-foss-2020b.eb --- .../RepeatModeler-2.0.2a-foss-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb new file mode 100644 index 0000000000..44ec3867af --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb @@ -0,0 +1,40 @@ +# Author: Jasper Grimm (UoY) + +name = 'RepeatModeler' +version = '2.0.2a' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatModeler is a de novo transposable element (TE) family identification and modeling package. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://www.repeatmasker.org/RepeatModeler'] +sources = ['RepeatModeler-%(version)s.tar.gz'] +checksums = ['8a9d69c8d7afbfb07f8bb6560c5f2fd35e61e5e7ccd01361e4f9a63f4ef3e50c'] + +dependencies = [ + ('Perl', '5.32.0'), + ('TRF', '4.09.1'), + ('RMBlast', '2.11.0'), + ('RepeatMasker', '4.1.2-p1'), + ('RepeatScout', '1.0.6'), + ('RECON', '1.08'), + ('Kent_tools', '411'), + ('CD-HIT', '4.8.1'), + # Optional (required for LTR pipeline): + ('MAFFT', '7.475', '-with-extensions'), + ('GenomeTools', '1.6.1'), # for LTRHarvest + ('LTR_retriever', '2.9.0'), + ('NINJA', '0.97-cluster_only'), +] + +exts_defaultclass = 'PerlModule' +exts_list = [ + ('Devel::Size', '0.83', { + 'source_tmpl': 'Devel-Size-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3'], + }), +] + +moduleclass = 'bio' From b834c45300bae11ecf7a5a95ee1a36278c11daf9 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 11 Jun 2021 14:36:05 +0100 Subject: [PATCH 1094/2365] author --- .../easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb index 5bfb6c8830..f66e55a398 100644 --- a/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb @@ -1,3 +1,5 @@ +# Author: Jasper Grimm (UoY) + easyblock = 'ConfigureMake' name = 'RepeatScout' From c865f91d79af5ebf14cd55f31f1459af00bbcd18 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 11 Jun 2021 16:07:04 +0200 Subject: [PATCH 1095/2365] adding easyconfigs: hypothesis-4.53.1-GCCcore-10.2.0.eb, PyTorch-1.3.1-fosscuda-2020b.eb, torchvision-0.4.2-fosscuda-2020b-PyTorch-1.3.1.eb and patches: PyTorch-1.3.1_add-Python3.8-compat.patch, PyTorch-1.3.1_add-support-for-cuda11.patch, PyTorch-1.3.1_add-support-for-cudnn8.patch, PyTorch-1.3.1_fix-for-nccl-error.patch, PyTorch-1.3.1_skip-nccl-error-tests.patch --- .../hypothesis-4.53.1-GCCcore-10.2.0.eb | 24 ++ .../p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb | 309 ++++++++++++++++++ ...sion-0.4.2-fosscuda-2020b-PyTorch-1.3.1.eb | 26 ++ 3 files changed, 359 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2020b-PyTorch-1.3.1.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b02cdc7690 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '4.53.1' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ff4b9b8286437eb323a3e0a62adb00039c4207038c229c3f5f1eff6051e376b1'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..7516bbe2ba --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb @@ -0,0 +1,309 @@ +name = 'PyTorch' +version = '1.3.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +local_pytorchthirdpartydir = 'pytorch-%(version)s/third_party' +local_extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' + +source_urls = ['https://github.com/pytorch/pytorch/archive'] + +# PyTorch pulls in a bunch of submodules that are not releases. We download the submodule revisions from their repos. +# determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.3.1/third_party +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': 'ca528e32fea9ca8f2b16053cff17160290fc84ce.tar.gz', + 'filename': 'gloo-20190930.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'gloo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'googletest'), + }, + { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], + 'download_filename': '25abf7efba0b2990f5a6dfb0a31bc65c0f2f4d17.tar.gz', + 'filename': 'pybind11-20190204.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'pybind11'), + }, + { + 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], + 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', + 'filename': 'clang-cindex-python3-20170330.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'pybind11/tools/clang'), + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': '89fe1695edf9ee14c22f815f24bac45577a4f135.tar.gz', + 'filename': 'cpuinfo-20190117.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'cpuinfo'), + }, + { + 'source_urls': ['https://github.com/onnx/onnx/archive'], + 'download_filename': '034921bd574cc84906b7996c07873454b7dd4135.tar.gz', + 'filename': 'onnx-20190926.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx'), + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': 'e776aa0275e293707b6a0901e0e8d8a8a3679508.tar.gz', + 'filename': 'benchmark-20180525.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx/third_party/benchmark'), + }, + { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], + 'download_filename': '09f082940113661256310e3f4811aa7261a9fa05.tar.gz', + 'filename': 'pybind11-20170919.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx/third_party/pybind11'), + }, + { + 'source_urls': ['https://github.com/onnx/onnx-tensorrt/archive'], + 'download_filename': 'cb3d8066f20e6bca306454934d09d6abd826264a.tar.gz', + 'filename': 'onnx-tensorrt-20190425.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx-tensorrt'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], + 'download_filename': '13da0b4c21d17f94150713366420baaf1b5a46f4.tar.gz', + 'filename': 'pthreadpool-20181008.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'pthreadpool'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], + 'download_filename': 'b742d1143724d646cd0f914646f1240eacf5bd73.tar.gz', + 'filename': 'FXdiv-20181016.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'FXdiv'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], + 'download_filename': '90a938f30ba414ada2f4b00674ee9631d7d85e19.tar.gz', + 'filename': 'psimd-20180906.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'psimd'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], + 'download_filename': 'febbb1c163726b5db24bed55cc9dc42529068997.tar.gz', + 'filename': 'FP16-20181128.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'FP16'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], + 'download_filename': 'c039579abe21f5756e0f0e45e8e767adccc11852.tar.gz', + 'filename': 'NNPACK-20190323.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'NNPACK'), + }, + { + 'source_urls': ['https://github.com/shibatch/sleef/archive'], + 'download_filename': '7f523de651585fe25cade462efccca647dcc8d02.tar.gz', + 'filename': 'sleef-20190730.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'sleef'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], + 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', + 'filename': 'PeachPy-20180219.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'python-peachpy'), + }, + { + 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], + 'download_filename': '7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz', + 'filename': 'QNNPACK-20190828.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'QNNPACK'), + }, + { + 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], + 'download_filename': '60e318d48dd72a22a1f63fa625387d4b7363bd23.tar.gz', + 'filename': 'fbgemm-20200521.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm'), + }, + { + 'source_urls': ['https://github.com/asmjit/asmjit/archive'], + 'download_filename': '4da474ac9aa2689e88d5e40a2f37628f302d7e3c.tar.gz', + 'filename': 'asmjit-20190814.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm/third_party/asmjit'), + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': 'd5e37adf1406cf899d7d9ec1d317c47506ccb970.tar.gz', + 'filename': 'cpuinfo-20190201.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm/third_party/cpuinfo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '0fc5466dbb9e623029b1ada539717d10bd45e99e.tar.gz', + 'filename': 'googletest-20180920.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm/third_party/googletest'), + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', + 'filename': 'benchmark-20180606.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'benchmark'), + }, + { + 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], + 'download_filename': 'd41dc4dd74acce21fb210e7625d5d135751fa9e5.tar.gz', + 'filename': 'eigen-20190126.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'eigen'), + }, + { + 'source_urls': ['https://github.com/google/gemmlowp/archive'], + 'download_filename': '3fb5c176c17c765a3492cd2f0321b0dab712f350.tar.gz', + 'filename': 'gemmlowp-20181127.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'gemmlowp/gemmlowp'), + }, + { + 'source_urls': ['https://github.com/NVlabs/cub/archive'], + 'download_filename': '285aeebaa34b0e8a7670867a2e66c1a52d998d6a.tar.gz', + 'filename': 'cub-20170829.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'cub'), + }, + { + 'source_urls': ['https://github.com/houseroad/foxi/archive'], + 'download_filename': '8f74bc4df3a4cfc69b1a3eadf62aa29d9961c72d.tar.gz', + 'filename': 'foxi-20190424.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'foxi'), + }, + { + 'source_urls': ['https://github.com/intel/ideep/archive'], + 'download_filename': '78eafa5d231924e3d525d4dc46de880015257618.tar.gz', + 'filename': 'ideep-20190912.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'ideep'), + }, + { + 'source_urls': ['https://github.com/intel/tbb/archive'], + 'download_filename': 'a51a90bc609bb73db8ea13841b5cf7aa4344d4a9.tar.gz', + 'filename': 'tbb-20181009.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'tbb'), + }, + { + 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], + 'download_filename': '0125f28c61c1f822fd48570b4c1066f96fcb9b2e.tar.gz', + 'filename': 'mkl-dnn-20190905.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'ideep/mkl-dnn'), + }, +] +patches = [ + '%(name)s-1.2.0_fix-findAVX.patch', + '%(name)s-1.2.0_disable-tests-ppc64le.patch', + '%(name)s-1.2.0_add-cuda11-support.patch', + 'PyTorch-1.3.1_add-Python3.8-compat.patch', + 'PyTorch-1.3.1_add-support-for-cuda11.patch', + 'PyTorch-1.3.1_add-support-for-cudnn8.patch', + 'PyTorch-1.3.1_fix-for-nccl-error.patch', + '%(name)s-%(version)s_fix-missing-sleef_h.patch', + 'PyTorch-1.3.1_skip-nccl-error-tests.patch', + '%(name)s-1.4.0_fix-missing-source-dir.patch', + 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', +] +checksums = [ + 'ab6feb5044f7d36f6e93dce4668d8c593e89d34aca7023fd99a38d215ca9dfc0', # v1.3.1.tar.gz + '1354079f38459bc8f322d1f5808eb5c57059a473e77489e981fb5debeadf0ad0', # gloo-20190930.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + '1a1ccf8779332a7d6d0db9034d42df188867cbaf52eb71d74451f79aa8ce2040', # pybind11-20190204.tar.gz + '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz + 'b84c49b4bdc12b0e8f1bff365dcefd50e5a2a25eeef8c928aeb2dab9fda4d599', # cpuinfo-20190117.tar.gz + 'eaa2d4b70aa0003fdab136ae26b5e0aebabcf6421df7fef69fec9ce005a09586', # onnx-20190926.tar.gz + 'c7682e9007ddfd94072647abab3e89ffd9084089460ae47d67060974467b58bf', # benchmark-20180525.tar.gz + '02407529fd8431cf627d45638b4d9a6c02b8aa5bf50d73b8fa12217918c57ff4', # pybind11-20170919.tar.gz + '1a98c6fece7878c88b59ffe651b427c15b4929c801a09655cd14ca44553787c3', # onnx-tensorrt-20190425.tar.gz + '90ab4f60ae0e99c0172dd5201dccc6de6c8f384a21b3d959588f4c1e00beec0f', # pthreadpool-20181008.tar.gz + '07625551202a1f35fe5e826669ad495962b26f6a139290e90b321c5996f002ef', # FXdiv-20181016.tar.gz + 'afd27417c6df1c85f79a68361055dd3adc292174913c39c1f58b698b9cfd7926', # psimd-20180906.tar.gz + '3e71681e0a67cd28552aa0bbb78ec6a6bd238216df15336dc1326280f7958de2', # FP16-20181128.tar.gz + '2c276e6cc9e3fb7a79bc337662aba738a638975381bac6d393254ec288d6269e', # NNPACK-20190323.tar.gz + '8cb5fae822077ca9cbc14dcc7bba9a3a35ad519284fc5169f9a176672c63860a', # sleef-20190730.tar.gz + '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180219.tar.gz + '0d752bd75f46ce4d7c6f0a60b0d6c0e5918a7b4683c825284f8db3706dd24f76', # QNNPACK-20190828.tar.gz + '5669f25fe8b550a44edbaf35bb7bb4a549474940f6b3291d988ffac5cc6a2d4f', # fbgemm-20200521.tar.gz + 'a6de3e1604b46b2e37ae31c0896e90f4962e887e0a3bcf1bd2fb8cc55a5c59cf', # asmjit-20190814.tar.gz + '3f2dc1970f397a0e59db72f9fca6ff144b216895c1d606f6c94a507c1e53a025', # cpuinfo-20190201.tar.gz + 'e99b904983d08ac8e9bddb5b0d21196b78ad9499e3c5d12192cee2ddd2b7515c', # googletest-20180920.tar.gz + '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz + '2ec954f18cec50a7063a7358ce555f7e11788a7f6d4e7e597d83687dc2f3b989', # eigen-20190126.tar.gz + 'fdd6f08bdb33d33f4df516ffb91730fdb163479c19502cfc983083fd9cf43bfa', # gemmlowp-20181127.tar.gz + '7224b03af4acbc54525105bb42e3ecd75c66a3a5b47e8a725ab008467c4109f9', # cub-20170829.tar.gz + 'b444b4428adc4befc777d9a1af2fd9bbf5f5a2339913668357196c5133e9cc7b', # foxi-20190424.tar.gz + 'b8fb8b4871cc3da4bded01c476957a08f51949c20f834f39f90f9e10811d6dfe', # ideep-20190912.tar.gz + ('dc0a8d8d96cb8765782aa6ac1b509ad4db955d9bbb58fa5cc2265f0292756d72', + 'be111cf161b587812fa3b106fe550efb6f129b8b0b702fef32fac23af9580e5e'), # tbb-20181009.tar.gz + ('d16c64ab2ce654f0a21e51f933ae9ee480a8873717d0bd10e0f2a2f658a7095b', + 'bf096e6b3f17925ebe7802e0fa7dcc246319210b6ea3645b3ed52899a474fafc'), # mkl-dnn-20190905.tar.gz + '001c9bf604aebe4b39ccad15332a71130b07b780c539ceca84d6c64cd6fc8a68', # PyTorch-1.2.0_fix-findAVX.patch + 'c4183bcb29a8bcbadea0341e93a3a32afdf860aa31331b768e787d899183da92', # PyTorch-1.2.0_disable-tests-ppc64le.patch + '5a8289ced3ea448c61b2c417bb6118cb73da67eb6b9a58ac14376c65f7151906', # PyTorch-1.2.0_add-cuda11-support.patch + '2a743d0fc52a6f7239e6750a7cd59148417546b45a0b10ad1a15e526b94c4434', # PyTorch-1.3.1_add-Python3.8-compat.patch + 'e379846cb0bccb7e6143bf21b1fa517771842c7ca165cb35d60e507edd38b6ce', # PyTorch-1.3.1_add-support-for-cuda11.patch + '2560bf24f40aa981c9d3802313b67c4d2378082a9fdd919c499de10793da7e64', # PyTorch-1.3.1_add-support-for-cudnn8.patch + '064801bf29f07524a93d17fc0ca6004adc4a506232b33077ac43bdbe3f3a9f7d', # PyTorch-1.3.1_fix-for-nccl-error.patch + '1337647ff64a1208d1e401fc84052d0bc6174b133cec2f3521319cb593f524fa', # PyTorch-1.3.1_fix-missing-sleef_h.patch + '5743ac23a0d0f40373baeb026bb5656a84ca1417fcce10be8370ec3f4c9e80a6', # PyTorch-1.3.1_skip-nccl-error-tests.patch + '797987fb9c9bf9f1d75a1be878ddf9f418f9524006b0985ca8e6d65d4e2b6998', # PyTorch-1.4.0_fix-missing-source-dir.patch + # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch + '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '4.53.1'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +excluded_tests = { + '': [ + # SEGV + 'autograd', + # https://github.com/pytorch/pytorch/issues/42498 + 'cpp_extensions', + ], + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/41186 + 'autograd', + # https://github.com/pytorch/pytorch/issues/41400 + 'jit', + # https://github.com/pytorch/pytorch/issues/41469 + 'nn', + # Sporadically fails for unknown reason. Fixed in newer versions + 'torch', + # Unknown + 'cuda', + ], +} + +# OpenMP causes e.g. torch.matmul to return invalid results at least on POWER +# See e.g. https://github.com/pytorch/pytorch/issues/3716#issuecomment-387776917 +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2020b-PyTorch-1.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2020b-PyTorch-1.3.1.eb new file mode 100644 index 0000000000..32ef599a46 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2020b-PyTorch-1.3.1.eb @@ -0,0 +1,26 @@ +name = 'torchvision' +version = '0.4.2' +local_pytorch_version = '1.3.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1184a27eab85c9e784bacc6f9d6fec99e168ab4eda6047ef9f709e7fdb22d8f9'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('PyTorch', local_pytorch_version), +] + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'vis' From 9464b53f6ffc391b714824256f0ee0b4dfa8eb4f Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 11 Jun 2021 15:10:13 +0100 Subject: [PATCH 1096/2365] use https --- .../easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb index f66e55a398..1b471ca34d 100644 --- a/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb @@ -5,13 +5,13 @@ easyblock = 'ConfigureMake' name = 'RepeatScout' version = '1.0.6' -homepage = 'http://www.repeatmasker.org/' +homepage = 'https://www.repeatmasker.org/' description = """De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.6 )""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['http://www.repeatmasker.org'] +source_urls = ['https://www.repeatmasker.org'] sources = ['RepeatScout-%(version)s.tar.gz'] checksums = ['31a44cf648d78356aec585ee5d3baf936d01eaba43aed382d9ac2d764e55b716'] From 22257959e842ffe6f611259d56db281273fee4b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Jun 2021 21:39:59 +0200 Subject: [PATCH 1097/2365] add missing Doxygen build dependency for GenomeWorks --- .../g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 101b0be39c..280fb4af01 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -23,7 +23,10 @@ sources = [{ # no checksum for source tarball because it's created locally via 'git clone' checksums = [None] -builddependencies = [('CMake', '3.18.4')] +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] dependencies = [ ('Python', '3.8.6'), From abb5444d37084e23a04f65a080ebb6053fcbb3ab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 12 Jun 2021 00:46:43 +0200 Subject: [PATCH 1098/2365] adding easyconfigs: nvtop-1.2.1-GCCcore-10.2.0.eb --- .../n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8eae3bff05 --- /dev/null +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'nvtop' +version = '1.2.1' + +homepage = 'https://github.com/Syllo/nvtop' +description = 'htop-like GPU usage monitor' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/Syllo/nvtop/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('CUDAcore', '11.1.1', '', True), + ('ncurses', '6.2'), +] + +separate_build_dir = True + +configopts = '-DNVML_INCLUDE_DIRS=$EBROOTCUDA/include -DNVML_LIBRARIES=$EBROOTCUDA/lib64/stubs/libnvidia-ml.so' + +sanity_check_paths = { + 'files': ['bin/nvtop'], + 'dirs': [], +} + +sanity_check_commands = ["nvtop --help"] + +moduleclass = 'tools' From c857f09ee5b9f9b810d8aa60054390ecacc90eff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 12 Jun 2021 15:59:53 +0200 Subject: [PATCH 1099/2365] adding easyconfigs: NiBabel-3.2.1-fosscuda-2020b.eb --- .../n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..cf9d4e9046 --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '3.2.1' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Pillow', '8.0.1'), + ('pydicom', '2.1.2'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['4d2ff9426b740011a1c916b54fc25da9348282e727eaa2ea163f42e00f1fc29e'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' From 5992928a49e74d745876dc92e48ca991f461d427 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 12 Jun 2021 16:06:27 +0200 Subject: [PATCH 1100/2365] add checksum --- easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb index 8eae3bff05..d8de7f1805 100644 --- a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/Syllo/nvtop/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['9b9d8159b95be5cbd9bf6904b44c212e820f17c9009e36e5cfeac43bbb059340'] builddependencies = [ ('binutils', '2.35'), From efee982db4706192da638973e0c63474baff2de3 Mon Sep 17 00:00:00 2001 From: Bennet Fauber Date: Sat, 12 Jun 2021 15:42:52 -0400 Subject: [PATCH 1101/2365] Updating Subread to 2.0.2 GCC-10.2.0 --- .../s/Subread/Subread-2.0.2-GCC-10.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..17cdbfec0d --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'Subread' +version = '2.0.2' + +# HTTPS is not valid +homepage = 'http://%(namelower)s.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] + +checksums = [ # source subread-2.0.2-source.tar.gz + '0b64bd51f39f8d322c4594697fa5f0f64fbe60283113eadadff9f4268f897079'] + +start_dir = 'src' + +prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && " +prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && " + +buildopts = " -f Makefile.Linux" + +files_to_copy = ['bin'] + +local_binaries_list = [ + 'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', 'subread-align', 'subread-buildindex', +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_binaries_list], + 'dirs': ['bin/utilities'], +} + +sanity_check_commands = [ + 'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh' +] + +moduleclass = 'bio' From 157c0f3f1579cec290b9b1bb76f4d9b8cff6f086 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 14 Jun 2021 13:18:17 +0200 Subject: [PATCH 1102/2365] adding easyconfigs: naturalsort-0.1.3-foss-2020b.eb, pysamstats-1.1.2-foss-2020b.eb, Excel-Writer-XLSX-1.09-foss-2020b.eb --- .../Excel-Writer-XLSX-1.09-foss-2020b.eb | 24 +++++++++++++++ .../pysamstats/pysamstats-1.1.2-foss-2020b.eb | 30 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb new file mode 100644 index 0000000000..134d149bbc --- /dev/null +++ b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PerlModule' + +name = 'Excel-Writer-XLSX' +version = '1.09' + +homepage = 'https://metacpan.org/pod/Excel::Writer::XLSX' +description = """The Excel::Writer::XLSX module can be used to create an Excel file in the 2007+ XLSX format. +Multiple worksheets can be added to a workbook and formatting can be applied to cells. Text, numbers, and formulas +can be written to the cells.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['d679c6ac19e93c32ab77594c793e41b948c7bb3873b600e70ad637d093dca187'] + +dependencies = [ + ('Perl', '5.32.0'), + ('Archive-Zip', '1.68'), +] + +options = {'modulename': 'Excel::Writer::XLSX'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb new file mode 100644 index 0000000000..6233dc44ab --- /dev/null +++ b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'pysamstats' +version = '1.1.2' + +homepage = 'https://github.com/alimanfoo/pysamstats' +description = """A Python utility for calculating statistics +against genome positions based on sequence alignments from a SAM or BAM file.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d8b41934fdc700552d689f473860c64525a88600460344d0cac2095424750c6'] + +use_pip = True + +dependencies = [ + ('Python', '3.8.6'), + ('Pysam', '0.16.0.1'), + ('SciPy-bundle', '2020.11'), + ('PyTables', '3.6.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.8/site-packages'], +} + +moduleclass = 'bio' From 681bdfeb8977692ed5e6c141f8c3db11945ebb48 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 14 Jun 2021 13:38:26 +0200 Subject: [PATCH 1103/2365] less strict requirements of pysamstats --- .../easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb index 6233dc44ab..1211730884 100644 --- a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb @@ -9,11 +9,13 @@ against genome positions based on sequence alignments from a SAM or BAM file.""" toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6d8b41934fdc700552d689f473860c64525a88600460344d0cac2095424750c6'] use_pip = True +download_dep_fail = True + +preinstallopts = "sed -i -e 's/ (<0.16)//g' setup.py && " dependencies = [ ('Python', '3.8.6'), @@ -22,6 +24,7 @@ dependencies = [ ('PyTables', '3.6.1'), ] +sanity_pip_check = True sanity_check_paths = { 'files': [], 'dirs': ['lib/python3.8/site-packages'], From 06f1175fc40b8e4678fcd0ce1231d4854110cf37 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 14 Jun 2021 15:37:41 +0200 Subject: [PATCH 1104/2365] repaired source file name --- .../Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb index 134d149bbc..d259f3941a 100644 --- a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb +++ b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -11,7 +11,7 @@ can be written to the cells.""" toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/'] -sources = ['%(name)s-v%(version)s.tar.gz'] +sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['d679c6ac19e93c32ab77594c793e41b948c7bb3873b600e70ad637d093dca187'] dependencies = [ @@ -21,4 +21,9 @@ dependencies = [ options = {'modulename': 'Excel::Writer::XLSX'} +sanity_check_paths = { + 'files': ['bin/extract_vba'], + 'dirs': ['lib', 'bin'], +} + moduleclass = 'tools' From 3b472fff9e093a4cbbcdc88dd1625a83caaf387e Mon Sep 17 00:00:00 2001 From: c3-builder Date: Mon, 14 Jun 2021 18:17:56 +0200 Subject: [PATCH 1105/2365] adding easyconfigs: libcint-4.4.0-foss-2020b.eb and patches: libcint-4.4.0_remove_pyscftest.patch --- .../l/libcint/libcint-4.4.0-foss-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb new file mode 100644 index 0000000000..dce8ca3120 --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '4.4.0' + +homepage = 'https://github.com/sunqm/libcint' +description = """libcint is an open source library for analytical Gaussian integrals.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/sunqm/libcint/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_remove_pyscftest.patch'] +checksums = [ + '39a831e9131395e7ac312608981495aed3e44d0511b0700b2a1fb163b32c89c1', # v4.4.0.tar.gz + '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d', # libcint-4.4.0_remove_pyscftest.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + # Python with numpy only required for 'make test' + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +separate_build_dir = False # Must use the same directory for tests + +configopts = '-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on' + +buildopts = "VERBOSE=1" + +runtest = 'test ' +#postinstallcmds = ['ln -s . build && cd testsuite && python test_rys_roots.py && foobar'] + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/libcint.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' From 9fd27aae60298c4cf760ddbed699558bdb5930d0 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Mon, 14 Jun 2021 18:43:31 +0200 Subject: [PATCH 1106/2365] Fix style --- easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb index dce8ca3120..f8db3f095f 100644 --- a/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-foss-2020b.eb @@ -30,7 +30,6 @@ configopts = '-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENAB buildopts = "VERBOSE=1" runtest = 'test ' -#postinstallcmds = ['ln -s . build && cd testsuite && python test_rys_roots.py && foobar'] sanity_check_paths = { 'files': ['include/cint.h', 'lib/libcint.%s' % SHLIB_EXT], From a72390a70e2f3588aebd274fb79bcb52c457c1a0 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 15 Jun 2021 08:25:30 +0200 Subject: [PATCH 1107/2365] Add patch to remove faulty AVX512 optimizations --- .../t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 9 +++------ .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 8 +++----- 2 files changed, 6 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 62e87e01cd..b55f05fb04 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -8,10 +8,6 @@ description = "An open-source software library for Machine Intelligence" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True} -if ARCH == 'x86_64': - # required workaround for failing tests on Intel Skylake and Cascade Lake, - # see https://github.com/tensorflow/tensorflow/issues/49944 - toolchainopts['extra_cxxflags'] = '-mno-avx512f' builddependencies = [ ('Bazel', '3.7.2'), @@ -158,6 +154,7 @@ exts_list = [ 'TensorFlow-2.4.0_dont-use-var-lock.patch', 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_disable_avx512-extensions.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', ], @@ -170,6 +167,8 @@ exts_list = [ '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', # TensorFlow-2.5.0_add-protobuf-deps.patch '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_disable_avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch @@ -199,8 +198,6 @@ exts_list = [ '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", - 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + - "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", 'with_xla': True, }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index f6ad95836c..4a90995824 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -8,11 +8,6 @@ description = "An open-source software library for Machine Intelligence" toolchain = {'name': 'fosscuda', 'version': '2020b'} toolchainopts = {'pic': True} -if ARCH == 'x86_64': - # required workaround for failing tests on Intel Skylake and Cascade Lake, - # see https://github.com/tensorflow/tensorflow/issues/49944 - toolchainopts['extra_cxxflags'] = '-mno-avx512f' - builddependencies = [ ('Bazel', '3.7.2'), @@ -163,6 +158,7 @@ exts_list = [ 'TensorFlow-2.4.1_fix-min-priority-test.patch', 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_disable_avx512-extensions.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', @@ -179,6 +175,8 @@ exts_list = [ '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', # TensorFlow-2.5.0_add-protobuf-deps.patch '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_disable_avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch From 5f69e4ff520e513a3a0225ff3fef10eaf93d8ddb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 15 Jun 2021 10:34:39 +0200 Subject: [PATCH 1108/2365] Add support for large CPU nodes --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 3 +++ .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index b55f05fb04..ad2ff05cc2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -154,6 +154,7 @@ exts_list = [ 'TensorFlow-2.4.0_dont-use-var-lock.patch', 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_add_support_for_large_core_systems.patch', 'TensorFlow-2.5.0_disable_avx512-extensions.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', @@ -167,6 +168,8 @@ exts_list = [ '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', # TensorFlow-2.5.0_add-protobuf-deps.patch '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_add_support_for_large_core_systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', # TensorFlow-2.5.0_disable_avx512-extensions.patch '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 4a90995824..6e3e754f93 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -158,6 +158,7 @@ exts_list = [ 'TensorFlow-2.4.1_fix-min-priority-test.patch', 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_add_support_for_large_core_systems.patch', 'TensorFlow-2.5.0_disable_avx512-extensions.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', @@ -175,6 +176,8 @@ exts_list = [ '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', # TensorFlow-2.5.0_add-protobuf-deps.patch '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_add_support_for_large_core_systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', # TensorFlow-2.5.0_disable_avx512-extensions.patch '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch From 39d2897fd2921a4d7bc1cf98cd7cfbaf2114b660 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 15 Jun 2021 10:50:30 +0200 Subject: [PATCH 1109/2365] adding easyconfigs: molecularGSM-20190826-intel-2020b.eb and patches: molecularGSM-20190826_fix_ase_test.patch, molecularGSM-20190826_fix_intel.patch --- .../molecularGSM-20190826-intel-2020b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb diff --git a/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb new file mode 100644 index 0000000000..e7ef463af9 --- /dev/null +++ b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'molecularGSM' +version = '20190826' +_commit_moleculargsm = '02ae717' +_commit_tribits = '5308a8e' + +homepage = 'https://github.com/ZimmermanGroup/molecularGSM' +description = """Code for single-ended and double-ended molecular GSM. +The growing string method is a reaction path and transition state finding method developed in c++.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'debug': True, 'noopt': True, 'extra_cxxflags': '-traceback', 'optarch': False} + +sources = [ + { + 'source_urls': ['https://github.com/ZimmermanGroup/molecularGSM/archive/'], + 'download_filename': '%s.tar.gz' % _commit_moleculargsm, + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/TriBITSPub/TriBITS/archive'], + 'download_filename': '%s.tar.gz' % _commit_tribits, + 'filename': 'TriBITS-%s.tar.gz' % _commit_tribits, + 'extract_cmd': 'tar -xzf %s -C %(name)s-* && cd %(name)s-* && mv TriBITS-* TriBITS', + }, +] +patches = [ + 'molecularGSM-20190826_fix_intel.patch', + 'molecularGSM-20190826_fix_ase_test.patch', +] +checksums = [ + '7bb7fd30d4220f720c25a0c6f761eba2b62f94b3be91b15eb536e49778245afc', # molecularGSM-20190826.tar.gz + '121c3885f8b8d2080a299db7f3f527520c985671280e69cb7beb00cd9e9f3e00', # TriBITS-5308a8e.tar.gz + '64b81dec0380db1d350c6ab33d10acb4364ad929544596025e6c7dfea6144a70', # molecularGSM-20190826_fix_intel.patch + '13b4f207af96749a118dee66a5b1fa9606c65c4c39b1b9981edfe713b46dd9c5', # molecularGSM-20190826_fix_ase_test.patch +] + +builddependencies = [('CMake', '3.18.4')] + +# parallel = 1 + +configopts = [ + # '', # default is MOPAC + # '-DGSM_ENABLE_QCHEM=1', + # '-DGSM_ENABLE_QCHEM_SF=1', + # '-DGSM_ENABLE_ORCA=1', + '-DGSM_ENABLE_GAUSSIAN=1', + # '-DGSM_ENABLE_MOLPRO=1', + # '-DGSM_ENABLE_ASE=1', +] + +install_cmd = 'mkdir -p %(installdir)s/bin && cp -a GSM/*.exe %(installdir)s/bin/' + +# _bins = ['ase', 'gaussian', 'molpro', 'mopac', 'orca', 'qchem', 'qchem_sf'] +_bins = ['gaussian'] + +sanity_check_paths = { + 'files': ['bin/gsm.%s.exe' % x for x in _bins], + 'dirs': [], +} + +moduleclass = 'chem' From 4d9d77e6b444196147f9fa6949d560fdaf18d35a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 15 Jun 2021 10:51:31 +0200 Subject: [PATCH 1110/2365] adding easyconfigs: geopy-2.1.0-GCCcore-10.2.0.eb --- .../g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3c5929e842 --- /dev/null +++ b/easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'geopy' +version = '2.1.0' + +homepage = 'https://geopy.readthedocs.io/en/stable/' +description = """ +geopy is a Python client for several popular geocoding web services. +geopy makes it easy for Python developers to locate the coordinates of addresses, cities, countries, +and landmarks across the globe using third-party geocoders and other data sources. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [('Python', '3.8.6')] + +use_pip = True + +exts_list = [ + ('geographiclib', '1.50', { + 'checksums': ['12bd46ee7ec25b291ea139b17aa991e7ef373e21abd053949b75c0e9ca55c632'], + }), + (name, version, { + 'checksums': ['892b219413e7955587b029949af3a1949c6fbac9d5ad17b79d850718f6a9550f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From e37e6fe76e272fcd9a7a54b3d8d2e4942067f6eb Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 15 Jun 2021 10:53:26 +0200 Subject: [PATCH 1111/2365] adding easyconfigs: CAMPARI-4.0-intel-2020b.eb --- .../c/CAMPARI/CAMPARI-4.0-intel-2020b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb new file mode 100644 index 0000000000..53ec1b1698 --- /dev/null +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'CAMPARI' +version = '4.0' +_date = '12202020' + +homepage = 'http://campari.sourceforge.net/V4/index.html' +description = """ +CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological +relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte +Carlo and molecular dynamics in seamless fashion.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['campari_v%s_%s.zip' % (version.split('.')[0], _date)] +checksums = ['bc627fb286b5461a5c68aa3e1a551ecd81016495163685800163c734f7c4f1bd'] + +dependencies = [('netCDF-Fortran', '4.5.3')] + +start_dir = 'source' + +configopts = '--enable-mpi=auto LIBS="$LIBS $LIBFFT"' + +buildopts = 'all LIBS="$LIBS $LIBFFT"' + +maxparallel = 10 + +postinstallcmds = ['cp -a %(builddir)s/campari/{data,doc,examples,params,tools,LICENSE} %(installdir)s/'] + +_binaries = ['campari', 'campari_mpi', 'campari_mpi_threads', 'campari_threads', 'camp_ncminer', 'camp_ncminer_threads'] +_libraries = ['lcampari.a', 'lcampari_mpi.a', 'lcampari_mpi_threads.a', 'lcampari_threads.a', 'libxdrf.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/%s' % x for x in _libraries], + 'dirs': [], +} + +sanity_check_commands = ['campari -h | grep "USAGE: CAMPARI"'] + +moduleclass = 'bio' From 9c5eec438405fe24ef75fd25f2a1a2fef68512c9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 15 Jun 2021 11:01:26 +0200 Subject: [PATCH 1112/2365] adding easyconfigs: AIMAll-19.10.12-intel-2020b-linux_64bit.eb --- ...AIMAll-19.10.12-intel-2020b-linux_64bit.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb diff --git a/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb b/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb new file mode 100644 index 0000000000..92c0827777 --- /dev/null +++ b/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb @@ -0,0 +1,39 @@ +easyblock = 'Tarball' + +name = 'AIMAll' +version = '19.10.12' +versionsuffix = '-linux_64bit' + +homepage = 'http://aim.tkgristmill.com' +description = """ +AIMAll is an easy to use, accurate, reliable and efficient quantum chemistry software package for performing +comprehensive, quantitative and visual QTAIM analyses of molecular systems - starting from molecular wavefunction +data.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +# download sources from http://aim.tkgristmill.com/download/download.html (requires login) +# to run in professional mode, add required license files to the main AIMAll directory +sources = [ + {'filename': 'aimall_%s_linux_64bit.tar.gz' % version.replace('.', '_'), + 'extract_cmd': 'tar -xzf %s --strip-components=1'}, + # {'filename': 'license_file_b.lslicb', 'extract_cmd': 'cp %s .'}, + # {'filename': 'license_file_a.lslica', 'extract_cmd': 'cp %s .'}, +] +checksums = [ + 'bf369ec8dd829c23a954b1c405edc7d8a01034d106cabc9c332bf7c4c177a54c', # aimall_19_10_12_linux_64bit.tar.gz +] + +buildininstalldir = True +skipsteps = ['install'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['bin/%s.exe' % x for x in ['aimext', 'aimint', 'aimqb', 'aimstudio', 'aimsum', 'aimutil']], + 'dirs': [], +} + +sanity_check_commands = ['aimqb.ish -nogui -help'] + +moduleclass = 'chem' From 6c7a7cc1078f28aedd0002d281b4f904b361c0ad Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 15 Jun 2021 11:19:49 +0200 Subject: [PATCH 1113/2365] adding easyconfigs: IOR-3.3.0-gompi-2020b.eb, IOR-3.3.0-gompi-2021a.eb --- .../i/IOR/IOR-3.3.0-gompi-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb new file mode 100644 index 0000000000..aae6519b94 --- /dev/null +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = "IOR" +version = "3.3.0" + +homepage = 'https://github.com/hpc/ior' +description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, + or HDF5 interfaces. """ + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = [('https://github.com/hpc/ior/archive')] +sources = ['%(version)s.tar.gz'] +checksums = ['701f2167f81ef963e227d4c036c4a947a98b5642b7c14c87c8ae657849891528'] + +builddependencies = [('Autotools', '20200321')] + +preconfigopts = "./bootstrap && " + +sanity_check_paths = { + 'files': ["bin/ior"], + 'dirs': ["share"] +} + +moduleclass = 'tools' From 774555c3c6b7bcc20e804e22cffc19729720d628 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 15 Jun 2021 11:24:38 +0200 Subject: [PATCH 1114/2365] Add patch and fix naming --- .../t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 8 ++++---- .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index ad2ff05cc2..b8b0fe831f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -154,8 +154,8 @@ exts_list = [ 'TensorFlow-2.4.0_dont-use-var-lock.patch', 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', - 'TensorFlow-2.5.0_add_support_for_large_core_systems.patch', - 'TensorFlow-2.5.0_disable_avx512-extensions.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', ], @@ -168,9 +168,9 @@ exts_list = [ '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', # TensorFlow-2.5.0_add-protobuf-deps.patch '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', - # TensorFlow-2.5.0_add_support_for_large_core_systems.patch + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', - # TensorFlow-2.5.0_disable_avx512-extensions.patch + # TensorFlow-2.5.0_disable-avx512-extensions.patch '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 6e3e754f93..da18013c78 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -158,8 +158,8 @@ exts_list = [ 'TensorFlow-2.4.1_fix-min-priority-test.patch', 'TensorFlow-2.5.0_add-default-shell-env.patch', 'TensorFlow-2.5.0_add-protobuf-deps.patch', - 'TensorFlow-2.5.0_add_support_for_large_core_systems.patch', - 'TensorFlow-2.5.0_disable_avx512-extensions.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', @@ -176,9 +176,9 @@ exts_list = [ '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', # TensorFlow-2.5.0_add-protobuf-deps.patch '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', - # TensorFlow-2.5.0_add_support_for_large_core_systems.patch + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', - # TensorFlow-2.5.0_disable_avx512-extensions.patch + # TensorFlow-2.5.0_disable-avx512-extensions.patch '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', From f40384cba4ac2c8dd952602a5b166a4bfe042693 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 15 Jun 2021 12:33:28 +0200 Subject: [PATCH 1115/2365] adding easyconfigs: AMS-2020.102-iimpi-2020b-intelmpi.eb --- .../AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb diff --git a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb new file mode 100644 index 0000000000..0e032547e3 --- /dev/null +++ b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'AMS' +version = '2020.102' +versionsuffix = '-intelmpi' + +homepage = 'https://www.scm.com/amsterdam-modeling-suite/' +description = """ +The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials +science, from quantum mechanics to fluid thermodynamics. +""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} + +sources = ['ams%(version)s.pc64_linux.intelmpi.bin.tgz'] +checksums = ['8a68eef268d7eb53ea1e10f66a48a8280f4dadae585999096ba1c246e88989db'] + +dependencies = [('libGLU', '9.0.1')] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +modextrapaths = { + 'AMSHOME': '', + 'AMSBIN': 'bin', + 'AMSRESOURCES': 'atomicdata', +} + +modloadmsg = """These environment variables need to be defined before using AMS: + * $SCMLICENSE: path to AMS license file + * $SCM_TMPDIR: path to user scratch directory +""" + +moduleclass = 'chem' From e6740e19ed4a03f3d7a7f9c7e35e9063a8347378 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 15 Jun 2021 13:25:40 +0200 Subject: [PATCH 1116/2365] adding easyconfigs: IOR-3.3.0-gompi-2020b.eb --- .../i/IOR/IOR-3.3.0-gompi-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb new file mode 100644 index 0000000000..da2da4d12f --- /dev/null +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb @@ -0,0 +1,28 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = "IOR" +version = "3.3.0" + +homepage = 'https://github.com/hpc/ior' +description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, + or HDF5 interfaces. """ + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = [('https://github.com/hpc/ior/archive')] +sources = ['%(version)s.tar.gz'] +checksums = ['701f2167f81ef963e227d4c036c4a947a98b5642b7c14c87c8ae657849891528'] + +builddependencies = [('Autotools', '20200321')] + +preconfigopts = "./bootstrap && " + +sanity_check_paths = { + 'files': ["bin/ior"], + 'dirs': ["share"] +} + +moduleclass = 'tools' From 924c4cc65fdec615a81ca321016bf5e9cdedeba3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 15 Jun 2021 14:44:39 +0200 Subject: [PATCH 1117/2365] [GCCcore/10.2.0] groff requires makeinfo as a build dep, which requires Perl, which requires groff. Break cyclic redundancy by adding Perl-minimal and makeinfo-minimal. --- .../g/groff/groff-1.22.4-GCCcore-10.2.0.eb | 2 +- .../makeinfo-6.7-GCCcore-10.2.0-minimal.eb | 35 +++++++++++++++++++ .../Perl-5.32.0-GCCcore-10.2.0-minimal.eb | 26 ++++++++++++++ 3 files changed, 62 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0-minimal.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb index 4d08613ba5..76c7be899c 100644 --- a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-10.2.0.eb @@ -15,7 +15,7 @@ checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] builddependencies = [ ('binutils', '2.35'), - ('makeinfo', '6.7'), + ('makeinfo', '6.7', '-minimal'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0-minimal.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0-minimal.eb new file mode 100644 index 0000000000..bd55c1413d --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0-minimal.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.7' +versionsuffix = '-minimal' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project. + +This is a minimal build with very basic functionality. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('Perl', '5.32.0', '-minimal'), +] + +configopts = '--disable-perl-xs --disable-perl-api-texi-build --disable-pod-simple-texinfo-tests ' + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb new file mode 100644 index 0000000000..882c2de902 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb @@ -0,0 +1,26 @@ +name = 'Perl' +version = '5.32.0' +versionsuffix = '-minimal' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' From c7df05458557fea95671d9bfbc101457d477e127 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 15 Jun 2021 14:50:38 +0200 Subject: [PATCH 1118/2365] makeinfo requires Perl as a dependency --- easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb index 9af1d073ea..f24d92de95 100644 --- a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb @@ -13,6 +13,7 @@ sources = ['texinfo-%(version)s.tar.xz'] checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] builddependencies = [('binutils', '2.35')] +dependencies = [('Perl', '5.32.0')] sanity_check_paths = { 'files': ['bin/makeinfo'], From 6656d666f32eee05031f72531af48a9f2955bbb5 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 15 Jun 2021 15:10:50 +0200 Subject: [PATCH 1119/2365] changes according to review --- .../e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb | 3 +++ .../easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb | 5 +---- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb index d259f3941a..c5eb8676cc 100644 --- a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb +++ b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -26,4 +26,7 @@ sanity_check_paths = { 'dirs': ['lib', 'bin'], } +sanity_check_commands = ['extract_vba --help 2>&1 | grep "This utility is used to extract the VBA project binary from an Excel"'] + + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb index 1211730884..b0cebf283a 100644 --- a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb @@ -15,6 +15,7 @@ checksums = ['6d8b41934fdc700552d689f473860c64525a88600460344d0cac2095424750c6'] use_pip = True download_dep_fail = True +# acceptance of pysam>0.16 preinstallopts = "sed -i -e 's/ (<0.16)//g' setup.py && " dependencies = [ @@ -25,9 +26,5 @@ dependencies = [ ] sanity_pip_check = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python3.8/site-packages'], -} moduleclass = 'bio' From f38c66d5aa2e9d122a3f829998e05a7b736735b7 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 15 Jun 2021 15:23:25 +0200 Subject: [PATCH 1120/2365] adding easyconfigs: LMfit-1.0.2-foss-2020b.eb, LMfit-1.0.2-intel-2020b.eb --- .../l/LMfit/LMfit-1.0.2-foss-2020b.eb | 33 +++++++++++++++++++ .../l/LMfit/LMfit-1.0.2-intel-2020b.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb new file mode 100644 index 0000000000..3e11982630 --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.2' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.23', { + 'checksums': ['f5096a924b1d2f147e70327245d95fc8f534dbe94277b6828ce2a8c049d3a438'], + }), + ('uncertainties', '3.1.5', { + 'checksums': ['9122c1e7e074196883b4a7a946e8482807b2f89675cb5e3798b87e0608ede903'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['67090ce56685cf7f92bd7358a1e7d4ad862b3758988109ec440e9825e5184b45'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb new file mode 100644 index 0000000000..2c4a3881dd --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.2' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.23', { + 'checksums': ['f5096a924b1d2f147e70327245d95fc8f534dbe94277b6828ce2a8c049d3a438'], + }), + ('uncertainties', '3.1.5', { + 'checksums': ['9122c1e7e074196883b4a7a946e8482807b2f89675cb5e3798b87e0608ede903'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['67090ce56685cf7f92bd7358a1e7d4ad862b3758988109ec440e9825e5184b45'], + }), +] + +moduleclass = 'math' From 325718bf47b848606b0ddb608a8228062411747a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Jun 2021 08:25:53 +0200 Subject: [PATCH 1121/2365] adding easyconfigs: tabixpp-1.1.0-GCC-10.2.0.eb --- .../t/tabixpp/tabixpp-1.1.0-GCC-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..fc3261b743 --- /dev/null +++ b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'tabixpp' +version = '1.1.0' + +homepage = 'https://github.com/ekg/tabixpp' +description = """C++ wrapper to tabix indexer""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1.0_use-external-HTSlib.patch'] +checksums = [ + '56c8f1b07190aba5e1d0b738e380e726d380f0ad8b2d0df133200b0ab1f8ed88', # v1.1.0.tar.gz + '65496b6e042cf54290386a33cf0de26cb1160b3ddb35216765999d790b99cab4', # tabixpp-1.1.0_use-external-HTSlib.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('HTSlib', '1.12'), + ('PCRE', '8.44'), +] + +skipsteps = ['configure'] + +preinstallopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/tabix++', 'lib/libtabixpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From a74dcfa05c715cb5ddc14272256f1a38b1a3b6ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Jun 2021 09:17:11 +0200 Subject: [PATCH 1122/2365] {bio}[gompi/2020b,GCC/10.2.0] MrBayes v3.2.7, Beast v2.6.4, beagle-lib v3.1.2 --- .../b/Beast/Beast-2.6.4-GCC-10.2.0.eb | 39 +++++++++++++++++++ .../beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb | 35 +++++++++++++++++ .../m/MrBayes/MrBayes-3.2.7-gompi-2020b.eb | 30 ++++++++++++++ 3 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2020b.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..6a056e1d19 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'Tarball' + +name = 'Beast' +version = '2.6.4' + +homepage = 'http://beast2.org' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%(version)s.Linux.tgz'] +checksums = ['4f80e2920eb9d87f3e9f64433119774dc67aca390fbd13dd480f852e3f8701a4'] + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '3.1.2'), +] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': ['bin/beast'], + 'dirs': [] +} + +sanity_check_commands = ["beast -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..f40b3b1712 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '3.1.2' + +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('Java', '11', '', True), + ('pkg-config', '0.29.2'), + ('pocl', '1.6'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--with-opencl=$EBROOTPOCL --with-cuda=$EBROOTCUDA " + +sanity_check_paths = { + 'files': ['include/libhmsbeagle-1/libhmsbeagle/%s' % x for x in ['beagle.h', 'platform.h']] + + ['lib/libhmsbeagle%s.%s' % (x, SHLIB_EXT) for x in ['-cpu', '-cpu-sse', '-jni', '']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2020b.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2020b.eb new file mode 100644 index 0000000000..a0ef1f5ec7 --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2020b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MrBayes' +version = '3.2.7' + +homepage = "https://nbisweden.github.io/MrBayes/" +description = """MrBayes is a program for Bayesian inference and model choice across + a wide range of phylogenetic and evolutionary models.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://github.com/NBISweden/MrBayes/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['39d9eb269969b501268d5c27f77687c6eaa2c71ccf15c724e6f330fc405f24b9'] + +dependencies = [ + ('libreadline', '8.0'), + ('beagle-lib', '3.1.2'), +] + +configopts = "--with-mpi --with-readline --with-beagle=$EBROOTBEAGLEMINLIB " + +sanity_check_paths = { + 'files': ['bin/mb'], + 'dirs': ['share'] +} + +sanity_check_commands = ["mb -help"] + +moduleclass = 'bio' From 9ed6320c4cf10fd159bb7b1831e96747411c7be6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Jun 2021 09:48:05 +0200 Subject: [PATCH 1123/2365] adding easyconfigs: tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb, torchvision-0.8.2-foss-2020b-PyTorch-1.7.1.eb --- ...nsorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb | 43 +++++++++++++++++++ ...chvision-0.8.2-foss-2020b-PyTorch-1.7.1.eb | 26 +++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-foss-2020b-PyTorch-1.7.1.eb diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..5083f88938 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'tensorboardX' +version = '2.2' +local_pytorch_ver = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_ver + +homepage = 'https://github.com/lanpa/tensorboardX' +description = "Tensorboard for PyTorch." + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'lanpa' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['dff39191ca26bce9c5c82b9a013558e8c17602d17279f70270ca3341f127c4cf'] + +# tensorboardX v2.x works with tensorboards generated with TensorFlow 2, +# but TensorFlow is not needed to use tensorboardX +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('protobuf-python', '3.14.0'), + ('PyTorch', local_pytorch_ver), + ('torchvision', '0.8.2', versionsuffix), +] + +options = {'modulename': '%(name)s'} + +use_pip = True +download_dep_fail = True + +postinstallcmds = ["cp -r %s %%(installdir)s" % d for d in ['docs', 'examples', 'tests']] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'docs', 'examples', 'tests'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-foss-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..081b0a5212 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.8.2-foss-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,26 @@ +name = 'torchvision' +version = '0.8.2' +local_pytorch_version = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9a866c3c8feb23b3221ce261e6153fc65a98ce9ceaa71ccad017016945c178bf'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('PyTorch', local_pytorch_version), +] + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'vis' From 59e5fb2e37de633541cb597c3f6b66dbe6d5ed02 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Jun 2021 10:11:08 +0200 Subject: [PATCH 1124/2365] adding easyconfigs: mapDamage-2.2.1-foss-2020b-R-4.0.4.eb --- .../inline-0.3.19-foss-2020b-R-4.0.4.eb | 29 +++++++++++++++++ .../mapDamage-2.2.1-foss-2020b-R-4.0.4.eb | 29 +++++++++++++++++ .../RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb | 30 ++++++++++++++++++ .../s/seqtk/seqtk-1.3-GCC-10.2.0.eb | 31 +++++++++++++++++++ 4 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb create mode 100644 easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb create mode 100644 easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..2881300bf9 --- /dev/null +++ b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'inline' +version = '0.3.19' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://cran.r-project.org/web/packages/inline' +description = """Functionality to dynamically define R functions and S4 methods + with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling + conventions.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('R', '4.0.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['inline'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..d640e4d3be --- /dev/null +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'mapDamage' +version = '2.2.1' +versionsuffix = '-R-%(rver)s' + +github_account = 'ginolhac' + +homepage = 'https://ginolhac.github.io/mapDamage/' +description = '''mapDamage2 is a computational framework written in Python and + R, which tracks and quantifies DNA damage patterns among ancient DNA + sequencing reads generated by Next-Generation Sequencing platforms.''' + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c'] + +dependencies = [ + ('Python', '3.8.6'), + ('seqtk', '1.3'), + ('Pysam', '0.16.0.1'), + ('R', '4.0.4'), + ('inline', '0.3.19', versionsuffix), + ('RcppGSL', '0.3.8', versionsuffix), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..754d7a89fe --- /dev/null +++ b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'RcppGSL' +version = '0.3.8' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://cran.r-project.org/web/packages/RcppGSL' +description = """The 'RcppGSL' package provides an easy-to-use interface + between 'GSL' data structures and R using concepts from 'Rcpp' which is itself + a package that eases the interfaces between R and C++.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('R', '4.0.4'), + ('GSL', '2.6'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['RcppGSL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..de96dba8af --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'seqtk' +version = '1.3' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563'] + +dependencies = [('zlib', '1.2.11')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BINDIR=%(installdir)s/bin/' + +sanity_check_paths = { + 'files': ['bin/seqtk'], + 'dirs': [], +} + +moduleclass = 'bio' From 27d4e7b33176e5e7898dd9e8f914c72357010965 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 16 Jun 2021 11:54:11 +0200 Subject: [PATCH 1125/2365] adding easyconfigs: gperftools-2.9.1-GCCcore-10.2.0.eb --- .../gperftools-2.9.1-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e29ea9698a --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.9.1' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'gperftools' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['484a88279d2fa5753d7e9dea5f86954b64975f20e796a6ffaf2f3426a674a06a'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), +] + +dependencies = [ + ('libunwind', '1.4.0'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From eff96bc4addca69094e99a715b35d1461162e290 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 16 Jun 2021 12:38:47 +0200 Subject: [PATCH 1126/2365] adding easyconfigs: RE2-2021-06-01-GCCcore-10.2.0.eb --- .../r/RE2/RE2-2021-06-01-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/r/RE2/RE2-2021-06-01-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/r/RE2/RE2-2021-06-01-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2021-06-01-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c1e9c7de09 --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2021-06-01-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = "CMakeMake" + +name = 'RE2' +version = '2021-06-01' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['26155e050b10b5969e986dab35654247a3b1b295e0532880b5a9c13c0a700ceb'] + +builddependencies = { + ('CMake', '3.18.4'), + ('binutils', '2.35'), +} + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' From dcc34e0987c65184a202898de1194778ca96b288 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Jun 2021 12:58:14 +0200 Subject: [PATCH 1127/2365] adding easyconfigs: tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb --- ...boardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..e398062f1d --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'tensorboardX' +version = '2.2' +local_pytorch_ver = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_ver + +homepage = 'https://github.com/lanpa/tensorboardX' +description = "Tensorboard for PyTorch." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +github_account = 'lanpa' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['dff39191ca26bce9c5c82b9a013558e8c17602d17279f70270ca3341f127c4cf'] + +# tensorboardX v2.x works with tensorboards generated with TensorFlow 2, +# but TensorFlow is not needed to use tensorboardX +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('protobuf-python', '3.14.0'), + ('PyTorch', local_pytorch_ver), + ('torchvision', '0.8.2', versionsuffix), +] + +options = {'modulename': '%(name)s'} + +use_pip = True +download_dep_fail = True + +postinstallcmds = ["cp -r %s %%(installdir)s" % d for d in ['docs', 'examples', 'tests']] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'docs', 'examples', 'tests'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From 43deb4a50a38281a4f152f16bce660591c2c8c88 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 16 Jun 2021 12:54:52 +0100 Subject: [PATCH 1128/2365] Add missing rgdal dep to R-INLA --- .../easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb index 2bb0ece82c..79229f933d 100644 --- a/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb @@ -19,6 +19,7 @@ dependencies = [ ('muParser', '2.3.2'), ('Rmath', '%(rver)s'), ('X11', '20201008'), + ('rgdal', '1.5-23', versionsuffix), ] default_easyblock = 'ConfigureMake' From f3eea7d0c64cf1e26a994192ee9c61866795a2bc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 16 Jun 2021 15:24:28 +0200 Subject: [PATCH 1129/2365] Exclude failing test --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb index 7516bbe2ba..75c89f5263 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb @@ -284,6 +284,8 @@ excluded_tests = { 'autograd', # https://github.com/pytorch/pytorch/issues/42498 'cpp_extensions', + # Precision issues. Maybe actual failures or "just" the new cuDNN + 'nn', ], 'POWER': [ # https://github.com/pytorch/pytorch/issues/41186 From 03416f05d84425fee2c26a01c2bd1090fd13f7d8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 16 Jun 2021 16:53:14 +0200 Subject: [PATCH 1130/2365] Add patch to fix alias violation in abseil --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 3 +++ .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index b8b0fe831f..c458718562 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -156,6 +156,7 @@ exts_list = [ 'TensorFlow-2.5.0_add-protobuf-deps.patch', 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', ], @@ -172,6 +173,8 @@ exts_list = [ '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', # TensorFlow-2.5.0_disable-avx512-extensions.patch '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index da18013c78..cc2dbfb5e6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -160,6 +160,7 @@ exts_list = [ 'TensorFlow-2.5.0_add-protobuf-deps.patch', 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', @@ -180,6 +181,8 @@ exts_list = [ '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', # TensorFlow-2.5.0_disable-avx512-extensions.patch '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch From e6efda45dae5e4449913fc0893e7ec431782d0b8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Jun 2021 20:44:02 +0200 Subject: [PATCH 1131/2365] adding easyconfigs: PnetCDF-1.12.2-gompi-2020b.eb, PnetCDF-1.12.2-gompic-2020b.eb --- .../p/PnetCDF/PnetCDF-1.12.2-gompi-2020b.eb | 35 +++++++++++++++++++ .../p/PnetCDF/PnetCDF-1.12.2-gompic-2020b.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompic-2020b.eb diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2020b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2020b.eb new file mode 100644 index 0000000000..2132d9c00f --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = "1.12.2" + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://parallel-netcdf.github.io/Release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ef1411875b07955f519a5b03278c31e566976357ddfc74c2493a1076e7d7c74'] + +builddependencies = [ + ('Autotools', '20200321'), + ('Perl', '5.32.0'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompic-2020b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompic-2020b.eb new file mode 100644 index 0000000000..fc395be789 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompic-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = "1.12.2" + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['https://parallel-netcdf.github.io/Release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ef1411875b07955f519a5b03278c31e566976357ddfc74c2493a1076e7d7c74'] + +builddependencies = [ + ('Autotools', '20200321'), + ('Perl', '5.32.0'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' From 71d217e21c2a5e662ce0899b313274a69c1c9409 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Jun 2021 22:05:52 +0200 Subject: [PATCH 1132/2365] adding easyconfigs: Amber-20.11-foss-2020b-AmberTools-21.3.eb --- .../Amber-20.11-foss-2020b-AmberTools-21.3.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb new file mode 100644 index 0000000000..4747d5bb52 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb @@ -0,0 +1,60 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 21 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 11) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', +] +checksums = [ + 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # mpi4py required for MMPBSA + ('Perl', '5.32.0'), + ('Boost', '1.74.0'), + ('libreadline', '8.0'), + ('matplotlib', '3.3.3'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.2'), + ('Tkinter', '3.8.6'), + ('X11', '20201008'), +] + +# All tests are expected to pass or be skipped +runtest = True + +static = False + +moduleclass = 'chem' From 3ff38177ab9e895d162027bae9beb34ed9db8028 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 17 Jun 2021 08:03:59 +0200 Subject: [PATCH 1133/2365] adding easyconfigs: Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb --- ...er-20.11-fosscuda-2020b-AmberTools-21.3.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb new file mode 100644 index 0000000000..5a6f3ea50d --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb @@ -0,0 +1,61 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 21 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 11) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', +] +checksums = [ + 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # mpi4py required for MMPBSA + ('Perl', '5.32.0'), + ('Boost', '1.74.0'), + ('libreadline', '8.0'), + ('matplotlib', '3.3.3'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.2'), + ('Tkinter', '3.8.6'), + ('X11', '20201008'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), +] + +# Some CUDA tests differs from expected results +runtest = False + +static = False + +moduleclass = 'chem' From 2d853a333cc9409a99e31b8f67191433f9ff5dcc Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 17 Jun 2021 09:59:38 +0200 Subject: [PATCH 1134/2365] IOR: Adds headers --- easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb index aae6519b94..da2da4d12f 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb @@ -1,3 +1,6 @@ +## +# Author: Robert Mijakovic +## easyblock = 'ConfigureMake' name = "IOR" From 129819196127da88078c133a93603273085bedf4 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 17 Jun 2021 11:47:54 +0200 Subject: [PATCH 1135/2365] IOR: removes already merged file --- .../i/IOR/IOR-3.3.0-gompi-2020b.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb deleted file mode 100644 index da2da4d12f..0000000000 --- a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2020b.eb +++ /dev/null @@ -1,28 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'ConfigureMake' - -name = "IOR" -version = "3.3.0" - -homepage = 'https://github.com/hpc/ior' -description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, - or HDF5 interfaces. """ - -toolchain = {'name': 'gompi', 'version': '2020b'} - -source_urls = [('https://github.com/hpc/ior/archive')] -sources = ['%(version)s.tar.gz'] -checksums = ['701f2167f81ef963e227d4c036c4a947a98b5642b7c14c87c8ae657849891528'] - -builddependencies = [('Autotools', '20200321')] - -preconfigopts = "./bootstrap && " - -sanity_check_paths = { - 'files': ["bin/ior"], - 'dirs': ["share"] -} - -moduleclass = 'tools' From 52571ee1ad09e766de8499a88624ab1e8ccc1e23 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Thu, 17 Jun 2021 15:07:43 +0200 Subject: [PATCH 1136/2365] adding easyconfigs: PySCF-1.7.6-foss-2020b.eb --- .../p/PySCF/PySCF-1.7.6-foss-2020b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-foss-2020b.eb b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-foss-2020b.eb new file mode 100644 index 0000000000..d83b01a813 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMakeCp' + +name = 'PySCF' +version = '1.7.6' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1805819557cf78fb5938a2141a429c74dabb3ba664b60420032584d7a876c2ab'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy, scipy + ('h5py', '3.1.0'), + ('libcint', '4.4.0'), + ('libxc', '4.3.4'), + ('XCFun', '2.1.1'), +] + +start_dir = 'pyscf/lib' + +separate_build_dir = True + +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" + +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +files_to_copy = ['pyscf'] + +sanity_check_paths = { + 'files': ['pyscf/__init__.py'], + 'dirs': ['pyscf/data', 'pyscf/lib'], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'chem' From 85f5ca3e6b7a515e6a1da0852527e24cc839fc1a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 17 Jun 2021 16:18:58 +0200 Subject: [PATCH 1137/2365] Add missing checksums --- .../easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb | 1 + .../easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb index 2881300bf9..4e64588e85 100644 --- a/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb @@ -16,6 +16,7 @@ source_urls = [ 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', ] sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'] dependencies = [ ('R', '4.0.4'), diff --git a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb index 754d7a89fe..14a33d56d5 100644 --- a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb @@ -16,6 +16,7 @@ source_urls = [ 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', ] sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'] dependencies = [ ('R', '4.0.4'), From a869b10e1deea99a0491089c157101775c128dcd Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 17 Jun 2021 16:41:24 +0200 Subject: [PATCH 1138/2365] mapDamage/2.2.1: Add missing use_pip/sanity_pip_check --- .../m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb index d640e4d3be..047f62ce97 100644 --- a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb @@ -26,4 +26,7 @@ dependencies = [ ('RcppGSL', '0.3.8', versionsuffix), ] +use_pip = True +sanity_pip_check = True + moduleclass = 'bio' From 5f8db5ab9a3880180cd01c92df702e3edcbf740d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 17 Jun 2021 18:09:41 +0200 Subject: [PATCH 1139/2365] mapDamage/2.2.1: Add missing download_dep_fail --- .../m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb index 047f62ce97..5ea38038f5 100644 --- a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb @@ -28,5 +28,6 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True moduleclass = 'bio' From 8c7d3d8e3d4381bf7cf2825e62ab8488d250c53f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 17 Jun 2021 18:51:18 +0200 Subject: [PATCH 1140/2365] inline and RcppGSL: Use https for homepage/source_urls --- .../i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb | 6 +++--- .../r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb index 4e64588e85..8f55b4abbf 100644 --- a/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb @@ -4,7 +4,7 @@ name = 'inline' version = '0.3.19' versionsuffix = '-R-%(rver)s' -homepage = 'http://cran.r-project.org/web/packages/inline' +homepage = 'https://cran.r-project.org/web/packages/inline' description = """Functionality to dynamically define R functions and S4 methods with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling conventions.""" @@ -12,8 +12,8 @@ description = """Functionality to dynamically define R functions and S4 methods toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ - 'http://cran.r-project.org/src/contrib/', - 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', ] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'] diff --git a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb index 14a33d56d5..1d6a13798f 100644 --- a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb @@ -4,7 +4,7 @@ name = 'RcppGSL' version = '0.3.8' versionsuffix = '-R-%(rver)s' -homepage = 'http://cran.r-project.org/web/packages/RcppGSL' +homepage = 'https://cran.r-project.org/web/packages/RcppGSL' description = """The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data structures and R using concepts from 'Rcpp' which is itself a package that eases the interfaces between R and C++.""" @@ -12,8 +12,8 @@ description = """The 'RcppGSL' package provides an easy-to-use interface toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ - 'http://cran.r-project.org/src/contrib/', - 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', ] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'] From 2336a23c960a39f6d27962d8b8ed9eaabeebedfa Mon Sep 17 00:00:00 2001 From: Max Voit Date: Fri, 18 Jun 2021 06:57:57 +0200 Subject: [PATCH 1141/2365] adding easyconfigs: Exonerate-2.4.0-GCC-10.2.0.eb --- .../e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..39bd452716 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [('GLib', '2.66.1')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' From 46ff486f75f8dadfba4ca9e17d5d0122a5eabd7e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 18 Jun 2021 10:36:09 +0200 Subject: [PATCH 1142/2365] Add JIT support for CUDA 11 to PyTorch 1.7.1 --- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 12289d484d..23ffcc8888 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -245,6 +245,7 @@ patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_add-jit-support-for-cuda11.patch', 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', 'PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch', 'PyTorch-1.7.1_dont-use-gpu-ccc-in-test.patch', @@ -258,6 +259,7 @@ patches = [ 'PyTorch-1.7.1_relax_precision_in_test_nn.patch', 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', 'PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch', + 'PyTorch-1.7.1_add_test_times.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz @@ -307,6 +309,8 @@ checksums = [ # PyTorch-1.7.0_increase-distributed-test-timeout.patch '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_add-jit-support-for-cuda11.patch + '7a5a6ca64196f5fe0dc954d387e188695a683cc37790da67f903c52a5dd5a1e7', # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', # PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch From 28a16358ff19710239bf095a1af219259c54d491 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 18 Jun 2021 10:51:09 +0200 Subject: [PATCH 1143/2365] Remove wrong patch --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 23ffcc8888..5b00155d13 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -259,7 +259,6 @@ patches = [ 'PyTorch-1.7.1_relax_precision_in_test_nn.patch', 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', 'PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch', - 'PyTorch-1.7.1_add_test_times.patch', ] checksums = [ 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz From bdb4f42b4e344afebdd1fcbff577c8c7bfb93dfb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Jun 2021 15:59:19 +0200 Subject: [PATCH 1144/2365] add cSEM extension to R 4.0.x + 4.1.0 easyconfigs (+ sync extension list) --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 18 ++++++ .../easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 21 +++++++ .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 18 ++++++ .../easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 21 +++++++ .../easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 59 +++++++++++++++++++ .../easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 59 +++++++++++++++++++ 6 files changed, 196 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 9bb63be795..b0565b8698 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2849,6 +2849,24 @@ exts_list = [ ('GxEScanR', '2.0.2', { 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 6b48ef208c..ec36f55ab3 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2856,6 +2856,27 @@ exts_list = [ ('semPLS', '1.0-10', { 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index af2ecce031..caaeb1ad52 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2885,6 +2885,24 @@ exts_list = [ ('GxEScanR', '2.0.2', { 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index f0b431cd09..5641d1979d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2887,6 +2887,27 @@ exts_list = [ ('semPLS', '1.0-10', { 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 83657b8665..4ef48f8b96 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2853,6 +2853,65 @@ exts_list = [ '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', ], }), + ('miceadds', '3.11-6', { + 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], + }), + ('visdat', '0.5.3', { + 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('naniar', '0.6.0', { + 'checksums': ['9c93c64f51dd8c3002c930c276ef57651e91c8db12f885a03113753c604e7e54'], + }), + ('stringdist', '0.9.6.3', { + 'checksums': ['cd6d98f982e9ae7c4154a040c3a3f959bce19abf0229d64d22efef41f85b3f1b'], + }), + ('image.binarization', '0.1.1', { + 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], + }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.10', { + 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.6.2', { + 'checksums': ['b65201c730e10b0a80d1dd788e0c370372a1f22f314f2e49ce4dc63cb3ffd992'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 545eb8a4f7..a9bf1536ef 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2864,6 +2864,65 @@ exts_list = [ '67259a76722717f29577d7a25c822a4fb9c1b5ce45699d02aa53ab0ffa1d0b2a', ], }), + ('miceadds', '3.11-6', { + 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], + }), + ('visdat', '0.5.3', { + 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('naniar', '0.6.0', { + 'checksums': ['9c93c64f51dd8c3002c930c276ef57651e91c8db12f885a03113753c604e7e54'], + }), + ('stringdist', '0.9.6.3', { + 'checksums': ['cd6d98f982e9ae7c4154a040c3a3f959bce19abf0229d64d22efef41f85b3f1b'], + }), + ('image.binarization', '0.1.1', { + 'checksums': ['f1d0c5e54b62b77249d6adf3e37b5fabec0dd6bb6a3b4a8a9c2152d59dab52b5'], + }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.10', { + 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.6.2', { + 'checksums': ['b65201c730e10b0a80d1dd788e0c370372a1f22f314f2e49ce4dc63cb3ffd992'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('progressr', '0.8.0', { + 'checksums': ['8224d397cea450d97a08ed94ecc76f6e46fd46faa89882834e71b654ba07f7d4'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From 83bce5078031a4a64f655e0335f24f28668f2b2b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 19 Jun 2021 14:43:57 +0100 Subject: [PATCH 1145/2365] adding easyconfigs: Hypre-2.21.0-fosscuda-2020b.eb and patches: Hypre-2.21.0_use-c++14-for-nvcc.patch --- .../h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..de1ee211cf --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb @@ -0,0 +1,25 @@ +name = 'Hypre' +version = '2.21.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use-c++14-for-nvcc.patch'] +checksums = [ + 'e380f914fe7efe22afc44cdf553255410dc8a02a15b2e5ebd279ba88817feaf5', # v2.21.0.tar.gz + 'e7914139e0a8b8804f22d75b135a1457849558bc57800b7845fea0f318b76bff', # Hypre-2.21.0_use-c++14-for-nvcc.patch +] + +start_dir = 'src' + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'numlib' From 08318f32855679636e356332c6b6c49ebc68d4fd Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 19 Jun 2021 18:15:09 +0200 Subject: [PATCH 1146/2365] adding easyconfigs: ABINIT-9.4.1-foss-2020b.eb --- .../a/ABINIT/ABINIT-9.4.1-foss-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-foss-2020b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-foss-2020b.eb new file mode 100644 index 0000000000..57583831e0 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.1-foss-2020b.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.4.1' + +homepage = 'https://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ec74133ef9d247cb6ad44c205675694919cf36d7f1682a9b85cae8bdecdc22a8'] + +builddependencies = [ + ('Python', '3.8.6'), +] +dependencies = [ + ('libxc', '4.3.4'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('HDF5', '1.10.7'), + ('Wannier90', '3.1.0'), +] + +# Needed due to changes in GCC10. +configopts = 'FCFLAGS="-fallow-argument-mismatch -ffree-line-length-none $FCFLAGS" ' +configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" ' + +# Ensure MPI +configopts += '--with-mpi="yes" --enable-openmp="no" ' +# configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# BLAS/Lapack from OpenBLAS +configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="${LIBLAPACK_MT}" ' + +# FFTW +configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From 6b64184ed4962d70c1a18e3305aefb2700fcf723 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 19 Jun 2021 19:12:46 +0200 Subject: [PATCH 1147/2365] add 'ninja --version' as sanity check command in Ninja easyconfigs --- easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb index 82f318c76b..afa160c101 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ninja --version"] + moduleclass = 'tools' From 9301c90a178ad912b9a18244597eae1a71e0c435 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 21 Jun 2021 09:44:24 +0200 Subject: [PATCH 1148/2365] adding easyconfigs: Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb, torchvision-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb --- ...vod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb | 46 +++++++++++++++++++ ...sion-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb | 26 +++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb new file mode 100644 index 0000000000..450a4626c5 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.22.0' +local_pt_version = '1.8.1' +versionsuffix = '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('flatbuffers', '1.12.0'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('PyTorch', local_pt_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + 'checksums': ['ed7526eeb5a9aca8a8a49a04a41a4648cb7b0a265857875fc5d6a04a739fdb37'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb new file mode 100644 index 0000000000..c07d776f19 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb @@ -0,0 +1,26 @@ +name = 'torchvision' +version = '0.9.1' +local_pytorch_version = '1.8.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['79964773729880e0eee0e6af13f336041121d4cc8491a3e2c0e5f184cac8a718'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('PyTorch', local_pytorch_version), +] + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'vis' From 5790f870ed03a47e696c745aa5602b100ef6e328 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 21 Jun 2021 11:56:42 +0100 Subject: [PATCH 1149/2365] adding easyconfigs: Seurat-4.0.3-foss-2020b-R-4.0.3.eb --- .../Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..331b937181 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb @@ -0,0 +1,60 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.0.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} + +exts_list = [ + ('spatstat.utils', '2.2-0', { + 'checksums': ['5ad87e524285621dc4ef75c941eba933d980125293ee8f2bef5b7db02f63d7ab'], + }), + ('spatstat.data', '2.1-0', { + 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], + }), + ('spatstat.geom', '2.2-0', { + 'checksums': ['70b063a7f317f531b2afb3afaedb047fce81b39ee481a4067962529d6069634c'], + }), + ('spatstat.sparse', '2.0-0', { + 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], + }), + ('spatstat.core', '2.2-0', { + 'checksums': ['0ecbc1ae688c8d4f41db3efa6253ac8db5c432ef714240d01a2b195950d65253'], + }), + ('Matrix', '1.3-4', { + 'checksums': ['ab42179d44545e99bbdf44bb6d04cab051dd2aba552b1f6edd51ed71b55f6c39'], + }), + ('SeuratObject', '4.0.2', { + 'checksums': ['64ee97a221ccaa0bbdc1890da9d3e9cf5b3b9fab037095cfb757db5bbb69cb1c'], + }), + (name, version, { + 'checksums': ['75d98696d0cee22eac5154ac26ef94accde5a5b0a140f3bdd60265322d9edfc9'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 7dfb70813a8e361dce0523162d775cd90c8b5aac Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 21 Jun 2021 13:10:38 +0200 Subject: [PATCH 1150/2365] Use """ around description. --- .../m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb index 5ea38038f5..a949307ab3 100644 --- a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb @@ -7,9 +7,9 @@ versionsuffix = '-R-%(rver)s' github_account = 'ginolhac' homepage = 'https://ginolhac.github.io/mapDamage/' -description = '''mapDamage2 is a computational framework written in Python and +description = """mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA - sequencing reads generated by Next-Generation Sequencing platforms.''' + sequencing reads generated by Next-Generation Sequencing platforms.""" toolchain = {'name': 'foss', 'version': '2020b'} From a26b6a37d6d870dd7e20eac753a511eda340abb6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 21 Jun 2021 14:17:12 +0200 Subject: [PATCH 1151/2365] Fix some more bugs --- .../easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb index 75c89f5263..65f738407c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb @@ -195,6 +195,7 @@ patches = [ '%(name)s-1.2.0_fix-findAVX.patch', '%(name)s-1.2.0_disable-tests-ppc64le.patch', '%(name)s-1.2.0_add-cuda11-support.patch', + 'PyTorch-1.3.1_add-jit-support-for-cuda11.patch', 'PyTorch-1.3.1_add-Python3.8-compat.patch', 'PyTorch-1.3.1_add-support-for-cuda11.patch', 'PyTorch-1.3.1_add-support-for-cudnn8.patch', @@ -202,6 +203,7 @@ patches = [ '%(name)s-%(version)s_fix-missing-sleef_h.patch', 'PyTorch-1.3.1_skip-nccl-error-tests.patch', '%(name)s-1.4.0_fix-missing-source-dir.patch', + 'PyTorch-1.6.0_fix-test-cuda.patch', 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', ] checksums = [ @@ -240,6 +242,8 @@ checksums = [ '001c9bf604aebe4b39ccad15332a71130b07b780c539ceca84d6c64cd6fc8a68', # PyTorch-1.2.0_fix-findAVX.patch 'c4183bcb29a8bcbadea0341e93a3a32afdf860aa31331b768e787d899183da92', # PyTorch-1.2.0_disable-tests-ppc64le.patch '5a8289ced3ea448c61b2c417bb6118cb73da67eb6b9a58ac14376c65f7151906', # PyTorch-1.2.0_add-cuda11-support.patch + # PyTorch-1.3.1_add-jit-support-for-cuda11.patch + '3dfff6835b0edeae2ad91f36ea5e9ee9dcdef82f5bf27aca27b8db98fed15939', '2a743d0fc52a6f7239e6750a7cd59148417546b45a0b10ad1a15e526b94c4434', # PyTorch-1.3.1_add-Python3.8-compat.patch 'e379846cb0bccb7e6143bf21b1fa517771842c7ca165cb35d60e507edd38b6ce', # PyTorch-1.3.1_add-support-for-cuda11.patch '2560bf24f40aa981c9d3802313b67c4d2378082a9fdd919c499de10793da7e64', # PyTorch-1.3.1_add-support-for-cudnn8.patch @@ -247,6 +251,7 @@ checksums = [ '1337647ff64a1208d1e401fc84052d0bc6174b133cec2f3521319cb593f524fa', # PyTorch-1.3.1_fix-missing-sleef_h.patch '5743ac23a0d0f40373baeb026bb5656a84ca1417fcce10be8370ec3f4c9e80a6', # PyTorch-1.3.1_skip-nccl-error-tests.patch '797987fb9c9bf9f1d75a1be878ddf9f418f9524006b0985ca8e6d65d4e2b6998', # PyTorch-1.4.0_fix-missing-source-dir.patch + 'adf21e77dbc5e60fd46fe21fceb908633b0da7d4fc9b6a3ea7f7cfb0c4a44678', # PyTorch-1.6.0_fix-test-cuda.patch # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', ] @@ -280,8 +285,6 @@ cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7 excluded_tests = { '': [ - # SEGV - 'autograd', # https://github.com/pytorch/pytorch/issues/42498 'cpp_extensions', # Precision issues. Maybe actual failures or "just" the new cuDNN From a0a7397d30553b2291926b87088da53db81446c6 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 21 Jun 2021 16:05:05 +0200 Subject: [PATCH 1152/2365] adding easyconfigs: Octave-6.2.0-foss-2020b.eb, GL2PS-1.4.2-GCCcore-10.2.0.eb, Qhull-2020.2-GCCcore-10.2.0.eb, qrupdate-1.1.2-GCCcore-10.2.0.eb, GraphicsMagick-1.3.36-foss-2020b.eb --- .../g/GL2PS/GL2PS-1.4.2-GCCcore-10.2.0.eb | 34 ++++++++ .../GraphicsMagick-1.3.36-foss-2020b.eb | 48 ++++++++++++ .../o/Octave/Octave-6.2.0-foss-2020b.eb | 78 +++++++++++++++++++ .../q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb | 46 +++++++++++ .../qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb | 35 +++++++++ 5 files changed, 241 insertions(+) create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..173f65d0fc --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('freeglut', '3.2.1'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb new file mode 100644 index 0000000000..da19daca51 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.36' + +homepage = 'https://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] +patches = [ + 'GraphicsMagick_pkgconfig_libtiff.patch' +] +checksums = [ + '1e6723c48c4abbb31197fadf8396b2d579d97e197123edc70a4f057f0533d563', # GraphicsMagick-1.3.36.tar.gz + '25b4c5361f30e23c809a078ac4b26e670d2b8341496323480037e2095d969294', # GraphicsMagick_pkgconfig_libtiff.patch +] + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('X11', '20201008'), + ('bzip2', '1.0.8'), + ('freetype', '2.10.3'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('LibTIFF', '4.1.0'), + ('libxml2', '2.9.10'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('Ghostscript', '9.53.3'), +] + +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + +sanity_check_paths = { + 'files': ['bin/gm', 'lib/libGraphicsMagick.a', 'lib/libGraphicsMagick++.a', + 'lib/libGraphicsMagickWand.a'], + 'dirs': ['include/GraphicsMagick', 'lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb new file mode 100644 index 0000000000..3da5bd86b4 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb @@ -0,0 +1,78 @@ +name = 'Octave' +version = '6.2.0' + +homepage = 'https://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['457d1fda8634a839e2fd7cfc55b98bd56f36b6ae73d31bb9df43dde3012caa7c'] + +builddependencies = [ + ('Bison', '3.7.1'), + ('flex', '2.6.4'), + ('Autotools', '20200321'), + ('gperf', '3.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20201008'), + ('PCRE', '8.44'), + ('ncurses', '6.2'), + ('libreadline', '8.0'), + ('arpack-ng', '3.8.0'), + ('cURL', '7.72.0'), + ('FLTK', '1.3.5'), + ('fontconfig', '2.13.92'), + ('freetype', '2.10.3'), + ('GLPK', '4.65'), + ('GL2PS', '1.4.2'), + ('gnuplot', '5.4.1'), + ('Java', '11', '', True), + ('zlib', '1.2.11'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('Qhull', '2020.2'), + ('Qt5', '5.14.2'), + ('HDF5', '1.10.7'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('texinfo', '6.7'), + ('libsndfile', '1.0.28'), + ('GraphicsMagick', '1.3.36'), +] + +configopts = '--disable-docs ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' + +local_pkg_url = 'https://downloads.sourceforge.net/' +local_pkg_url += 'project/octave/Octave%20Forge%20Packages/Individual%20Package%20Releases/' +exts_default_options = {'source_urls': [local_pkg_url]} + +exts_list = [ + ('control', '3.2.0', { + 'checksums': ['faf1d510d16ab46e4fa91a1288f4a7839ee05469c33e4698b7a007a0bb965e3e'], + }), + ('general', '2.1.1', { + 'checksums': ['fbd09409950c8b95e02ccb3895ec78f52cc8589a08a65d8c512a7cacf567bb4a'], + }), + ('io', '2.6.3', { + 'checksums': ['6bc63c6498d79cada01a6c4446f793536e0bb416ddec2a5201dd8d741d459e10'], + }), + ('signal', '1.4.1', { + 'checksums': ['d978600f8b8f61339b986136c9862cad3e8f7015f84132f214bf63e9e281aeaa'], + }), + ('statistics', '1.4.2', { + 'checksums': ['7976814f837508e70367548bfb0a6d30aa9e447d4e3a66914d069efb07876247'], + }), + ('struct', '1.0.17', { + 'checksums': ['0137bbb5df650f29104f6243502f3a2302aaaa5e42ea9f02d8a3943aaf668433'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7f4aaf8b6b --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +#patches = [ +# 'Qhull_pkgconfig.patch', +#] +checksums = [ + 'b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e', # qhull-2020-src-8.0.2.tgz +# 'b87d9aeff9fc4d4d1e31924fa486f94b6e1d6221a2b38dfa989991c4ad2bbc74', # Qhull_pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..81525546aa --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makeconf.patch'] +checksums = [ + 'e2a1c711dc8ebc418e21195833814cb2f84b878b90a2774365f0166402308e08', # qrupdate-1.1.2.tar.gz + '4aa0e61a18bd14c76048f7b2f1f52875f7bac4bc3426ce9a37dfdb5b2b0d2379', # qrupdate-1.1.2_makeconf.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' From 5a46623a89945d5e3a3f425413aaae604e2bbee0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Jun 2021 18:16:30 +0200 Subject: [PATCH 1153/2365] add libtirpc dep --- easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb index 53ec1b1698..ad23693077 100644 --- a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb @@ -16,7 +16,10 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['campari_v%s_%s.zip' % (version.split('.')[0], _date)] checksums = ['bc627fb286b5461a5c68aa3e1a551ecd81016495163685800163c734f7c4f1bd'] -dependencies = [('netCDF-Fortran', '4.5.3')] +dependencies = [ + ('netCDF-Fortran', '4.5.3'), + ('libtirpc', '1.3.1'), +] start_dir = 'source' From ab81a2c8e77923a9e42e498f761d1c2b485fd778 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Jun 2021 18:22:08 +0200 Subject: [PATCH 1154/2365] fix draft stuff --- .../molecularGSM-20190826-intel-2020b.eb | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb index e7ef463af9..ce073ff093 100644 --- a/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb +++ b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb @@ -38,22 +38,19 @@ checksums = [ builddependencies = [('CMake', '3.18.4')] -# parallel = 1 - configopts = [ - # '', # default is MOPAC - # '-DGSM_ENABLE_QCHEM=1', - # '-DGSM_ENABLE_QCHEM_SF=1', - # '-DGSM_ENABLE_ORCA=1', + '', # default is MOPAC + '-DGSM_ENABLE_QCHEM=1', + '-DGSM_ENABLE_QCHEM_SF=1', + '-DGSM_ENABLE_ORCA=1', '-DGSM_ENABLE_GAUSSIAN=1', - # '-DGSM_ENABLE_MOLPRO=1', - # '-DGSM_ENABLE_ASE=1', + '-DGSM_ENABLE_MOLPRO=1', + '-DGSM_ENABLE_ASE=1', ] install_cmd = 'mkdir -p %(installdir)s/bin && cp -a GSM/*.exe %(installdir)s/bin/' -# _bins = ['ase', 'gaussian', 'molpro', 'mopac', 'orca', 'qchem', 'qchem_sf'] -_bins = ['gaussian'] +_bins = ['ase', 'gaussian', 'molpro', 'mopac', 'orca', 'qchem', 'qchem_sf'] sanity_check_paths = { 'files': ['bin/gsm.%s.exe' % x for x in _bins], From 1c3c7e907562ac3aad79c2fa7cc6c7e1bdc375be Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 21 Jun 2021 18:31:29 +0200 Subject: [PATCH 1155/2365] adding easyconfigs: PETSc-3.14.4-intel-2020b.eb --- .../p/PETSc/PETSc-3.14.4-intel-2020b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-intel-2020b.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-intel-2020b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-intel-2020b.eb new file mode 100644 index 0000000000..5e792a3e97 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-intel-2020b.eb @@ -0,0 +1,47 @@ +name = 'PETSc' +version = '3.14.4' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + '2fb431434b91e054cc3a176f7cb008951088243b5dcb3efc8eec8ce589a2658e', # petsc-3.14.4.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('MUMPS', '5.3.5', '-metis'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('Hypre', '2.20.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' From f92a6605c8f22c41dfa29740caef79d0ccabb8af Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 22 Jun 2021 09:50:30 +0200 Subject: [PATCH 1156/2365] add libtirpc link flags --- easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb index ad23693077..8ce474d08a 100644 --- a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb @@ -23,9 +23,9 @@ dependencies = [ start_dir = 'source' -configopts = '--enable-mpi=auto LIBS="$LIBS $LIBFFT"' +configopts = '--enable-mpi=auto LIBS="$LIBS $LIBFFT -ltirpc"' -buildopts = 'all LIBS="$LIBS $LIBFFT"' +buildopts = 'all LIBS="$LIBS $LIBFFT -ltirpc"' maxparallel = 10 From 0d81a1ba6f2836104d4f07ab1d4dc182e8ea3053 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Tue, 22 Jun 2021 11:51:15 +0200 Subject: [PATCH 1157/2365] adding easyconfigs: CubeWriter-4.6-GCCcore-10.2.0.eb, CubeLib-4.6-GCCcore-10.2.0.eb, CubeGUI-4.6-GCCcore-10.2.0.eb --- .../c/CubeGUI/CubeGUI-4.6-GCCcore-10.2.0.eb | 53 ++++++++++++++++++ .../c/CubeLib/CubeLib-4.6-GCCcore-10.2.0.eb | 56 +++++++++++++++++++ .../CubeWriter-4.6-GCCcore-10.2.0.eb | 55 ++++++++++++++++++ 3 files changed, 164 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..99955038a6 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeGUI' +version = '4.6' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube graphical report explorer. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '1871c6736121d94a22314cb5daa8f3cbb978b58bfe54f677c4c9c9693757d0c5', # cubegui-4.6.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.35'), + ('CubeLib', '4.6'), +] + +dependencies = [ + ('Qt5', '5.14.2'), +] + +sanity_check_paths = { + 'files': ['bin/cube', 'bin/cubegui-config', + 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], + 'dirs': ['include/cubegui', 'lib/cube-plugins'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a669ee8b3f --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.2.0.eb @@ -0,0 +1,56 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.6' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '36eaffa7688db8b9304c9e48ca5dc4edc2cb66538aaf48657b9b5ccd7979385b', # cubelib-4.4.4.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2d3fc4b8b4 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.2.0.eb @@ -0,0 +1,55 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.6' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = [ + '99fe58ce7ab13061ebfbc360aedaecc28099a30636c5269a42c0cbaf57149aa8', # cubew-4.6.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' From ede50086ba00fb30d5b5dcbbcbceb2b71cc88970 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Tue, 22 Jun 2021 12:03:45 +0200 Subject: [PATCH 1158/2365] adding easyconfigs: datamash-1.5-GCCcore-10.2.0.eb --- .../d/datamash/datamash-1.5-GCCcore-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100755 easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb new file mode 100755 index 0000000000..cfb866c453 --- /dev/null +++ b/easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'datamash' +version = '1.5' + +homepage = 'https://www.gnu.org/software/datamash/' +description = "GNU datamash performs basic numeric, textual and statistical operations on input data files" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['226249d5fe54024f96404798778f45963a3041714229d4225cd5d9acdaba21ad'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/datamash'], + 'dirs': ['share/man'] +} + +moduleclass = 'data' From c4b9736c134eaf1d5d513ed28b70af784befe97a Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Tue, 22 Jun 2021 12:06:40 +0200 Subject: [PATCH 1159/2365] adding easyconfigs: HDF-EOS-2.20-GCCcore-10.2.0.eb, HDF-EOS-2.20-GCCcore-10.2.0.eb, h4toh5-2.2.3-gompi-2020b.eb --- .../h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ .../h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb | 29 ++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb diff --git a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6f42eeb5aa --- /dev/null +++ b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'HDF-EOS' +version = '2.20' + +homepage = 'https://hdfeos.org/' +description = """HDF-EOS libraries are software libraries built on HDF libraries. + It supports three data structures for remote sensing data: Grid, Point and Swath.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos/latest_release/', + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos/previous_releases/', +] + +sources = ['%(name)s%(version)sv1.00.tar.Z'] + +checksums = ['cb0f900d2732ab01e51284d6c9e90d0e852d61bba9bce3b43af0430ab5414903'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('HDF', '4.2.15'), + ('Szip', '2.1.1'), +] + +preconfigopts = 'export CC="$EBROOTHDF/bin/h4cc -Df2cFortran" && ' + +configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" + +sanity_check_paths = { + 'files': ['include/HdfEosDef.h', 'include/HDFEOSVersion.h', 'lib/libGctp.a', 'lib/libhdfeos.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb new file mode 100644 index 0000000000..8e8e8c7f70 --- /dev/null +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'h4toh5' +version = '2.2.3' + +homepage = 'http://www.hdfgroup.org/h4toh5/' +description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, + as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] + +dependencies = [ + ('HDF', '4.2.15'), + ('HDF5', '1.10.7'), + ('HDF-EOS', '2.20'), +] + +configopts = "CC=$EBROOTHDF/bin/h4cc --with-hdf5=$EBROOTHDF5 --with-hdfeos2=$EBROOTHDFMINEOS " + +sanity_check_paths = { + 'files': ['bin/h4toh5', 'bin/h5toh4', 'include/h4toh5.h', 'lib/libh4toh5.a'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'data' From a4adb019675563a5c5fbf386beee4ff1879baa14 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Tue, 22 Jun 2021 12:18:51 +0200 Subject: [PATCH 1160/2365] added HDF-EOS5-1.16-gompi-2020b.eb --- .../h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb diff --git a/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb new file mode 100644 index 0000000000..20f1019fff --- /dev/null +++ b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'HDF-EOS5' +version = '1.16' + +homepage = 'https://hdfeos.org/' +description = """HDF-EOS libraries are software libraries built on HDF libraries. + It supports three data structures for remote sensing data: Grid, Point and Swath.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos5/latest_release/', + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos5/previous_releases/', +] + +sources = ['%(name)s.%(version)s.tar.Z'] + +checksums = ['7054de24b90b6d9533329ef8dc89912c5227c83fb447792103279364e13dd452'] + +dependencies = [ + ('HDF5', '1.10.7'), + ('Szip', '2.1.1'), +] + +preconfigopts = 'export CC="$EBROOTHDF5/bin/h5pcc -Df2cFortran" && ' + +configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" + +sanity_check_paths = { + 'files': ['include/HE5_HdfEosDef.h', 'include/HE5_GctpFunc.h', 'lib/libGctp.a', 'lib/libhe5_hdfeos.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' From 81e019fd5c01735eeb0d5c5fc187d8c57cbeebed Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 22 Jun 2021 16:53:44 +0200 Subject: [PATCH 1161/2365] adding easyconfigs: PyTorch-1.9.0-foss-2020b.eb, PyTorch-1.9.0-fosscuda-2020b.eb and patches: PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch, PyTorch-1.9.0_fix-testnn-on-A100.patch, PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch, PyTorch-1.9.0_fix-vsx-vector-functions.patch, PyTorch-1.9.0_increase_test_cuda_tolerance.patch, PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch, PyTorch-1.9.0_limit_world_size_for_zero_redundancy_opt_test.patch, PyTorch-1.9.0_skip-nccl-error-tests.patch --- .../p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 89 +++++++++++++ .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 118 ++++++++++++++++++ 2 files changed, 207 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb new file mode 100644 index 0000000000..8dd7b6ca99 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -0,0 +1,89 @@ +name = 'PyTorch' +version = '1.9.0' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', + 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + # PyTorch-1.8.1_dont-sync-gpu-for-cpu-test.patch + 'a5bc86837c59a36d59311be9cbd0c6d86ea6be235c2a7ffb400b89c758b28490', + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch + 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', + '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), +] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..8a44a2c5db --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -0,0 +1,118 @@ +name = 'PyTorch' +version = '1.9.0' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', + 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', + 'PyTorch-1.9.0_fix-testnn-on-A100.patch', + 'PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.9.0_increase_test_cuda_tolerance.patch', + 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', + 'PyTorch-1.9.0_limit_world_size_for_zero_redundancy_opt_test.patch', + 'PyTorch-1.9.0_skip-nccl-error-tests.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch + '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', + # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch + 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', + '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch + # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch + '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', + '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + # PyTorch-1.9.0_increase_test_cuda_tolerance.patch + '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', + # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch + '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', + # PyTorch-1.9.0_limit_world_size_for_zero_redundancy_opt_test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From dd05674e42c0142a07a6d98d8eac8db1bd67861b Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 22 Jun 2021 08:58:49 -0700 Subject: [PATCH 1162/2365] {data}[GCCcore/10.2.0] bsddb3 6.9 --- .../b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d6c4183a15 --- /dev/null +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'bsddb3' +version = '6.2.9' + +homepage = 'https://pypi.org/project/bsddb3/' +description = """bsddb3 is a nearly complete Python binding of the +Oracle/Sleepycat C API for the Database Environment, Database, Cursor, +Log Cursor, Sequence and Transaction objects.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['70d05ec8dc568f42e70fc919a442e0daadc2a905a1cfb7ca77f549d49d6e7801'] + +osdependencies = [('libdb-dev', 'libdb-devel')] + +builddependencies = [('binutils', '2.35')] +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True + +# Need to unset LIBS or pip install crashes. +preinstallopts = 'unset LIBS && ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' From 233e4e139a837812ad5126ee518da7d04ac208e7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 22 Jun 2021 18:38:33 +0100 Subject: [PATCH 1163/2365] adding easyconfigs: PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb, imageio-2.9.0-fosscuda-2020b.eb --- .../i/imageio/imageio-2.9.0-fosscuda-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..a67dbeea4c --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.9.0' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 88b01c45345dca89248f56d4a9cbe9621305a5c4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 23 Jun 2021 08:42:09 +0200 Subject: [PATCH 1164/2365] Mark test_lstm as xfail --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 8dd7b6ca99..2d760bbcaf 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -27,6 +27,7 @@ patches = [ 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.9.0_mark_lstm_serialization_test_as_xfail.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -46,6 +47,8 @@ checksums = [ # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + # PyTorch-1.9.0_mark_lstm_serialization_test_as_xfail.patch + 'b91e587f6391bb27b439a5b4050f6f014a8019abf703b0481c93eb40e2e76cfb', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index 8a44a2c5db..6c8a1c3fbc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -34,6 +34,7 @@ patches = [ 'PyTorch-1.9.0_increase_test_cuda_tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', 'PyTorch-1.9.0_limit_world_size_for_zero_redundancy_opt_test.patch', + 'PyTorch-1.9.0_mark_lstm_serialization_test_as_xfail.patch', 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] checksums = [ @@ -66,6 +67,8 @@ checksums = [ '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', # PyTorch-1.9.0_limit_world_size_for_zero_redundancy_opt_test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.9.0_mark_lstm_serialization_test_as_xfail.patch + 'b91e587f6391bb27b439a5b4050f6f014a8019abf703b0481c93eb40e2e76cfb', '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch ] From bfdeafa9b6be5b043b8fd4382dfcb4d434db795f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 23 Jun 2021 09:56:08 +0200 Subject: [PATCH 1165/2365] Add device patch and fix patch naming --- .../p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 4 ++-- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 15 +++++++++------ 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 2d760bbcaf..3869b3f9a2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -27,7 +27,7 @@ patches = [ 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', - 'PyTorch-1.9.0_mark_lstm_serialization_test_as_xfail.patch', + 'PyTorch-1.9.0_mark-lstm-serialization-test-as-xfail.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -47,7 +47,7 @@ checksums = [ # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch - # PyTorch-1.9.0_mark_lstm_serialization_test_as_xfail.patch + # PyTorch-1.9.0_mark-lstm-serialization-test-as-xfail.patch 'b91e587f6391bb27b439a5b4050f6f014a8019abf703b0481c93eb40e2e76cfb', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index 6c8a1c3fbc..5abc2728a8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -28,13 +28,14 @@ patches = [ 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', + 'PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch', 'PyTorch-1.9.0_fix-testnn-on-A100.patch', 'PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', - 'PyTorch-1.9.0_increase_test_cuda_tolerance.patch', + 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', - 'PyTorch-1.9.0_limit_world_size_for_zero_redundancy_opt_test.patch', - 'PyTorch-1.9.0_mark_lstm_serialization_test_as_xfail.patch', + 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.9.0_mark-lstm-serialization-test-as-xfail.patch', 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] checksums = [ @@ -57,17 +58,19 @@ checksums = [ '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', + # PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch + 'edb180d6967c507c147400a64422ff4499bcd5519f9be8d332890c317359dbad', '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch - # PyTorch-1.9.0_increase_test_cuda_tolerance.patch + # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', - # PyTorch-1.9.0_limit_world_size_for_zero_redundancy_opt_test.patch + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.9.0_mark_lstm_serialization_test_as_xfail.patch + # PyTorch-1.9.0_mark-lstm-serialization-test-as-xfail.patch 'b91e587f6391bb27b439a5b4050f6f014a8019abf703b0481c93eb40e2e76cfb', '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch ] From 6513a78d09b003bdc058fcbb2c2670f8db6446f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Jun 2021 11:06:39 +0200 Subject: [PATCH 1166/2365] adding easyconfigs: FDS-6.7.6-intel-2020b.eb --- .../f/FDS/FDS-6.7.6-intel-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.7.6-intel-2020b.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.7.6-intel-2020b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.7.6-intel-2020b.eb new file mode 100644 index 0000000000..9b15ca6c7b --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.7.6-intel-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.7.6' + +homepage = 'https://pages.nist.gov/fds-smv' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS%(version)s.tar.gz'] +checksums = ['33432cc31d9f75d3904c2b89f197016bb5c73d6b108878d804ebf055d3cafdc1'] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'impi_intel_linux_64 FFLAGS="$FFLAGS -fpp" FCOMPL="$FC" obj=fds' + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { + 'files': ['Build/fds'], + 'dirs': [], +} + +sanity_check_commands = [ + "fds 2>&1 | grep 'MPI Enabled;'", + "fds 2>&1 | grep 'OpenMP Enabled;'", +] + +moduleclass = 'phys' From e46c3f3584ac1c0e116dc9b2cdfb40506b992f6e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 23 Jun 2021 15:37:39 +0200 Subject: [PATCH 1167/2365] functional crispr-dav --- .../a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb | 48 +++++++++ .../f/FLASH/FLASH-2.2.00-foss-2020b.eb | 28 ++++++ .../PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb | 99 +++++++++++++++++++ 3 files changed, 175 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb new file mode 100644 index 0000000000..734e544fc9 --- /dev/null +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'ABRA2' +version = '2.23' + +homepage = 'https://github.com/mozack/abra2' +description = "Assembly Based ReAligner" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/mozack/abra2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ABRA2-2.22_fix-Makefile.patch'] +checksums = [ + '3993f66a493070ee49df2865b6786a45a0cf6c379bae83e94b8339abbe673289', # v2.23.tar.gz + '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch +] + +builddependencies = [('Maven', '3.6.3', '', True)] + +dependencies = [ + ('Java', '11', '', True), + ('BWA', '0.7.17'), +] + +parallel = 1 + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' +buildopts += '&& make standalone CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +files_to_copy = [ + (['abra'], 'bin'), + (['target/libAbra.%s' % SHLIB_EXT], 'lib'), + 'target/abra2-%(version)s-jar-with-dependencies.jar', +] + +postinstallcmds = ["cd %(installdir)s && mv abra2-%(version)s-jar-with-dependencies.jar abra2-%(version)s.jar"] + +sanity_check_paths = { + 'files': ['abra2-%(version)s.jar', 'bin/abra', 'lib/libAbra.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextravars = { + "LC_ALL": "en_US.UTF-8", +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb new file mode 100644 index 0000000000..da47c15d06 --- /dev/null +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'FLASH' +version = '2.2.00' + +homepage = 'https://ccb.jhu.edu/software/FLASH/' +description = """FLASH (Fast Length Adjustment of SHort reads) is a very fast +and accurate software tool to merge paired-end reads from next-generation +sequencing experiments. FLASH is designed to merge pairs of reads when the +original DNA fragments are shorter than twice the length of reads. The +resulting longer reads can significantly improve genome assemblies. They can +also improve transcriptome assembly when FLASH is used to merge RNA-seq data. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/dstreett/FLASH2/archive/'] +sources = ['%(version)s.zip'] +checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] + +files_to_copy = [(['flash2'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/flash2'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb new file mode 100644 index 0000000000..c7576441ae --- /dev/null +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb @@ -0,0 +1,99 @@ +# author: Denis Kristak + +easyblock = 'Tarball' + +name = 'PRINSEQ' +version = '0.20.4' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://prinseq.sourceforge.net' +description = """A bioinformatics tool to PRe-process and show INformation of SEQuence data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] +sources = ['%(namelower)s-lite-%(version)s.tar.gz'] +checksums = ['9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f'] + +dependencies = [ + ('Perl', '5.32.0'), + ('cairo', '1.16.0'), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::Depends', '0.8001', { + 'source_tmpl': 'ExtUtils-Depends-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['673c4387e7896c1a216099c1fbb3faaa7763d7f5f95a1a56a60a2a2906c131c5'], + }), + ('ExtUtils::PkgConfig', '1.16', { + 'source_tmpl': 'ExtUtils-PkgConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], + }), + ('Pod::Usage', '2.0', { + 'source_tmpl': 'Pod-Usage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + 'checksums': ['530943a9ac3ba00404d7be8ee8572f30f6db9de123cd725af3647333a87d4fea'], + }), + ('Cairo', '1.109', { + 'source_tmpl': 'Cairo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['8219736e401c2311da5f515775de43fd87e6384b504da36a192f2b217643077f'], + }), + ('Statistics::PCA', '0.0.1', { + 'source_tmpl': 'Statistics-PCA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSTH/'], + 'checksums': ['f8adb10b00232123d103a5b49161ad46370f47fe0f752e5462a4dc15f9d46bc4'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + 'checksums': ['7f863566a6a9cb93eda93beadb77d9aa04b9304d769cea3bb921b9a91b3a1eb9'], + }), + ('Math::Cephes::Matrix', '0.5305', { + 'source_tmpl': 'Math-Cephes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['561a800a4822e748d2befc366baa4b21e879a40cc00c22293c7b8736caeb83a1'], + }), + ('Math::MatrixReal', '2.13', { + 'source_tmpl': 'Math-MatrixReal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LETO/'], + 'checksums': ['4f9fa1a46dd34d2225de461d9a4ed86932cdd821c121fa501a15a6d4302fb4b2'], + }), + ('Text::SimpleTable', '2.07', { + 'source_tmpl': 'Text-SimpleTable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRAMBERG/'], + 'checksums': ['256d3f38764e96333158b14ab18257b92f3155c60d658cafb80389f72f4619ed'], + }), + ('Contextual::Return', '0.2.1', { + 'source_tmpl': 'Contextual-Return-v%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], + 'checksums': ['17a1ed1043a2abe123920894d6023709e834de66ef766be86e4cfbb96b1dd16c'], + }), +] + +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +postinstallcmds = [ + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", + "chmod +x %(installdir)s/*.pl", +] + +sanity_check_paths = { + 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], + 'dirs': [] +} + + +moduleclass = 'bio' From 2b09905c0e40317dc99d8bafe10e191b2899da6b Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Wed, 23 Jun 2021 15:45:31 +0200 Subject: [PATCH 1168/2365] adding easyconfigs: RagTag-2.0.1-foss-2020b.eb --- .../r/RagTag/RagTag-2.0.1-foss-2020b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb b/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb new file mode 100644 index 0000000000..72d2449db4 --- /dev/null +++ b/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonPackage' + +name = 'RagTag' +version = '2.0.1' + +homepage = 'https://github.com/malonge/RagTag' +description = """RagTag is a collection of software tools for scaffolding and +improving modern genome assemblies. Tasks include: homology-based misassembly +correction, homology-based assembly scaffolding and patching, and scaffold +merging. RagTag also provides command line utilities for working with common +genome assembly file formats.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/malonge/RagTag/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ragtag-2.0.1-scripts.patch'] +checksums = [ + 'fc3022d744cabdc2f492c0aa353af7c07fc71efd1b07c5ca5d333601868862c4', # v2.0.1.tar.gz + '01d1623fade21fb838904334fc2afc93351e66241c612939c619714658f43687', # ragtag-2.0.1-scripts.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Pysam', '0.16.0.1'), + ('networkx', '2.5'), + ('MUMmer', '4.0.0beta2'), + # Minimap2, Unimap, or Nucmer (via MUMmer?) try installing all 3? +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/ragtag.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['ragtag.py updategff --help'] + +options = {'modulename': 'ragtag_utilities'} + +moduleclass = 'bio' From 817846e2e9777d46cc5b94fd5a468db78de8a51c Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Wed, 23 Jun 2021 16:01:36 +0200 Subject: [PATCH 1169/2365] RagTag: add unimap --- .../r/RagTag/RagTag-2.0.1-foss-2020b.eb | 11 ++++- .../u/unimap/unimap-0.1-GCCcore-10.2.0.eb | 42 +++++++++++++++++++ 2 files changed, 51 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb b/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb index 72d2449db4..df5c5723b8 100644 --- a/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb @@ -26,7 +26,8 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('networkx', '2.5'), ('MUMmer', '4.0.0beta2'), - # Minimap2, Unimap, or Nucmer (via MUMmer?) try installing all 3? + ('minimap2', '2.20'), + ('unimap', '0.1'), ] download_dep_fail = True @@ -37,7 +38,13 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ['ragtag.py updategff --help'] +sanity_check_commands = [ + 'ragtag.py updategff --help', + # Ragtag exec()s these commands + 'nucmer --help', + 'minimap2 --help', + 'unimap --help', +] options = {'modulename': 'ragtag_utilities'} diff --git a/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c03b77d5db --- /dev/null +++ b/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'unimap' +version = '0.1' + +homepage = 'https://github.com/lh3/unimap' +description = """Unimap is a fork of minimap2 optimized for assembly-to-reference +alignment. It integrates the minigraph chaining algorithm and can align through +long INDELs (up to 100kb by default) much faster than minimap2. Unimap is a +better fit for resolving segmental duplications and is recommended over minimap2 +for alignment between high-quality assemblies. + +Unimap does not replace minimap2 for other types of alignment. It drops the +support of multi-part index and short-read mapping. Its long-read alignment is +different from minimap2 but is not necessarily better. Unimap is more of a +specialized minimap2 at the moment.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/lh3/unimap/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d5d7831e1fa78c943a96ef78ba22ec88eebf39368bdb135c30554f052f0dbc5c'] + +builddependencies = [('binutils', '2.35')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "unimap --help", + "cd %(builddir)s/unimap-%(version)s && unimap -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' From 09907bb036443f2c5d9f41428c6c3001de9ffc7f Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Wed, 23 Jun 2021 16:16:05 +0200 Subject: [PATCH 1170/2365] RagTag: downgrade minimap2 to pass tests --- easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb b/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb index df5c5723b8..fa1a05370a 100644 --- a/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb @@ -26,12 +26,13 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('networkx', '2.5'), ('MUMmer', '4.0.0beta2'), - ('minimap2', '2.20'), + ('minimap2', '2.18'), ('unimap', '0.1'), ] download_dep_fail = True use_pip = True +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/ragtag.py'], From 8bb6ad3c66f279d4f75982e064dffd208dd46039 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 24 Jun 2021 10:35:35 +0200 Subject: [PATCH 1171/2365] Move xfail mark --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 2 +- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 3869b3f9a2..371976b5c9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -48,7 +48,7 @@ checksums = [ 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_mark-lstm-serialization-test-as-xfail.patch - 'b91e587f6391bb27b439a5b4050f6f014a8019abf703b0481c93eb40e2e76cfb', + '56304b2a98b253f3ffa6e2cbc6d43cc6febf19bea8ce68355b8d072bdb9a60d1', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index 5abc2728a8..98289b27cc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -71,7 +71,7 @@ checksums = [ # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', # PyTorch-1.9.0_mark-lstm-serialization-test-as-xfail.patch - 'b91e587f6391bb27b439a5b4050f6f014a8019abf703b0481c93eb40e2e76cfb', + '56304b2a98b253f3ffa6e2cbc6d43cc6febf19bea8ce68355b8d072bdb9a60d1', '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch ] From b1309e1f410b435905971f0afe2d8a70a59f82d3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 24 Jun 2021 12:25:34 +0200 Subject: [PATCH 1172/2365] Skip lstm test for good --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 371976b5c9..d614502526 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -27,7 +27,7 @@ patches = [ 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', - 'PyTorch-1.9.0_mark-lstm-serialization-test-as-xfail.patch', + 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -47,8 +47,8 @@ checksums = [ # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch - # PyTorch-1.9.0_mark-lstm-serialization-test-as-xfail.patch - '56304b2a98b253f3ffa6e2cbc6d43cc6febf19bea8ce68355b8d072bdb9a60d1', + # PyTorch-1.9.0_skip-lstm-serialization-test.patch + '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', ] osdependencies = [OS_PKG_IBVERBS_DEV] From 8ca2068761941c1814646a48fe04590fe82df1fe Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 24 Jun 2021 12:30:48 +0200 Subject: [PATCH 1173/2365] Skip lstm test for good --- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index 98289b27cc..ede9dfd996 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -35,7 +35,7 @@ patches = [ 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.9.0_mark-lstm-serialization-test-as-xfail.patch', + 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] checksums = [ @@ -70,8 +70,8 @@ checksums = [ '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.9.0_mark-lstm-serialization-test-as-xfail.patch - '56304b2a98b253f3ffa6e2cbc6d43cc6febf19bea8ce68355b8d072bdb9a60d1', + # PyTorch-1.9.0_skip-lstm-serialization-test.patch + '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch ] From 6568388c011f06f319570a369140c477cdd256bf Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 25 Jun 2021 11:19:15 +0200 Subject: [PATCH 1174/2365] SentencePiece: bumps version --- .../SentencePiece-0.1.96-GCC-10.2.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb new file mode 100644 index 0000000000..3e5db3aca3 --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.1.96' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('gperftools', '2.9.1'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['1c0bd83e03f71a10fc934b7ce996e327488b838587f03159fd392c77c7701389'], +} + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'separate_build_dir': True, + 'start_dir': '%(namelower)s-%(version)s', + }), + ('sentencepiece', version, { + 'easyblock': 'PythonPackage', + 'start_dir': '%(namelower)s-%(version)s/python', + 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] + +sanity_check_paths = { + 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + + ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + + ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], +} + +sanity_check_commands = [ + 'spm_train --help', + "python -c 'import sentencepiece'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'lib' From 59c96864a954f4ca20751c955149a312ad90abad Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 25 Jun 2021 13:28:02 +0200 Subject: [PATCH 1175/2365] SentencePiece: fixes checksum --- .../s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb index 3e5db3aca3..c578663248 100644 --- a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb @@ -24,7 +24,7 @@ dependencies = [ default_component_specs = { 'source_urls': [GITHUB_LOWER_SOURCE], 'sources': ['v%(version)s.tar.gz'], - 'checksums': ['1c0bd83e03f71a10fc934b7ce996e327488b838587f03159fd392c77c7701389'], + 'checksums': ['5198f31c3bb25e685e9e68355a3bf67a1db23c9e8bdccc33dc015f496a44df7a'], } components = [ From 4492671abc23969efa1754e3ce88b003350014db Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 25 Jun 2021 13:36:55 +0200 Subject: [PATCH 1176/2365] adding easyconfigs: torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb --- ...text-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..0cb1c698d9 --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,42 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.8.1' +local_pytorch_version = '1.7.1' +local_python_suffix = '-Python-%(pyver)s' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['128f3c9ea6d774fca26d838f71b86adf32c2978ab092882454df598be5e8ce37'] + +builddependencies = [ + ('RE2', '2021-06-01'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SentencePiece', '0.1.96'), + ('tqdm', '4.60.0'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.1.5'), +] + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/BuildExtension/d' setup.py &&" + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 049ecbe0088264cf857ce0375547205e32e35be9 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 25 Jun 2021 16:17:35 +0200 Subject: [PATCH 1177/2365] torchtext: aligns the dependency version of tqdm --- .../t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb index 0cb1c698d9..e9c3ae26bc 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb @@ -27,7 +27,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('SentencePiece', '0.1.96'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('PyTorch', local_pytorch_version), ('double-conversion', '3.1.5'), ] From 901c825237b8f39f4beeb29de508b6a4f0476add Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 25 Jun 2021 17:55:38 +0200 Subject: [PATCH 1178/2365] adding easyconfigs: ASE-3.22.0-foss-2020b.eb, ASE-3.22.0-intel-2020b.eb, GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb, GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb --- .../a/ASE/ASE-3.22.0-foss-2020b.eb | 66 +++++++++++++++++ .../a/ASE/ASE-3.22.0-intel-2020b.eb | 70 +++++++++++++++++++ .../GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb | 49 +++++++++++++ .../GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb | 52 ++++++++++++++ 4 files changed, 237 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb new file mode 100644 index 0000000000..ccc4271110 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.3.3'), + ('spglib-python', '1.16.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '2.0.1', { + 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], + }), + ('Jinja2', '3.0.1', { + 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], + }), + ('Werkzeug', '2.0.1', { + 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('itsdangerous', '2.0.1', { + 'checksums': ['9e724d68fc22902a1435351f84c3fb8623f303fffcc566a4cb952df8c572cff0'], + }), + ('Flask', '1.1.2', { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['e60259c7b50867b1cb817caf938fcc1ed383702413df6d2e1afe7ea07f65acee'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb new file mode 100644 index 0000000000..fa2e15624a --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.3.3'), + ('spglib-python', '1.16.0'), +] + +use_pip = True +sanity_pip_check = True + +# required because we're building Python packages (MarkupSafe, +# ase-ext) using Intel compilers on top of Python built with GCC. +check_ldshared = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '2.0.1', { + 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], + }), + ('Jinja2', '3.0.1', { + 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], + }), + ('Werkzeug', '2.0.1', { + 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('itsdangerous', '2.0.1', { + 'checksums': ['9e724d68fc22902a1435351f84c3fb8623f303fffcc566a4cb952df8c572cff0'], + }), + ('Flask', '1.1.2', { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['e60259c7b50867b1cb817caf938fcc1ed383702413df6d2e1afe7ea07f65acee'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..f2b603dd33 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '21.6.0' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('libxc', '4.3.4'), + ('libvdwxc', '0.4.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..362e25c782 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -0,0 +1,52 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '21.6.0' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', +] + +# The intel version is not built with libvdwxc support, as that library is incompatible with MKL. +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('libxc', '4.3.4'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC. +check_ldshared = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' From 7fbc7aa08a563b7b1f11e45ec22ed0a029ca33ee Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 25 Jun 2021 18:54:37 +0200 Subject: [PATCH 1179/2365] Style fix: remove superfluous pypi.org source specification. --- easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb | 2 -- easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb index ccc4271110..70498c9207 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '2.0.1', { 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb index fa2e15624a..09a4e22383 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb @@ -27,8 +27,6 @@ sanity_pip_check = True # ase-ext) using Intel compilers on top of Python built with GCC. check_ldshared = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '2.0.1', { 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], From 5cf3428caf536d6ffa5d7b811cb9062b9c3587eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Jun 2021 09:48:08 +0200 Subject: [PATCH 1180/2365] add grf extension to recent R easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 6 ++++++ 6 files changed, 36 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index b0565b8698..2ed3af32dc 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2867,6 +2867,12 @@ exts_list = [ ('cSEM', '0.4.0', { 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index ec36f55ab3..fb28ae26c5 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2877,6 +2877,12 @@ exts_list = [ ('cSEM', '0.4.0', { 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index caaeb1ad52..98a80a3a48 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2903,6 +2903,12 @@ exts_list = [ ('cSEM', '0.4.0', { 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 5641d1979d..e6f7562b5d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2908,6 +2908,12 @@ exts_list = [ ('cSEM', '0.4.0', { 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 4ef48f8b96..7c53fc26ba 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2912,6 +2912,12 @@ exts_list = [ ('cSEM', '0.4.0', { 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index a9bf1536ef..0747ce4d62 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2923,6 +2923,12 @@ exts_list = [ ('cSEM', '0.4.0', { 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From 8ac5f5c4a6e871892188a904b4a09f9cbf1dc47f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 26 Jun 2021 15:18:36 +0100 Subject: [PATCH 1181/2365] remove PYPI_SOURCE --- easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb index d6c4183a15..a1fed0243f 100644 --- a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb @@ -10,7 +10,6 @@ Log Cursor, Sequence and Transaction objects.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['70d05ec8dc568f42e70fc919a442e0daadc2a905a1cfb7ca77f549d49d6e7801'] From c3eacdac97c13b8d86bd701f79fbe2cae1784142 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 26 Jun 2021 15:29:48 +0100 Subject: [PATCH 1182/2365] set sanity_pip_check --- easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb index a1fed0243f..a0e546b185 100644 --- a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb @@ -20,6 +20,7 @@ dependencies = [('Python', '3.8.6')] use_pip = True download_dep_fail = True +sanity_pip_check = True # Need to unset LIBS or pip install crashes. preinstallopts = 'unset LIBS && ' From 9d0fb2b37ed2dc9097cad017a1c2d4bd084574e1 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 26 Jun 2021 15:30:23 +0100 Subject: [PATCH 1183/2365] stray space --- easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb index a0e546b185..a2429cf4d0 100644 --- a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ dependencies = [('Python', '3.8.6')] use_pip = True download_dep_fail = True -sanity_pip_check = True +sanity_pip_check = True # Need to unset LIBS or pip install crashes. preinstallopts = 'unset LIBS && ' From 60d81f532b2887a75e38cfe8c3f2cf16281144a3 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 28 Jun 2021 09:19:02 +0200 Subject: [PATCH 1184/2365] adding easyconfigs: HAL-2.1-foss-2020b.eb, Sibelia-3.0.7-foss-2020b.eb and patches: Sibelia-3.0.7-indeces.patch --- .../easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb | 116 ++++++++++++++++++ .../s/Sibelia/Sibelia-3.0.7-foss-2020b.eb | 40 ++++++ 2 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb new file mode 100644 index 0000000000..d393abafd9 --- /dev/null +++ b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb @@ -0,0 +1,116 @@ +easyblock = 'MakeCp' + +name = 'HAL' +version = '2.1' + +homepage = 'https://github.com/ComparativeGenomicsToolkit/hal' +description = """HAL is a structure to efficiently store and index multiple genome alignments +and ancestral reconstructions. HAL is a graph-based representation which +provides several advantages over matrix/block-based formats such as MAF, such as +improved scalability and the ability to perform queries with respect to an +arbitrary reference or subtree. + +This package includes the HAL API and several analysis and conversion tools +which are described below. HAL files are presently stored in either HDF5 or mmap +format, but we note that the tools and most of the API are format-independent, +so other databases could be implemented in the future. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +local_sonLibHash = '562a466e4570c93a647ffb10aa2628143b4ee9f4' +sources = [ + { + 'source_urls': ['https://github.com/ComparativeGenomicsToolkit/hal/archive/refs/tags/'], + 'filename': 'release-V%(version)s.tar.gz', + 'extract_cmd': 'tar xvf %s && mv hal-release-V%(version)s hal' + }, + { + 'source_urls': ['https://github.com/ComparativeGenomicsToolkit/sonLib/archive/'], + 'download_filename': '%s.tar.gz' % local_sonLibHash, + 'filename': 'sonLib-%s.tar.gz' % local_sonLibHash, + 'extract_cmd': 'tar xvf %s && mv sonLib-' + local_sonLibHash + ' hal/sonLib' + }, +] +checksums = [ + '540255be1af55abf390359fe034b82d7e61bdf6c3277df3cc01259cd450994e5', # release-V2.1.tar.gz + # sonLib-562a466e4570c93a647ffb10aa2628143b4ee9f4.tar.gz + '3ef2b1dd7805b636afae104728c74e0dff2cfee3a68166836300eff4d0952109', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('Sibelia', '3.0.7'), + ('PyYAML', '5.3.1'), +] + +prebuildopts = 'pushd sonLib && make && popd && ' +buildopts = 'sonLibRootDir=$(pwd)/sonLib' + +files_to_copy = [ + (['bin/*', 'sonLib/bin/*'], 'bin'), + (['lib/*', 'sonLib/lib/*'], 'lib'), + (['sonLib/src/sonLib/*'], 'lib/python%(pyshortver)s/site-packages/sonLib'), + ([ + '__init__.py', 'mutations', 'randgen', 'analysis', 'extract', 'modify', + 'phyloP', 'assemblyHub', 'extra', 'validate', 'blockViz', 'stats', 'maf', 'liftover' + ], 'lib/python%(pyshortver)s/site-packages/hal') +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], +} +exts_list = [ + ('addict', '2.2.1', { + 'checksums': ['f22493f056032f50e4931a82444fcba8ef74c8fc994c5d06aa546a1433c2b8b0'], + }), + ('dill', '0.3.4', { + 'source_tmpl': 'dill-%(version)s.zip', + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), + ('enlighten', '1.10.1', { + 'checksums': ['3391916586364aedced5d6926482b48745e4948f822de096d32258ba238ea984'], + }), + ('websocket-client', '1.1.0', { + 'modulename': 'websocket', + 'checksums': ['b68e4959d704768fa20e35c9d508c8dc2bbc041fd8d267c0d7345cffe2824568'], + }), + ('blessed', '1.18.1', { + 'checksums': ['8b09936def6bc06583db99b65636b980075733e13550cb6af262ce724a55da23'], + }), + ('prefixed', '0.3.2', { + 'checksums': ['ca48277ba5fa8346dd4b760847da930c7b84416387c39e93affef086add2c029'], + }), + ('docker', '4.3.1', { + 'checksums': ['bad94b8dd001a8a4af19ce4becc17f41b09f228173ffe6a4e0355389eef142f2'], + }), + ('toil', '5.3.0', { + 'checksums': ['4ea8f703ee697c4b5ff506db545d0dbb6e4753fbfc61c4230f1eccba8f860e7c'], + }), + ('newick', '1.3.0', { + 'checksums': ['a34010de5047481277dfad76b29f3db525d539f34d876437a861da6a24fca0c8'], + }), + ('pytest', '6.2.4', { + 'checksums': ['50bcad0a0b9c5a72c8e4e7c9855a3ad496ca6a881a3641b4260605450772c54b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/halValidate'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + "halValidate --help 2>&1 | grep 'halValidate v%(version)s'", + "python -c 'from sonLib.bioio import getTempFile'", + "python -c 'from hal.stats.halStats import getHalGenomes'" +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb b/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb new file mode 100644 index 0000000000..4ee05dcdc0 --- /dev/null +++ b/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = "CMakeMake" + +name = 'Sibelia' +version = '3.0.7' + +homepage = 'http://bioinf.spbau.ru/en/%(namelower)s' +description = """Sibelia: A comparative genomics tool: It assists biologists in analysing + the genomic variations that correlate with pathogens, or the genomic changes that help + microorganisms adapt in different environments. Sibelia will also be helpful for the + evolutionary and genome rearrangement studies for multiple strains of microorganisms.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [('http://sourceforge.net/projects/%(namelower)s-bio/files/', 'download')] +sources = ['%(name)s-%(version)s-Source.tar.gz'] +patches = ['Sibelia-3.0.7-indeces.patch'] +checksums = [ + '114d076dd9f381d7e856ea54414e8a53e9f6bad28d75bb530ee511584f53070e', # Sibelia-3.0.7-Source.tar.gz + 'c20badf609d38b10be26c0f4a6517f6805684d6fb24fe0d34f4794c9c365529e', # Sibelia-3.0.7-indeces.patch +] + +builddependencies = [('CMake', '3.18.4')] + +start_dir = 'src' + +separate_build_dir = True + +prebuildopts = 'sed -i.bak "s#gcc#$CC#g" ../Sibelia-%(version)s-Source/src/lagan/src/Makefile && ' +prebuildopts += 'sed -i.bak "s#g++#$CXX#g" ../Sibelia-%(version)s-Source/src/lagan/src/Makefile && ' +prebuildopts += 'sed -i.bak "s#gcc#$CC#g" ../Sibelia-%(version)s-Source/src/lagan/src/glocal/Makefile && ' +prebuildopts += 'sed -i.bak "s#g++#$CXX#g" ../Sibelia-%(version)s-Source/src/lagan/src/glocal/Makefile && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['C-%(name)s.py', '%(name)s', 'snpEffAnnotate.py']], + 'dirs': [''], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' From 1f3300ab096eedd2831f6d93111bb7d38bb26e15 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Jun 2021 09:44:36 +0200 Subject: [PATCH 1185/2365] Fix build on AVX512 machines --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb index 65f738407c..20dd004271 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb @@ -199,6 +199,7 @@ patches = [ 'PyTorch-1.3.1_add-Python3.8-compat.patch', 'PyTorch-1.3.1_add-support-for-cuda11.patch', 'PyTorch-1.3.1_add-support-for-cudnn8.patch', + 'PyTorch-1.3.1_fix-build-on-AVX512-cpus.patch', 'PyTorch-1.3.1_fix-for-nccl-error.patch', '%(name)s-%(version)s_fix-missing-sleef_h.patch', 'PyTorch-1.3.1_skip-nccl-error-tests.patch', @@ -247,6 +248,7 @@ checksums = [ '2a743d0fc52a6f7239e6750a7cd59148417546b45a0b10ad1a15e526b94c4434', # PyTorch-1.3.1_add-Python3.8-compat.patch 'e379846cb0bccb7e6143bf21b1fa517771842c7ca165cb35d60e507edd38b6ce', # PyTorch-1.3.1_add-support-for-cuda11.patch '2560bf24f40aa981c9d3802313b67c4d2378082a9fdd919c499de10793da7e64', # PyTorch-1.3.1_add-support-for-cudnn8.patch + 'daf8e2c49a5ecab37c583f9cc97688f4264d420adba23192b72184f268558676', # PyTorch-1.3.1_fix-build-on-AVX512-cpus.patch '064801bf29f07524a93d17fc0ca6004adc4a506232b33077ac43bdbe3f3a9f7d', # PyTorch-1.3.1_fix-for-nccl-error.patch '1337647ff64a1208d1e401fc84052d0bc6174b133cec2f3521319cb593f524fa', # PyTorch-1.3.1_fix-missing-sleef_h.patch '5743ac23a0d0f40373baeb026bb5656a84ca1417fcce10be8370ec3f4c9e80a6', # PyTorch-1.3.1_skip-nccl-error-tests.patch From 72791978bc1d21a064e7c94bde23db7405ca5bbe Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 24 Jun 2021 15:53:58 +0200 Subject: [PATCH 1186/2365] Remove superflous PYPI_SOURCE entries --- easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb | 1 - .../easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb | 1 - .../easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb | 1 - .../g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb | 1 - .../easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 5 ----- .../p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb | 1 - easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb | 1 - .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 2 +- .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 2 +- 10 files changed, 3 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb index 5e4aad028e..c9ac575179 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb @@ -68,7 +68,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { - 'source_urls': [PYPI_SOURCE], 'use_pip': True, 'download_dep_fail': True, 'sanity_pip_check': True, diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb index 5a529a9533..4603708413 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb @@ -67,7 +67,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { - 'source_urls': [PYPI_SOURCE], 'use_pip': True, 'download_dep_fail': True, 'sanity_pip_check': True, diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb index 13d039f411..40ef1e2f2b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb @@ -67,7 +67,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { - 'source_urls': [PYPI_SOURCE], 'use_pip': True, 'download_dep_fail': True, 'sanity_pip_check': True, diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 280fb4af01..54b87d3c57 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -66,7 +66,6 @@ local_genomeworks_preinstallopts += "export GW_ROOT_DIR=%(builddir)s/GenomeWorks exts_list = [ ('sortedcollections', '2.1.0', { - 'source_urls': [PYPI_SOURCE], 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], }), ('genomeworks', version, { diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb index 07596366dc..8cbb26767c 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -19,8 +19,8 @@ local_preinstallopts = './configure.py --cuda-root="$EBROOTCUDA" --boost-inc-dir local_preinstallopts += '--boost-lib-dir="$EBROOTBOOST/lib" --no-use-shipped-boost ' local_preinstallopts += '--boost-python-libname=boost_python38 && ' -sanity_pip_check = True use_pip = True +sanity_pip_check = True exts_default_options = { 'source_tmpl': SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index 2fc24f0a12..ba678e59e0 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -32,7 +32,6 @@ local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/si local_sipver = '5.4.0' components = [ ('SIP', local_sipver, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], 'start_dir': 'sip-%s' % local_sipver, @@ -40,21 +39,18 @@ components = [ 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.5.0', { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.8.1', { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], 'easyblock': 'Binary', @@ -63,7 +59,6 @@ components = [ 'install_cmd': local_setup_env + local_pyqt5_sip_install, }), ('PyQtWebEngine', version, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], 'easyblock': 'ConfigureMakePythonPackage', diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb index f7ba3e761c..854336b2eb 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb @@ -9,7 +9,6 @@ description = """pkgconfig is a Python module to interface with the pkg-config c toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f'] diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb index fff50e2e31..039c034486 100644 --- a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb @@ -31,7 +31,6 @@ runtest = False exts_defaultclass = 'PythonPackage' exts_default_options = { - 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index c458718562..015fdb2f97 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -41,8 +41,8 @@ dependencies = [ ('zlib', '1.2.11'), ] -sanity_pip_check = True use_pip = True +sanity_pip_check = True # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index cc2dbfb5e6..5e6c23ac57 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -43,8 +43,8 @@ dependencies = [ ('zlib', '1.2.11'), ] -sanity_pip_check = True use_pip = True +sanity_pip_check = True # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d From 70f816e26fc7ae87f47c33ff76c2a97a4488dc9c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 24 Jun 2021 16:31:27 +0200 Subject: [PATCH 1187/2365] Remove raw PyPi URLs --- .../easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb | 1 - .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb | 1 - .../easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb | 3 --- .../m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb | 3 --- .../easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb | 3 --- .../m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb | 3 --- .../n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb | 1 - .../n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb | 1 - easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 1 - 9 files changed, 17 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb index e16f7e4642..8e7eb5871f 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb @@ -37,7 +37,6 @@ exts_list = [ 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], }), ('BioPerl', version, { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], }), diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index e2f3288212..21aa4a17f7 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -35,7 +35,6 @@ exts_list = [ (name, version, { 'buildcmd': 'build_ext', 'modulename': 'pygpu', - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], }), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb index ed77f16aee..4a49f2dc22 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb index 8fb868afac..06ed98ff90 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb index d05fd348d9..a79ad30577 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb index f20755abf9..845af2bf73 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb @@ -30,17 +30,14 @@ exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), ('kiwisolver', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], }), ] diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb index b7343ccf1a..ed8e4eca0f 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb @@ -28,7 +28,6 @@ exts_list = [ (name, version, { 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], 'source_tmpl': 'netCDF4-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], 'checksums': [ 'd957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd', # netCDF4-1.5.5.1.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb index 01db361cc5..a65f8885a9 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb @@ -26,7 +26,6 @@ exts_list = [ (name, version, { 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], 'source_tmpl': 'netCDF4-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], 'checksums': [ 'd957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd', # netCDF4-1.5.5.1.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index d006f6a932..5862d89ed4 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -31,7 +31,6 @@ exts_default_options = { exts_list = [ ('py4j', '0.10.9.2', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], }), ] From ce352604d9a0a0a5103511ec92e7b2267b15d373 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Jun 2021 10:23:41 +0200 Subject: [PATCH 1188/2365] Remove more redundant default options (mostly sanity check) --- .../easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb index 8cbb26767c..3a973ddf49 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -22,10 +22,6 @@ local_preinstallopts += '--boost-python-libname=boost_python38 && ' use_pip = True sanity_pip_check = True -exts_default_options = { - 'source_tmpl': SOURCELOWER_TAR_GZ, -} - exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], @@ -34,6 +30,7 @@ exts_list = [ 'checksums': ['50f2d5b2196a18950fa1397d5ad7ea52daa5985e6196bfd06ba608a7caf93d07'], }), (name, version, { + 'source_tmpl': SOURCELOWER_TAR_GZ, 'preinstallopts': local_preinstallopts, 'checksums': ['effa3b99b55af67f3afba9b0d1b64b4a0add4dd6a33bdd6786df1aa4cc8761a5'], }), From 3ec61ecd4c4f1f47a752fee0b32ddff31b11c901 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 28 Jun 2021 12:13:30 +0200 Subject: [PATCH 1189/2365] Depend on the Flask module instead of duplicating it. --- .../a/ASE/ASE-3.22.0-foss-2020b.eb | 23 +++---------------- .../a/ASE/ASE-3.22.0-intel-2020b.eb | 23 +++---------------- 2 files changed, 6 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb index 70498c9207..87ef103fc6 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb @@ -15,33 +15,16 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Tkinter', '%(pyver)s'), + ('Flask', '1.1.2'), ('matplotlib', '3.3.3'), - ('spglib-python', '1.16.0'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional ] use_pip = True sanity_pip_check = True exts_list = [ - ('MarkupSafe', '2.0.1', { - 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], - }), - ('Jinja2', '3.0.1', { - 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], - }), - ('Werkzeug', '2.0.1', { - 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('itsdangerous', '2.0.1', { - 'checksums': ['9e724d68fc22902a1435351f84c3fb8623f303fffcc566a4cb952df8c572cff0'], - }), - ('Flask', '1.1.2', { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), ('pytest-mock', '3.6.1', { 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], }), diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb index 09a4e22383..a31426b7e1 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb @@ -15,9 +15,10 @@ toolchain = {'name': 'intel', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Tkinter', '%(pyver)s'), + ('Flask', '1.1.2'), ('matplotlib', '3.3.3'), - ('spglib-python', '1.16.0'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional ] use_pip = True @@ -28,24 +29,6 @@ sanity_pip_check = True check_ldshared = True exts_list = [ - ('MarkupSafe', '2.0.1', { - 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], - }), - ('Jinja2', '3.0.1', { - 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], - }), - ('Werkzeug', '2.0.1', { - 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('itsdangerous', '2.0.1', { - 'checksums': ['9e724d68fc22902a1435351f84c3fb8623f303fffcc566a4cb952df8c572cff0'], - }), - ('Flask', '1.1.2', { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), ('pytest-mock', '3.6.1', { 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], }), From 94b337c06ef1086f5d57e132ab4e94c5976b7e2e Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 28 Jun 2021 12:52:09 +0200 Subject: [PATCH 1190/2365] HAL: fix style --- .../easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb | 20 +++++++++---------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb index d393abafd9..9c9c33ee73 100644 --- a/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb @@ -18,7 +18,9 @@ so other databases could be implemented in the future. toolchain = {'name': 'foss', 'version': '2020b'} -local_sonLibHash = '562a466e4570c93a647ffb10aa2628143b4ee9f4' +local_sonLib_datetime = '20210415' +local_sonLib_hash = '562a466e4570c93a647ffb10aa2628143b4ee9f4' + sources = [ { 'source_urls': ['https://github.com/ComparativeGenomicsToolkit/hal/archive/refs/tags/'], @@ -27,9 +29,9 @@ sources = [ }, { 'source_urls': ['https://github.com/ComparativeGenomicsToolkit/sonLib/archive/'], - 'download_filename': '%s.tar.gz' % local_sonLibHash, - 'filename': 'sonLib-%s.tar.gz' % local_sonLibHash, - 'extract_cmd': 'tar xvf %s && mv sonLib-' + local_sonLibHash + ' hal/sonLib' + 'download_filename': '%s.tar.gz' % local_sonLib_hash, + 'filename': 'sonLib-%s-%s.tar.gz' % (local_sonLib_datetime, local_sonLib_hash), + 'extract_cmd': 'tar xvf %s && mv sonLib-' + local_sonLib_hash + ' hal/sonLib' }, ] checksums = [ @@ -53,10 +55,9 @@ files_to_copy = [ (['bin/*', 'sonLib/bin/*'], 'bin'), (['lib/*', 'sonLib/lib/*'], 'lib'), (['sonLib/src/sonLib/*'], 'lib/python%(pyshortver)s/site-packages/sonLib'), - ([ - '__init__.py', 'mutations', 'randgen', 'analysis', 'extract', 'modify', - 'phyloP', 'assemblyHub', 'extra', 'validate', 'blockViz', 'stats', 'maf', 'liftover' - ], 'lib/python%(pyshortver)s/site-packages/hal') + (['__init__.py', 'mutations', 'randgen', 'analysis', 'extract', 'modify', + 'phyloP', 'assemblyHub', 'extra', 'validate', 'blockViz', 'stats', 'maf', 'liftover'], + 'lib/python%(pyshortver)s/site-packages/hal') ] exts_defaultclass = 'PythonPackage' @@ -96,9 +97,6 @@ exts_list = [ ('newick', '1.3.0', { 'checksums': ['a34010de5047481277dfad76b29f3db525d539f34d876437a861da6a24fca0c8'], }), - ('pytest', '6.2.4', { - 'checksums': ['50bcad0a0b9c5a72c8e4e7c9855a3ad496ca6a881a3641b4260605450772c54b'], - }), ] sanity_check_paths = { From f3fa4430f938aaa306dd62fb6af01342bd2332e4 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 28 Jun 2021 14:02:15 +0200 Subject: [PATCH 1191/2365] flash2 should be accessible via `flash` cmd --- easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb index da47c15d06..858caac9c7 100644 --- a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb @@ -20,8 +20,9 @@ checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] files_to_copy = [(['flash2'], 'bin')] +postinstallcmds = ['ln -s %(installdir)s/bin/flash2 %(installdir)s/bin/flash'] sanity_check_paths = { - 'files': ['bin/flash2'], + 'files': ['bin/flash2', 'bin/flash'], 'dirs': [], } From 1d0ff6c0ce2913e27438cf705fe97d58d853b0e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Jun 2021 15:53:15 +0200 Subject: [PATCH 1192/2365] fix comment in checksums for HAL --- easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb index 9c9c33ee73..7753fb4bfa 100644 --- a/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb @@ -36,7 +36,7 @@ sources = [ ] checksums = [ '540255be1af55abf390359fe034b82d7e61bdf6c3277df3cc01259cd450994e5', # release-V2.1.tar.gz - # sonLib-562a466e4570c93a647ffb10aa2628143b4ee9f4.tar.gz + # sonLib-20210415-562a466e4570c93a647ffb10aa2628143b4ee9f4.tar.gz '3ef2b1dd7805b636afae104728c74e0dff2cfee3a68166836300eff4d0952109', ] From f1eed01e0d9c8d64ee137e574c38ffd127e3b23a Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 28 Jun 2021 19:03:05 +0200 Subject: [PATCH 1193/2365] adding easyconfigs: eggnog-mapper-2.1.4-foss-2020b.eb, MMseqs2-13-45111-gompi-2020b.eb --- .../eggnog-mapper-2.1.4-foss-2020b.eb | 47 +++++++++++++++++++ .../m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb | 26 ++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb new file mode 100644 index 0000000000..ce2ddd3295 --- /dev/null +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonPackage' + +name = 'eggnog-mapper' +version = '2.1.4' + +homepage = 'https://github.com/eggnogdb/eggnog-mapper' +description = """EggNOG-mapper is a tool for fast functional annotation of novel +sequences. It uses precomputed orthologous groups and phylogenies from the +eggNOG database (http://eggnog5.embl.de) to transfer functional information from +fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation +of novel genomes, transcriptomes or even metagenomic gene catalogs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'eggnogdb' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('HMMER', '3.3.2'), + ('DIAMOND', '2.0.7'), + ('prodigal', '2.6.3'), + ('wget', '1.20.3'), + ('MMseqs2', '13-45111'), + ('XlsxWriter', '1.4.0'), +] + +# Relax version constraings +preinstallopts = "sed -i 's/biopython==1.76/biopython==1.78/' setup.cfg && " +preinstallopts += "sed -i 's/xlsxwriter==1.4.3/xlsxwriter==1.4.0/' setup.cfg && " +preinstallopts += "sed -i 's/psutil==5.7.0/psutil==5.7.2/' setup.cfg && " + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_commands = [ + 'download_eggnog_data.py --help', + 'create_dbs.py --help', + 'emapper.py --version | grep %(version)s', +] + +options = {'modulename': 'eggnogmapper'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb new file mode 100644 index 0000000000..1f9c4aebf1 --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +version = '13-45111' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.18.4')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE' + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +moduleclass = 'bio' From ffde526042c2877eb6cae2e76570e8affaddab25 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 28 Jun 2021 21:22:44 +0200 Subject: [PATCH 1194/2365] eggnog: checksus --- .../e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb | 1 + easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb index ce2ddd3295..377293c19c 100644 --- a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} github_account = 'eggnogdb' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] +checksums = ['c131043eb3cf5c8f32a4f088dabcbe0eae8fbb3680c2a6ac997c3bcd2fa5f0f2'] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb index 1f9c4aebf1..38b876a77c 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'gompi', 'version': '2020b'} github_account = 'soedinglab' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] +checksums = ['6444bb682ebf5ced54b2eda7a301fa3e933c2a28b7661f96ef5bdab1d53695a2'] builddependencies = [('CMake', '3.18.4')] From 7983d66ef22cfdd0eb65643a4c15df3ae61e00d4 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 28 Jun 2021 21:24:47 +0200 Subject: [PATCH 1195/2365] Ragout: naming, checksums --- .../r/Ragout/Ragout-2.3-foss-2020b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb b/easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb new file mode 100644 index 0000000000..d86d97d9b0 --- /dev/null +++ b/easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Ragout' +version = '2.3' + +homepage = 'https://github.com/fenderglass/Ragout' +description = """Ragout (Reference-Assisted Genome Ordering UTility) is a tool +for chromosome-level scaffolding using multiple references. Given initial +assembly fragments (contigs/scaffolds) and one or multiple related references +(complete or draft), it produces a chromosome-scale assembly (as a set of +scaffolds).""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'fenderglass' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['69d50a7ff49f03821e0143449ee0dc3e80c73e2c24568cad71948a5492613bca'] + +dependencies = [ + ('Python', '3.8.6'), + ('Sibelia', '3.0.7'), + ('HAL', '2.1'), + ('networkx', '2.5'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_commands = ['ragout --help'] + +moduleclass = 'bio' From 1ed3216160c65163d5a020a9e1aa7a648e1c1015 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 28 Jun 2021 21:54:18 +0200 Subject: [PATCH 1196/2365] eggnog: add dataset download instructions --- .../e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb index 377293c19c..a4ddd4d2b4 100644 --- a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb @@ -1,3 +1,8 @@ +# Eggnog DB installation instructions: +# 1. 'export EGGNOG_DATA_DIR=//eggnog-mapper-data' +# 2. run 'download_eggnog_data.py' +# 3. Check the expected DB version with 'emapper.py --version' + easyblock = 'PythonPackage' name = 'eggnog-mapper' From 123b934bde160daa071287fb2cfd041a5f0e32a7 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 29 Jun 2021 10:29:06 +0200 Subject: [PATCH 1197/2365] adding versionsuffix --- ...SPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..5c267480b2 --- /dev/null +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'CRISPResso2' +version = '2.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pinellolab/CRISPResso2/' +description = """CRISPResso2 is a software pipeline designed to enable rapid and +intuitive interpretation of genome editing experiments.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [ + {'source_urls': ['https://github.com/pinellolab/CRISPResso2/archive/'], + 'filename': 'v%(version)s.tar.gz'}, + {'source_urls': ['https://crispresso.pinellolab.partners.org/static/demo/'], + 'filename': 'base_editor.fastq.gz', 'extract_cmd': 'cp %s %(builddir)s'}] +patches = ['CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch'] +checksums = [ + '29dfaaa65f66225faee4887376ea6b524355332fc6f7ca4d07bb7d63596ef5e6', # v2.1.2.tar.gz + '371aad07a164721188deaa80ca7589f5cd4b871119d90d55a984c6d9c8d31c7a', # base_editor.fastq.gz + # CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch + '87e4515d87c5e70fa65a8216a950dca5876948821ef5132a993102c168ece66a', +] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'), + ('matplotlib', '2.2.5', '-Python-%(pyver)s'), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('FLASH', '2.2.00'), + ('SAMtools', '1.12'), + ('Bowtie2', '2.4.2'), + ('Seaborn', '0.9.1', '-Python-%(pyver)s'), +] +download_dep_fail = True +use_pip = True +options = {'modulename': False} +sanity_pip_check = True + +local_seq_str = 'GGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTAC' +local_seq_str += 'AAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATG' +local_seq_str += 'GGGAGGACATCGATGTCACCTCCAATGACTAGGGTGG' +sanity_check_commands = [('CRISPResso -h'), + ("""CRISPResso --fastq_r1 %%(builddir)s/base_editor.fastq.gz --amplicon_seq %s \ + --guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 10 \ + --quantification_window_center -10 --base_editor_output""" % local_seq_str)] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} + +moduleclass = 'bio' From 43bcdf0c81e8996dc7806fab342227998690e25f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Jun 2021 09:31:17 +0100 Subject: [PATCH 1198/2365] adding easyconfigs: DosageConvertor-1.0.4-GCC-10.2.0.eb --- .../DosageConvertor-1.0.4-GCC-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb b/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..89c5ad2862 --- /dev/null +++ b/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +# Includes some material from the BEAR Software team at the University of Birmingham. + +easyblock = 'CMakeMake' + +name = 'DosageConvertor' +version = '1.0.4' +local_commit = 'c53a377bb6e03cd697f528cd74d97eb0c9f56e8b' + +homepage = 'http://genome.sph.umich.edu/wiki/DosageConvertor' +description = """DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 + to other formats such as MaCH or PLINK. Please note that this tool CANNOT handle missing values in + the input files and may NOT work for non-Minimac3/4 VCF files.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +builddependencies = [ + ('CMake', '3.18.4') +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libStatGen', '1.0.15'), +] + +source_urls = ['https://github.com/Santy-8128/%(name)s/archive'] +sources = ['%s.tar.gz' % local_commit] + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = [ + '%%(name)s --vcfDose %%(builddir)s/%%(name)s-%s/test/TestDataImputedVCF.dose.vcf.gz --prefix output --format 1' + ' --info %%(builddir)s/%%(name)s-%s/test/TestDataImputedVCF.info --type plink' % (local_commit, local_commit) +] + +moduleclass = 'bio' From 98d8e2f70e22bca6020eda5b3b6687d2743d25c2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Jun 2021 10:24:30 +0100 Subject: [PATCH 1199/2365] adding easyconfigs: libStatGen-1.0.15-GCCcore-10.2.0.eb --- .../libStatGen-1.0.15-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6cb6951226 --- /dev/null +++ b/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'MakeCp' + +name = 'libStatGen' +version = '1.0.15' +_hash = 'ff4f2fc' + +homepage = "https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen" +description = """Useful set of classes for creating statistical genetic programs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'statgen' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _hash, 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['68acb15b6c85f07b0dbf3f8b7a2a99a88fc97d3e29e80bebab82bd2a8e09121e'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +runtest = 'test' + +files_to_copy = [ + (['libStatGen.a'], 'lib'), + ('include'), +] + +sanity_check_paths = { + 'files': ['lib/libStatGen.a', 'include/VcfFile.h', 'include/SamFile.h', 'include/BamIndex.h', 'include/Cigar.h'], + 'dirs': [], +} + +moduleclass = 'bio' From 4469e961fa8b09271321d79de1e08aca0f95e634 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 29 Jun 2021 11:53:52 +0200 Subject: [PATCH 1200/2365] adding easyconfigs: QuantumESPRESSO-6.7-foss-2020b.eb --- .../QuantumESPRESSO-6.7-foss-2020b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb new file mode 100644 index 0000000000..43a880080a --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +name = 'QuantumESPRESSO' +version = '6.7' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s.0/', + 'https://github.com/dceresoli/qe-gipaw/archive/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + {'filename': 'qe-gipaw-%(version)sMaX.tar.gz', 'download_filename': '%(version)sMaX.tar.gz'}, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + '8f06ea31ae52ad54e900a2f51afd5c70f78096d9dcf39c86c2b17dccb1ec9c87', # qe-6.7-ReleasePack.tgz + '95d2ed2f4d27f044dba171bdf8c1913a67ebc8846ed3463462828f2d414a2a61', # qe-gipaw-6.7MaX.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('ELPA', '2020.11.001'), + ('libxc', '4.3.4'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From 45e8855c870607cc1f72a88368f9316d63b04519 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Jun 2021 12:44:43 +0200 Subject: [PATCH 1201/2365] Fix special cases of URLs --- .../easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb | 1 + .../g/GROMACS/GROMACS-2021-fosscuda-2020b.eb | 1 + .../g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb | 1 + .../GenomeWorks-2021.02.2-fosscuda-2020b.eb | 1 + .../netcdf4-python-1.5.5.1-fosscuda-2020b.eb | 1 + .../netcdf4-python-1.5.5.1-intel-2020b.eb | 1 + .../p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 11 ++--------- .../easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb | 2 +- 8 files changed, 9 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb index c9ac575179..5e4aad028e 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb @@ -68,6 +68,7 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'use_pip': True, 'download_dep_fail': True, 'sanity_pip_check': True, diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb index 4603708413..5a529a9533 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb @@ -67,6 +67,7 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'use_pip': True, 'download_dep_fail': True, 'sanity_pip_check': True, diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb index 40ef1e2f2b..13d039f411 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb @@ -67,6 +67,7 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'use_pip': True, 'download_dep_fail': True, 'sanity_pip_check': True, diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 54b87d3c57..280fb4af01 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -66,6 +66,7 @@ local_genomeworks_preinstallopts += "export GW_ROOT_DIR=%(builddir)s/GenomeWorks exts_list = [ ('sortedcollections', '2.1.0', { + 'source_urls': [PYPI_SOURCE], 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], }), ('genomeworks', version, { diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb index ed8e4eca0f..4970fc6590 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb @@ -27,6 +27,7 @@ exts_list = [ }), (name, version, { 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'checksums': [ 'd957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd', # netCDF4-1.5.5.1.tar.gz diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb index a65f8885a9..4877a91283 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb @@ -25,6 +25,7 @@ exts_list = [ }), (name, version, { 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'checksums': [ 'd957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd', # netCDF4-1.5.5.1.tar.gz diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index ba678e59e0..75f5f65a1e 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'PyQt5' version = '5.15.1' @@ -16,8 +16,6 @@ dependencies = [ ('Qt5', '5.14.2'), ] -default_easyblock = 'PythonPackage' - local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " @@ -30,7 +28,7 @@ local_pyqtweb_configopts += "--no-stubs --no-dist-info" local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.4.0' -components = [ +exts_list = [ ('SIP', local_sipver, { 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], @@ -39,19 +37,16 @@ components = [ 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.5.0', { - 'sources': [SOURCE_TAR_GZ], 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.8.1', { - 'sources': [SOURCE_TAR_GZ], 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { - 'sources': [SOURCE_TAR_GZ], 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], 'easyblock': 'Binary', 'start_dir': '%(name)s-%(version)s', @@ -59,7 +54,6 @@ components = [ 'install_cmd': local_setup_env + local_pyqt5_sip_install, }), ('PyQtWebEngine', version, { - 'sources': [SOURCE_TAR_GZ], 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', @@ -80,7 +74,6 @@ sanity_check_commands = [ ] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'QT_INSTALL_DATA': 'qsci', } diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb index 039c034486..9b5c672dad 100644 --- a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb @@ -31,13 +31,13 @@ runtest = False exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ ('cloudpickle', '1.6.0', { - 'sources': ['%(name)s-%(version)s.tar.gz'], 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), ('dill', '0.3.3', { From 3c1968337b1edbdb3c805ccc883c04dc528b186f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Jun 2021 12:31:35 +0100 Subject: [PATCH 1202/2365] Add checksum and fix long line --- .../d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb b/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb index 89c5ad2862..39e2802d80 100644 --- a/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb @@ -4,7 +4,7 @@ easyblock = 'CMakeMake' name = 'DosageConvertor' version = '1.0.4' -local_commit = 'c53a377bb6e03cd697f528cd74d97eb0c9f56e8b' +local_hash = 'c53a377bb6e03cd697f528cd74d97eb0c9f56e8b' homepage = 'http://genome.sph.umich.edu/wiki/DosageConvertor' description = """DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 @@ -23,7 +23,8 @@ dependencies = [ ] source_urls = ['https://github.com/Santy-8128/%(name)s/archive'] -sources = ['%s.tar.gz' % local_commit] +sources = ['%s.tar.gz' % local_hash] +checksums = ['3ee1f3ef23d7e7c04295a5fa43c3b59811cc8fe778f0f69c9759c2624ae3aa47'] configopts = '-DCMAKE_BUILD_TYPE=Release' @@ -34,7 +35,7 @@ sanity_check_paths = { sanity_check_commands = [ '%%(name)s --vcfDose %%(builddir)s/%%(name)s-%s/test/TestDataImputedVCF.dose.vcf.gz --prefix output --format 1' - ' --info %%(builddir)s/%%(name)s-%s/test/TestDataImputedVCF.info --type plink' % (local_commit, local_commit) + ' --info %%(builddir)s/%%(name)s-%s/test/TestDataImputedVCF.info --type plink' % (local_hash, local_hash) ] moduleclass = 'bio' From 4c07b65c27f2d2e593ce8f429c2aed81455d6a4e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 29 Jun 2021 14:21:14 +0200 Subject: [PATCH 1203/2365] review changes --- .../CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb new file mode 100644 index 0000000000..d6b5db719a --- /dev/null +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -0,0 +1,34 @@ +name = 'CRISPR-DAV' +version = '2.3.4' + +homepage = 'https://github.com/pinetree1/crispr-dav/' +description = """CRISPR-DAV is a pipeline to analyze +amplicon-based NGS data of CRISPR clones in a high throughput manner.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/pinetree1/crispr-dav/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch'] +checksums = [ + '49975cd48bdbf31fe5a9e2aaa3f5ed85d3cc6f65a422ee3aa8daed890159d2ae', # v2.3.4.tar.gz + # crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch + '41475a09754d65cc2c88d4161be6eacdfc98242bccbe49778c4f1f74210a6cb2', +] + +dependencies = [ + ('R', '4.0.3'), + ('Perl', '5.32.0'), + ('NGS', '2.10.9'), + ('Pysam', '0.16.0.1'), + ('Excel-Writer-XLSX', '1.09'), + ('naturalsort', '0.1.3'), + ('pysamstats', '1.1.2'), + ('ABRA2', '2.23'), + ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), + ('SAMtools', '1.12'), + ('BEDTools', '2.30.0'), + ('FLASH', '2.2.00'), +] + +moduleclass = 'bio' From dd55b632655100c82f6786f8ca7a5b86761da2fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Jun 2021 15:24:56 +0200 Subject: [PATCH 1204/2365] adding easyconfigs: Filtlong-0.2.0-GCC-10.2.0.eb --- .../f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..d03c231209 --- /dev/null +++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'Filtlong' +version = '0.2.0' + +homepage = 'https://github.com/rrwick/Filtlong' +description = """Filtlong is a tool for filtering long reads by quality. It can take a set + of long reads and produce a smaller, better subset. It uses both read length (longer is better) + and read identity (higher is better) when choosing which reads pass the filter""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/rrwick/Filtlong/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a4afb925d7ced8d083be12ca58911bb16d5348754e7c2f6431127138338ee02a'] + +unpack_options = '--strip-components=1' + +parallel = 1 + +dependencies = [ + ('zlib', '1.2.11'), +] + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ['bin/filtlong'], + 'dirs': [] +} + +sanity_check_commands = ["filtlong --help"] + +moduleclass = 'bio' From aad58649af43189b906301d67637790843392cfb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Jun 2021 15:27:45 +0200 Subject: [PATCH 1205/2365] add twang + xgboost extensions to recent R easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 6 ++++++ 6 files changed, 36 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 2ed3af32dc..e74cf716d9 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2873,6 +2873,12 @@ exts_list = [ ('grf', '2.0.0', { 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index fb28ae26c5..78709bbe06 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2883,6 +2883,12 @@ exts_list = [ ('grf', '2.0.0', { 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 98a80a3a48..6c95515829 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2909,6 +2909,12 @@ exts_list = [ ('grf', '2.0.0', { 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index e6f7562b5d..07da3391f8 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2914,6 +2914,12 @@ exts_list = [ ('grf', '2.0.0', { 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 7c53fc26ba..6128b88862 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2918,6 +2918,12 @@ exts_list = [ ('grf', '2.0.0', { 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 0747ce4d62..6f1241008d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2929,6 +2929,12 @@ exts_list = [ ('grf', '2.0.0', { 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From cdd4874f092d274b7dc1c8aec281462997a218cb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 29 Jun 2021 15:33:43 +0200 Subject: [PATCH 1206/2365] adding easyconfigs: CubeWriter-4.4.3-GCCcore-10.2.0.eb, OPARI2-2.0.6-GCCcore-10.2.0.eb, OTF2-2.3-GCCcore-10.2.0.eb, PDT-3.25-GCCcore-10.2.0.eb, Score-P-7.0-gompic-2020b.eb, SIONlib-1.7.6-GCCcore-10.2.0-tools.eb --- .../CubeWriter-4.4.3-GCCcore-10.2.0.eb | 51 +++++++++++++++++ .../o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb | 44 ++++++++++++++ .../o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb | 50 ++++++++++++++++ .../p/PDT/PDT-3.25-GCCcore-10.2.0.eb | 37 ++++++++++++ .../SIONlib-1.7.6-GCCcore-10.2.0-tools.eb | 51 +++++++++++++++++ .../s/Score-P/Score-P-7.0-gompic-2020b.eb | 57 +++++++++++++++++++ 6 files changed, 290 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompic-2020b.eb diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..198339522e --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.4.3' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['93fff6cc1e8b0780f0171ef5302a2e1a257f99b6383fbfc1b9b82f925ceff501'] + +builddependencies = [ + ('GCC', '%(toolchain_version)s', '', True), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/cubew-config', 'lib/libcube4w.a', 'lib/libcube4w.so'], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f0f645a58c --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.6' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['55972289ce66080bb48622110c3189a36e88a12917635f049b37685b9d3bbcb0'] + +builddependencies = [ + ('GCC', '%(toolchain_version)s', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bb9bb1ea3f --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '2.3' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['36957428d37c40d35b6b45208f050fb5cfe23c54e874189778a24b0e9219c7e3'] + +builddependencies = [ + ('GCC', '%(toolchain_version)s', '', True), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.6', '-tools'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..58d1e37b75 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +checksums = ['1037628d854edfeded3d847150d3e8fbd3774e8146407ce32f5021c80f6299be'] + +builddependencies = [ + ('GCC', '%(toolchain_version)s', '', True), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb new file mode 100644 index 0000000000..04f2ad8b5f --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.6' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['2c220390ef63d001f8ab02c380087187ea02ad2bfc5956e05ecaa0725a6f9942'] + +builddependencies = [ + ('GCC', '%(toolchain_version)s', '', True), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompic-2020b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompic-2020b.eb new file mode 100644 index 0000000000..e3bc0ac529 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompic-2020b.eb @@ -0,0 +1,57 @@ +# # +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Alexander Grund +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'Score-P' +version = '7.0' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['68f24a68eb6f94eaecf500e17448f566031946deab74f2cba072ee8368af0996'] + +dependencies = [ + ('CubeLib', '4.6'), + ('CubeWriter', '4.6'), + ('libunwind', '1.4.0'), + ('OPARI2', '2.0.6'), + ('OTF2', '2.3'), + # Hardware counter support (optional): + ('PAPI', '6.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'cuda_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 7466fcbca41398372957d98fdbdf68f7474ca688 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 29 Jun 2021 15:40:22 +0000 Subject: [PATCH 1207/2365] Backport "[nvptx] Set -misa=sm_35 by default" This adds a patch included in GCC 11.1.0 setting -misa=sm_35 by default for compatibility with CUDA 11 which no longer supports the previous default sm_30. Fixes #12518 --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 33e8317d38..65f6fc7c6c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -32,6 +32,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-9.3.0_nvptx_sm_35_default.patch', 'GCCcore-10.2.0_fix-has-include-Fortran.patch', 'GCCcore-10.2.0_fix-ice-on-arm.patch', 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', @@ -46,6 +47,7 @@ checksums = [ 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # nvptx-tools-20180301.tar.gz '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCCcore-10.2.0_fix-has-include-Fortran.patch '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278', # GCCcore-10.2.0_fix-ice-on-arm.patch # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch From b3ae14446e10a11cef2ed52410f4390746181797 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Jun 2021 18:38:12 +0200 Subject: [PATCH 1208/2365] enhance sanity check for MMseqs2 13.* and eggnog-mapper 2.1.4 + use simpler sed command to strip out too strict version requirements for eggnog-mapper dependencies --- .../e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb | 11 +++++++---- .../m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb | 4 ++++ 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb index a4ddd4d2b4..536eecf003 100644 --- a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb @@ -33,15 +33,18 @@ dependencies = [ ('XlsxWriter', '1.4.0'), ] -# Relax version constraings -preinstallopts = "sed -i 's/biopython==1.76/biopython==1.78/' setup.cfg && " -preinstallopts += "sed -i 's/xlsxwriter==1.4.3/xlsxwriter==1.4.0/' setup.cfg && " -preinstallopts += "sed -i 's/psutil==5.7.0/psutil==5.7.2/' setup.cfg && " +# strip out (too) strict version requirements for dependencies +preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " use_pip = True sanity_pip_check = True download_dep_fail = True +sanity_check_paths = { + 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + sanity_check_commands = [ 'download_eggnog_data.py --help', 'create_dbs.py --help', diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb index 38b876a77c..876e969d18 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb @@ -15,6 +15,8 @@ checksums = ['6444bb682ebf5ced54b2eda7a301fa3e933c2a28b7661f96ef5bdab1d53695a2'] builddependencies = [('CMake', '3.18.4')] +dependencies = [('bzip2', '1.0.8')] + separate_build_dir = True configopts = '-DCMAKE_BUILD_TYPE=RELEASE' @@ -24,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["mmseqs --help"] + moduleclass = 'bio' From e6d8a78534f64ec0b3190a851a9486c8878c0355 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Jun 2021 19:09:55 +0100 Subject: [PATCH 1209/2365] Remove obsolete configopts --- .../d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb b/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb index 39e2802d80..1076bd462a 100644 --- a/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb @@ -26,8 +26,6 @@ source_urls = ['https://github.com/Santy-8128/%(name)s/archive'] sources = ['%s.tar.gz' % local_hash] checksums = ['3ee1f3ef23d7e7c04295a5fa43c3b59811cc8fe778f0f69c9759c2624ae3aa47'] -configopts = '-DCMAKE_BUILD_TYPE=Release' - sanity_check_paths = { 'files': ['bin/%(name)s'], 'dirs': [] From c2a06bdb8f50d5487cfa3137d787913bb815812c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Jun 2021 22:40:54 +0200 Subject: [PATCH 1210/2365] add back source URL required for py4j extension in Spark easyconfigs --- easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index 5862d89ed4..71ff15224d 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -25,6 +25,7 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } From 976e9a46d958079e9a67a3d4b6b5a4f5208ec59f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 30 Jun 2021 03:32:24 +0200 Subject: [PATCH 1211/2365] Fix install step for glew --- .../easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb | 5 +++-- .../easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb | 5 +++-- .../easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb | 5 +++-- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb index 61dd4c138a..32893834e0 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb @@ -22,7 +22,8 @@ sources = ['%(name)s-%(version)s.tgz'] checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] builddependencies = [('binutils', '2.35')] -buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system dependencies = [ ('Mesa', '20.2.1'), ('X11', '20201008'), @@ -31,7 +32,7 @@ dependencies = [ skipsteps = ['configure'] preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' -install_cmd = 'make install.all' +install_cmd = 'make install.all ' + local_system sanity_check_paths = { 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb index b995d85444..083e28d457 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb @@ -22,7 +22,8 @@ sources = ['%(name)s-%(version)s.tgz'] checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] builddependencies = [('binutils', '2.35')] -buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system dependencies = [ ('Mesa', '20.2.1'), ('X11', '20201008'), @@ -31,7 +32,7 @@ dependencies = [ skipsteps = ['configure'] preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' -install_cmd = 'make install.all' +install_cmd = 'make install.all ' + local_system sanity_check_paths = { 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb index 77964f2f35..cb58df1067 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb @@ -22,7 +22,8 @@ sources = ['%(name)s-%(version)s.tgz'] checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] builddependencies = [('binutils', '2.35')] -buildopts = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system dependencies = [ ('Mesa', '20.2.1'), ('X11', '20201008'), @@ -31,7 +32,7 @@ dependencies = [ skipsteps = ['configure'] preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' -install_cmd = 'make install.all' +install_cmd = 'make install.all ' + local_system sanity_check_paths = { 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + From c22f7349c1e2738853efd3c692146ba995c07005 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 30 Jun 2021 11:01:57 +0200 Subject: [PATCH 1212/2365] adding easyconfigs: ParMETIS-4.0.3-gompi-2020b.eb --- .../p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb new file mode 100644 index 0000000000..f74f7c6ef0 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.18.4')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' From 024b76f5e108b41d9f1da216c772909284b8c0f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Jun 2021 11:55:10 +0200 Subject: [PATCH 1213/2365] update Boost 1.7.4.0 to use tagged_layout rather than boost_multi_thread --- easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 4 ++-- .../easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index 6d96a0ef07..faa5a1229d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -27,8 +27,8 @@ dependencies = [ configopts = '--without-libraries=python,mpi' -# disable MPI, enable threading support +# disable MPI, build Boost libraries with tagged layout boost_mpi = False -boost_multi_thread = True +tagged_layout = True moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb index 49052e5479..ab084d66fb 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb @@ -25,8 +25,8 @@ dependencies = [ configopts = '--without-libraries=python,mpi' -# disable MPI, enable threading support +# disable MPI, build Boost libraries with tagged layout boost_mpi = False -boost_multi_thread = True +tagged_layout = True moduleclass = 'devel' From 439f3c2e71b95de8ee84e2feee8978866f58dc9a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 30 Jun 2021 16:31:23 +0100 Subject: [PATCH 1214/2365] Port to GCC-10.2.0 --- .../b/Beast/Beast-1.10.4-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..799b63b5ea --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +# Author: Pablo Escobar Lopez (1/1) +# Biozentrum - University of Basel +easyblock = 'Tarball' + +name = 'Beast' +version = '1.10.4' + +homepage = 'https://beast.community' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/%(namelower)s-dev/%(namelower)s-mcmc/releases/download/v%(version)s/'] +sources = ['BEASTv%(version)s.tgz'] +checksums = ['be652c4d55953f7c6c7a9d3eb3de203c77dc380e81ad81cfe0492408990c36a8'] + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '3.1.2'), +] + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From f10f4f5f61b6e152979781683df117e8814fce4a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 1 Jul 2021 11:36:48 +0200 Subject: [PATCH 1215/2365] Use binutils --- .../easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb index 198339522e..4b3c1d7de0 100644 --- a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb @@ -33,7 +33,7 @@ sources = ['cubew-%(version)s.tar.gz'] checksums = ['93fff6cc1e8b0780f0171ef5302a2e1a257f99b6383fbfc1b9b82f925ceff501'] builddependencies = [ - ('GCC', '%(toolchain_version)s', '', True), + ('binutils', '2.35'), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb index f0f645a58c..0849295e0d 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['55972289ce66080bb48622110c3189a36e88a12917635f049b37685b9d3bbcb0'] builddependencies = [ - ('GCC', '%(toolchain_version)s', '', True), + ('binutils', '2.35'), ] diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb index bb9bb1ea3f..a59b3c5ca9 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb @@ -29,7 +29,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['36957428d37c40d35b6b45208f050fb5cfe23c54e874189778a24b0e9219c7e3'] builddependencies = [ - ('GCC', '%(toolchain_version)s', '', True), + ('binutils', '2.35'), ] dependencies = [ # SIONlib container support (optional): diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb index 58d1e37b75..4e8554240a 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ sources = ['pdtoolkit-%(version)s.tar.gz'] checksums = ['1037628d854edfeded3d847150d3e8fbd3774e8146407ce32f5021c80f6299be'] builddependencies = [ - ('GCC', '%(toolchain_version)s', '', True), + ('binutils', '2.35'), ] diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb index 04f2ad8b5f..92977478d5 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb @@ -34,7 +34,7 @@ sources = ['%(namelower)s-%(version)sl.tar.gz'] checksums = ['2c220390ef63d001f8ab02c380087187ea02ad2bfc5956e05ecaa0725a6f9942'] builddependencies = [ - ('GCC', '%(toolchain_version)s', '', True), + ('binutils', '2.35'), ] configopts = '--disable-cxx --disable-fortran --disable-ompi ' From a4d7fa54171c39725fb6c49c3379de60057e0b6f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 1 Jul 2021 11:39:47 +0200 Subject: [PATCH 1216/2365] changes from review --- ...SPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 25 ++++++++++++------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb index 5c267480b2..571c2db3c0 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -16,13 +16,11 @@ sources = [ {'source_urls': ['https://github.com/pinellolab/CRISPResso2/archive/'], 'filename': 'v%(version)s.tar.gz'}, {'source_urls': ['https://crispresso.pinellolab.partners.org/static/demo/'], - 'filename': 'base_editor.fastq.gz', 'extract_cmd': 'cp %s %(builddir)s'}] -patches = ['CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch'] + 'filename': 'base_editor_v%(version)s.fastq.gz', 'download_filename': 'base_editor.fastq.gz', + 'extract_cmd': 'cp %s %(builddir)s'}] checksums = [ '29dfaaa65f66225faee4887376ea6b524355332fc6f7ca4d07bb7d63596ef5e6', # v2.1.2.tar.gz - '371aad07a164721188deaa80ca7589f5cd4b871119d90d55a984c6d9c8d31c7a', # base_editor.fastq.gz - # CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch - '87e4515d87c5e70fa65a8216a950dca5876948821ef5132a993102c168ece66a', + '371aad07a164721188deaa80ca7589f5cd4b871119d90d55a984c6d9c8d31c7a', # base_editor_v2.1.2.fastq.gz ] dependencies = [ @@ -41,13 +39,22 @@ use_pip = True options = {'modulename': False} sanity_pip_check = True +# strip out too strict version requirements for dependencies +preinstallopts = "sed -i 's/,<=[0-9]*//g' setup.py && sed -i 's/==/>=/g' setup.py && " + +# this is an example command from: +# https://github.com/pinellolab/CRISPResso2#example-run-base-editing-experiment local_seq_str = 'GGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTAC' local_seq_str += 'AAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATG' local_seq_str += 'GGGAGGACATCGATGTCACCTCCAATGACTAGGGTGG' -sanity_check_commands = [('CRISPResso -h'), - ("""CRISPResso --fastq_r1 %%(builddir)s/base_editor.fastq.gz --amplicon_seq %s \ - --guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 10 \ - --quantification_window_center -10 --base_editor_output""" % local_seq_str)] +local_test_cmd = "CRISPResso --fastq_r1 %(builddir)s/base_editor_v%(version)s.fastq.gz " +local_test_cmd += "--amplicon_seq %s " % local_seq_str +local_test_cmd += "--guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 10 " +local_test_cmd += "--quantification_window_center -10 --base_editor_output" +sanity_check_commands = [ + "CRISPResso -h", + local_test_cmd, +] modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} From b39a1774872a51b11234e263a771bd3075a0cf18 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 1 Jul 2021 11:41:36 +0200 Subject: [PATCH 1217/2365] Fix missing dep in Ambers internal xblas Makefile. --- .../a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb index 4747d5bb52..ee8d80b627 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb @@ -20,6 +20,7 @@ sources = [ patches = [ 'AmberTools-20_cmake-locate-netcdf.patch', 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', ] checksums = [ 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 @@ -27,6 +28,8 @@ checksums = [ '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', ] builddependencies = [ From 356fc960fec06f0f8f39233b8e5270beb80d4e3a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 1 Jul 2021 12:07:16 +0200 Subject: [PATCH 1218/2365] Avoid OpenMPI 4 using PMIx from system instead of from --with-pmix --- .../easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 9 ++++++++- .../easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb | 9 ++++++++- .../o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb | 9 ++++++++- .../easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 9 ++++++++- 4 files changed, 32 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb index 15b78eb63e..66ef580c97 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -8,7 +8,14 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + 'f6ab980a07d65aee64985aae94d0ab47927ae3ee8bafe0aeb694fff701a8be17', # mca-btl-openib-device-params.ini-ZIH.patch + '2631e56718458cc8aefc26dd394b7d0c95f04dd7bd00d6ce6acaa64795a5f664', # mca-params.patch +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb index b83f21c664..54dd65b0ee 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -8,7 +8,14 @@ toolchain = {'name': 'gcccuda', 'version': '2020b'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + 'f6ab980a07d65aee64985aae94d0ab47927ae3ee8bafe0aeb694fff701a8be17', # mca-btl-openib-device-params.ini-ZIH.patch + '2631e56718458cc8aefc26dd394b7d0c95f04dd7bd00d6ce6acaa64795a5f664', # mca-params.patch +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb index b132e94d87..85223744f2 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -8,7 +8,14 @@ toolchain = {'name': 'iccifort', 'version': '2020.4.304'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + 'f6ab980a07d65aee64985aae94d0ab47927ae3ee8bafe0aeb694fff701a8be17', # mca-btl-openib-device-params.ini-ZIH.patch + '2631e56718458cc8aefc26dd394b7d0c95f04dd7bd00d6ce6acaa64795a5f664', # mca-params.patch +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index c80283a715..95741f972e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -8,11 +8,18 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch'] +patches = [ + 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch' +] checksums = [ '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a', # openmpi-4.1.0.tar.gz # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + 'f6ab980a07d65aee64985aae94d0ab47927ae3ee8bafe0aeb694fff701a8be17', # mca-btl-openib-device-params.ini-ZIH.patch + '2631e56718458cc8aefc26dd394b7d0c95f04dd7bd00d6ce6acaa64795a5f664', # mca-params.patch ] builddependencies = [ From 0d22040eb000ea415308ae4d0b0b93700a5460fc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 1 Jul 2021 12:17:03 +0200 Subject: [PATCH 1219/2365] Remove custom patch checksums --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 2 -- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb | 2 -- .../easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb | 2 -- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 2 -- 4 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb index 66ef580c97..de69437e30 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -13,8 +13,6 @@ checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - 'f6ab980a07d65aee64985aae94d0ab47927ae3ee8bafe0aeb694fff701a8be17', # mca-btl-openib-device-params.ini-ZIH.patch - '2631e56718458cc8aefc26dd394b7d0c95f04dd7bd00d6ce6acaa64795a5f664', # mca-params.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb index 54dd65b0ee..245532a13e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -13,8 +13,6 @@ checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - 'f6ab980a07d65aee64985aae94d0ab47927ae3ee8bafe0aeb694fff701a8be17', # mca-btl-openib-device-params.ini-ZIH.patch - '2631e56718458cc8aefc26dd394b7d0c95f04dd7bd00d6ce6acaa64795a5f664', # mca-params.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb index 85223744f2..6083f480cd 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -13,8 +13,6 @@ checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - 'f6ab980a07d65aee64985aae94d0ab47927ae3ee8bafe0aeb694fff701a8be17', # mca-btl-openib-device-params.ini-ZIH.patch - '2631e56718458cc8aefc26dd394b7d0c95f04dd7bd00d6ce6acaa64795a5f664', # mca-params.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index 95741f972e..fda533d6ab 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -18,8 +18,6 @@ checksums = [ 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - 'f6ab980a07d65aee64985aae94d0ab47927ae3ee8bafe0aeb694fff701a8be17', # mca-btl-openib-device-params.ini-ZIH.patch - '2631e56718458cc8aefc26dd394b7d0c95f04dd7bd00d6ce6acaa64795a5f664', # mca-params.patch ] builddependencies = [ From 3211818459124746dd8b5fa77209a72ab63e2df9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 1 Jul 2021 12:51:47 +0200 Subject: [PATCH 1220/2365] Fix missing dep in Ambers internal xblas Makefile. --- .../a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb index 5a6f3ea50d..fc45e8660c 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb @@ -20,6 +20,7 @@ sources = [ patches = [ 'AmberTools-20_cmake-locate-netcdf.patch', 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', ] checksums = [ 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 @@ -27,6 +28,8 @@ checksums = [ '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', ] builddependencies = [ From b6e6563ce8a7ec5afcc8afb7bcd6f1f925dc6697 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 2 Jul 2021 18:07:46 +0200 Subject: [PATCH 1221/2365] add neuralnet extension to recent R 4.x easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 +++ 6 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index e74cf716d9..4217885745 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2879,6 +2879,9 @@ exts_list = [ ('twang', '2.3', { 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 78709bbe06..d988cd20cc 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2889,6 +2889,9 @@ exts_list = [ ('twang', '2.3', { 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 6c95515829..1f05e7f1af 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2915,6 +2915,9 @@ exts_list = [ ('twang', '2.3', { 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 07da3391f8..f56ea3e03b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2920,6 +2920,9 @@ exts_list = [ ('twang', '2.3', { 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 6128b88862..b6cddf6bee 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2924,6 +2924,9 @@ exts_list = [ ('twang', '2.3', { 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 6f1241008d..ad61d8b44d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2935,6 +2935,9 @@ exts_list = [ ('twang', '2.3', { 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From 87d07eca0b40b8ac276884e863500bb2c137caab Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 2 Jul 2021 21:45:43 +0200 Subject: [PATCH 1222/2365] adding easyconfigs: GDAL-3.2.1-intel-2020b.eb, GEOS-3.9.1-iccifort-2020.4.304.eb and patches: GDAL-3.2.1_cpp-conformance.patch --- .../g/GDAL/GDAL-3.2.1-intel-2020b.eb | 67 +++++++++++++++++++ .../g/GEOS/GEOS-3.9.1-iccifort-2020.4.304.eb | 20 ++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb new file mode 100644 index 0000000000..f41af638de --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb @@ -0,0 +1,67 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.2.1' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = [ + 'GDAL-3.0.0_fix-python-CC-CXX.patch', + 'GDAL-3.2.1_cpp-conformance.patch', +] +checksums = [ + '6c588b58fcb63ff3f288eb9f02d76791c0955ba9210d98c3abd879c770ae28ea', # gdal-3.2.1.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch + 'fdf6a84d16141ccc9bc4ce98a762357ba374dea87d1f2a41a1a23be80b7ca69d', # GDAL-3.2.1_cpp-conformance.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('netCDF', '4.7.4'), + ('expat', '2.2.9'), + ('GEOS', '3.9.1'), + ('SQLite', '3.33.0'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('JasPer', '2.0.24'), + ('LibTIFF', '4.1.0'), + ('zlib', '1.2.11'), + ('cURL', '7.72.0'), + ('PCRE2', '10.35'), + ('PROJ', '7.2.1'), + ('libgeotiff', '1.6.0'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('HDF', '4.2.15'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +prebuildopts = "env LDSHARED='icc -shared' " + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..757f093e12 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-iccifort-2020.4.304.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.9.1' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7e630507dcac9dc07565d249a26f06a15c9f5b0c52dd29129a0e3d381d7e382a'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' From 4b038d50d5891dfce53046408cebfefd75efbc80 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 3 Jul 2021 08:41:46 +0100 Subject: [PATCH 1223/2365] Revert PyQt5 to a bundle with components --- .../p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index 75f5f65a1e..2fc24f0a12 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'Bundle' name = 'PyQt5' version = '5.15.1' @@ -16,6 +16,8 @@ dependencies = [ ('Qt5', '5.14.2'), ] +default_easyblock = 'PythonPackage' + local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " @@ -28,8 +30,9 @@ local_pyqtweb_configopts += "--no-stubs --no-dist-info" local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.4.0' -exts_list = [ +components = [ ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], 'start_dir': 'sip-%s' % local_sipver, @@ -37,16 +40,22 @@ exts_list = [ 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.5.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.8.1', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], 'easyblock': 'Binary', 'start_dir': '%(name)s-%(version)s', @@ -54,6 +63,8 @@ exts_list = [ 'install_cmd': local_setup_env + local_pyqt5_sip_install, }), ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', @@ -74,6 +85,7 @@ sanity_check_commands = [ ] modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'QT_INSTALL_DATA': 'qsci', } From a3dba87ee03e8cb033552eb4adeceec3c54041d4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 3 Jul 2021 08:53:25 +0100 Subject: [PATCH 1224/2365] using components is the important part --- .../easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index 2fc24f0a12..a44ceb27a7 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'PyQt5' version = '5.15.1' @@ -32,7 +32,6 @@ local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/si local_sipver = '5.4.0' components = [ ('SIP', local_sipver, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], 'start_dir': 'sip-%s' % local_sipver, @@ -40,21 +39,18 @@ components = [ 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.5.0', { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.8.1', { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], 'easyblock': 'Binary', @@ -63,7 +59,6 @@ components = [ 'install_cmd': local_setup_env + local_pyqt5_sip_install, }), ('PyQtWebEngine', version, { - 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], 'easyblock': 'ConfigureMakePythonPackage', From 5c9c36872c874a49f0d10caff3dbc492138dc885 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 3 Jul 2021 09:06:31 +0100 Subject: [PATCH 1225/2365] appease the CI --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index a44ceb27a7..d50e24ff28 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -18,6 +18,8 @@ dependencies = [ default_easyblock = 'PythonPackage' +use_pip = True + local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " @@ -69,6 +71,8 @@ components = [ }), ] +sanity_pip_check = True + sanity_check_paths = { 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 17065b86674d41819dca6cae7c1bb4e1420efea5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 3 Jul 2021 15:47:37 +0200 Subject: [PATCH 1226/2365] Remove unecessary commented lines --- .../easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb index 7f4aaf8b6b..f5dbae1ffe 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb @@ -18,13 +18,6 @@ toolchainopts = {'pic': True} source_urls = ['http://www.qhull.org/download/'] sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] -#patches = [ -# 'Qhull_pkgconfig.patch', -#] -checksums = [ - 'b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e', # qhull-2020-src-8.0.2.tgz -# 'b87d9aeff9fc4d4d1e31924fa486f94b6e1d6221a2b38dfa989991c4ad2bbc74', # Qhull_pkgconfig.patch -] builddependencies = [ ('binutils', '2.35'), From 13161ad10fb8552612b49a13f8cef9291897bcca Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 3 Jul 2021 15:54:56 +0200 Subject: [PATCH 1227/2365] MUMPS/5.3.5, SuiteSparse/5.8.1 and Hypre/2.20.0 for intel/2020b --- .../h/Hypre/Hypre-2.20.0-intel-2020b.eb | 18 ++++++++++++ .../m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb | 27 +++++++++++++++++ ...iteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb | 29 +++++++++++++++++++ 3 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-intel-2020b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-intel-2020b.eb new file mode 100644 index 0000000000..6b3ba1660e --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-intel-2020b.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.20.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5be77b28ddf945c92cde4b52a272d16fb5e9a7dc05e714fc5765948cba802c01'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb new file mode 100644 index 0000000000..162fb38b82 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -0,0 +1,27 @@ +name = 'MUMPS' +version = '5.3.5' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4'] + +dependencies = [ + ('SCOTCH', '6.1.0'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb new file mode 100644 index 0000000000..d26467a833 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '5.8.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['06726e471fbaa55f792578f9b4ab282ea9d008cf39ddcc3b42b73400acddef40'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From 15528af66fd7fd6e9d95c1b53682c35181b02518 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 3 Jul 2021 22:05:14 +0200 Subject: [PATCH 1228/2365] Add checksum for Qhull/2020.2-GCCcore-10.2.0 --- easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb index f5dbae1ffe..f55d1c11a2 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb @@ -18,6 +18,7 @@ toolchainopts = {'pic': True} source_urls = ['http://www.qhull.org/download/'] sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] builddependencies = [ ('binutils', '2.35'), From 868bb78ec24b606797bf4947a62d8ffde592f8a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 4 Jul 2021 10:39:52 +0200 Subject: [PATCH 1229/2365] fix build of manta 1.6.0 on top of Boost 1.74.0 (#13338) --- .../m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb index aef74b24d0..4587e8e91d 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb @@ -34,6 +34,11 @@ dependencies = [ ('zlib', '1.2.11'), ] +# workaround for bug in Boost 1.74.0 triggered by use of -Wundef, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/13337 +# and https://github.com/boostorg/type_traits/issues/107 +configopts = "-DBoost_NO_BOOST_CMAKE=ON" + buildopts = "FLAGS='-I$EBROOTPYTHON/include -L$EBROOTPYTHON/lib -lpython ' " # following are necessary should anyone try to make manta compatible with python3 From 49fac0720735e10e98209715d2c609717ab59f0d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 5 Jul 2021 08:59:23 +0100 Subject: [PATCH 1230/2365] adding easyconfigs: Control-FREEC-11.6-GCC-10.2.0.eb --- .../Control-FREEC-11.6-GCC-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb b/easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb new file mode 100644 index 0000000000..f705159c83 --- /dev/null +++ b/easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'Control-FREEC' +version = '11.6' + +homepage = 'https://github.com/BoevaLab/FREEC' +description = """Copy number and genotype annotation from whole +genome and whole exome sequencing data.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/BoevaLab/FREEC/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['36564f86a01236e720cf412780e87eb24f224470f5bae45a99edb2d4a3cd1734'] + +build_cmd = "cd src && make all" + +files_to_copy = ['src/freec', 'scripts', 'data', 'README.md'] + +sanity_check_paths = { + 'dirs': [''], + 'files': ['freec'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From aa1266d93422d5f03902738864d98868d8c74ea9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jul 2021 18:07:09 +0200 Subject: [PATCH 1231/2365] fix recent taxator-tk easyconfigs by adding (back) -DBoost_NO_BOOST_CMAKE=ON configure option --- .../easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb index d8f225d930..fa4ffd5008 100644 --- a/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('Boost', '1.74.0'), ] -separate_build_dir = True +configopts = "-DBoost_NO_BOOST_CMAKE=ON" buildopts = "&& mkdir -p %(installdir)s/bin" buildopts += " && cp -a {alignments-filter,binner,taxator,taxknife,unittest_ncbitaxonomy} %(installdir)s/bin/" From 2fff31cfd749b3b28e6f38c92d5114706f13966e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 6 Jul 2021 14:46:32 +0100 Subject: [PATCH 1232/2365] adding easyconfigs: LADR-2009-11A-GCCcore-10.2.0.eb --- .../l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e7a9e16bb5 --- /dev/null +++ b/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'LADR' +version = '2009-11A' + +homepage = 'https://www.cs.unm.edu/~mccune/mace4/download' +description = """Prover9, Mace4, and several related programs come packaged in + a system called LADR (Library for Automated Deduction Research). +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.cs.unm.edu/~mccune/mace4/download'] +sources = [SOURCE_TAR_GZ] +checksums = ['c32bed5807000c0b7161c276e50d9ca0af0cb248df2c1affb2f6fc02471b51d0'] + +dependencies = [('binutils', '2.35')] + +# parallel build fails +parallel = 1 + +buildopts = "all" + +runtest = "test1 && make test2 && make test3" + +files_to_copy = [(['manpages/*.1'], 'share/man/man1'), 'bin', 'Changelog', 'COPYING'] + +sanity_check_paths = { + 'files': ['bin/mace4', 'bin/prover9', 'bin/prover9-mace4'], + 'dirs': ['share'], +} + +sanity_check_commands = [("prover9 -h 2>&1 | grep 'Usage: prover9 \[-h\] \[-x\] \[-p\] \[-t \] \[-f \]'", '')] + +moduleclass = 'math' From edb2d35b4ad538567033bea6c8873c9e39e67ffd Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 6 Jul 2021 14:48:28 +0100 Subject: [PATCH 1233/2365] adding easyconfigs: Vampire-4.5.1-GCCcore-10.2.0.eb --- .../v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..edb6a8fe3b --- /dev/null +++ b/easybuild/easyconfigs/v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'CMakeMakeCp' + +name = 'Vampire' +version = '4.5.1' + +homepage = 'https://vprover.github.io/' +description = "The Vampire Theorem Prover." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'vprover' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f7bf491a2576a7fc6551eabf37763b2b6ffd36e87ad660ff191dcd88a8969ae7'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [('Z3', '4.8.10')] + +configopts = '-DZ3_DIR="$EBROOTZ3/lib64/cmake/z3"' + +files_to_copy = ['bin', 'scripts', 'LICENCE', 'README.md'] + +postinstallcmds = ["cd %(installdir)s/bin && ln -sf vampire_z3_Release vampire"] + +sanity_check_paths = { + 'files': ['bin/vampire_z3_Release', 'bin/vampire'], + 'dirs': ['scripts'], +} + +sanity_check_commands = [ + "%(namelower)s --help", + "%(namelower)s --show_options on", +] + +moduleclass = 'math' From 90e3b2250e9c8e082ca5315eacbe58fdbbe06ae5 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 6 Jul 2021 17:51:53 +0200 Subject: [PATCH 1234/2365] adding easyconfigs: freud-analysis-2.6.2-foss-2020b.eb --- .../freud-analysis-2.6.2-foss-2020b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb new file mode 100644 index 0000000000..877385766c --- /dev/null +++ b/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'freud-analysis' +version = '2.6.2' + +homepage = 'https://github.com/glotzerlab/freud' +description = """The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories +obtained from molecular dynamics or Monte Carlo simulations. High performance, parallelized C++ is used to compute +standard tools such as radial distribution functions, correlation functions, order parameters, and clusters, as well as +original analysis methods including potentials of mean force and torque (PMFTs) and local environment matching. The +freud library supports many input formats and outputs NumPy arrays, enabling integration with the scientific Python +ecosystem for many typical materials science workflows.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('CMake', '3.18.4'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('tbb', '2020.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('rowan', '1.3.0.post1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/rowan'], + 'checksums': ['8f1d0e3279f80c6ae1ee68a90955301853b5586f64e42ba4c27d85504d525e4f'], + }), + (name, version, { + 'modulename': 'freud', + 'source_urls': ['https://pypi.python.org/packages/source/f/freud-analysis'], + 'checksums': ['1cc1b95a8a386e0ac7162246b42be800cfdaf335684a614aae02841aa4df6614'], + }), +] + +moduleclass = 'vis' From 7219f51e600eb20b4aab6a40151c265359aa6275 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Wed, 7 Jul 2021 12:47:35 +0200 Subject: [PATCH 1235/2365] adding easyconfigs: Armadillo-10.5.3-foss-2020b.eb --- .../Armadillo/Armadillo-10.5.3-foss-2020b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-10.5.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-10.5.3-foss-2020b.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-10.5.3-foss-2020b.eb new file mode 100644 index 0000000000..8bc6b53c4d --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-10.5.3-foss-2020b.eb @@ -0,0 +1,24 @@ +name = 'Armadillo' +version = "10.5.3" + +homepage = 'http://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = [ + 'e6c51d8d52a6f78b9c6459f6986135093e0ee705a674307110f6175f2cd5ee37', +] + +dependencies = [ + ('Boost', '1.74.0'), + ('arpack-ng', '3.8.0'), +] + +builddependencies = [('CMake', '3.18.4')] + +moduleclass = 'numlib' From e5a9516ad7b43266793454188ddce70c3f53124f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Jul 2021 16:34:47 +0200 Subject: [PATCH 1236/2365] Fix PyQt 5.15.1 ECs --- .../p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index d50e24ff28..2fc24f0a12 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'Bundle' name = 'PyQt5' version = '5.15.1' @@ -18,8 +18,6 @@ dependencies = [ default_easyblock = 'PythonPackage' -use_pip = True - local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " @@ -34,6 +32,7 @@ local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/si local_sipver = '5.4.0' components = [ ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], 'start_dir': 'sip-%s' % local_sipver, @@ -41,18 +40,21 @@ components = [ 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.5.0', { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.8.1', { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], 'easyblock': 'Binary', @@ -61,6 +63,7 @@ components = [ 'install_cmd': local_setup_env + local_pyqt5_sip_install, }), ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], 'easyblock': 'ConfigureMakePythonPackage', @@ -71,8 +74,6 @@ components = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 0bd5817e3b2eed534514032de155b6d1d4b2b200 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 7 Jul 2021 17:10:47 +0200 Subject: [PATCH 1237/2365] adding easyconfigs: archspec-0.1.2-GCCcore-10.2.0.eb --- .../archspec/archspec-0.1.2-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..06b4ffb6c8 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.1.2' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = ['archspec-%(version)s-py2.py3-none-any.whl'] +checksums = ['71aef85b8114c357723b0ea455cba9a2bf567400dce25b0ee7f96eb4f1405d37'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +sanity_pip_check = True + +moduleclass = 'tools' From 22a46ade88a037d4df34122d272cb350a7350192 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 7 Jul 2021 17:12:06 +0200 Subject: [PATCH 1238/2365] adding easyconfigs: Voro++-0.4.6-GCCcore-10.2.0.eb --- .../v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6eb0971906 --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] +builddependencies = [('binutils', '2.35')] + + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +moduleclass = 'math' From 55a52826212f7ea3cbf1cf074a8feeaab4833eb7 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 7 Jul 2021 17:58:59 +0200 Subject: [PATCH 1239/2365] adding easyconfigs: ScaFaCoS-1.0.1-foss-2020b.eb --- .../s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb new file mode 100644 index 0000000000..c7c6f359df --- /dev/null +++ b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'ScaFaCoS' +version = '1.0.1' + +homepage = 'http://www.scafacos.de/' +description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '2b125f313795c81b0e87eb920082e91addf94c17444f9486d979e691aaded99b', # scafacos-1.0.1.tar.gz +] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GMP', '6.2.0'), + ('GSL', '2.6'), +] + +preconfigopts = 'unset F77 && ' + +configopts = 'FCFLAGS="-fallow-argument-mismatch $FCFLAGS" ' +configopts += '--enable-shared --enable-static --disable-doc ' +# tell it where to find provided FFTW +configopts += '--without-internal-fftw --with-fftw3-includedir=$EBROOTFFTW/include --with-fftw3-libdir=$EBROOTFFTW/lib ' +# only include the solvers supported for LAMMPS +# (for p2nfft we need an additonal dependency) +configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' + +sanity_check_paths = { + 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], + 'dirs': [], +} + +moduleclass = 'math' From e9d759dc81b44ac27786617dada6c385c363381d Mon Sep 17 00:00:00 2001 From: Max Voit Date: Thu, 8 Jul 2021 08:10:21 +0200 Subject: [PATCH 1240/2365] fix the libxml2 dependency (like #13030) which was broken due to #11065 --- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb index ea56b033af..a164b3b035 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -20,6 +20,10 @@ checksums = [ '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch ] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + dependencies = [ ('Python', '3.8.6'), ('netCDF', '4.7.4'), From ce5042c13171dd2ade9817ea13caa871986860c6 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Thu, 8 Jul 2021 12:21:49 +0200 Subject: [PATCH 1241/2365] fix download link --- .../h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb | 10 ++++------ .../h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb | 10 ++++------ 2 files changed, 8 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb index 6f42eeb5aa..801944ccbe 100644 --- a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb @@ -10,13 +10,11 @@ description = """HDF-EOS libraries are software libraries built on HDF libraries toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos/latest_release/', - 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos/previous_releases/', +source_urls = ['https://git.earthdata.nasa.gov/rest/git-lfs/storage/DAS/hdfeos/'] +sources = [ + {'download_filename': 'cb0f900d2732ab01e51284d6c9e90d0e852d61bba9bce3b43af0430ab5414903', + 'filename': '%(name)s%(version)sv1.00.tar.Z'} ] - -sources = ['%(name)s%(version)sv1.00.tar.Z'] - checksums = ['cb0f900d2732ab01e51284d6c9e90d0e852d61bba9bce3b43af0430ab5414903'] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb index 20f1019fff..49eb02b40f 100644 --- a/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb @@ -10,13 +10,11 @@ description = """HDF-EOS libraries are software libraries built on HDF libraries toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = [ - 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos5/latest_release/', - 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos5/previous_releases/', +source_urls = ['https://git.earthdata.nasa.gov/rest/git-lfs/storage/DAS/hdfeos5/'] +sources = [ + {'download_filename': '7054de24b90b6d9533329ef8dc89912c5227c83fb447792103279364e13dd452', + 'filename': '%(name)s.%(version)s.tar.Z'} ] - -sources = ['%(name)s.%(version)s.tar.Z'] - checksums = ['7054de24b90b6d9533329ef8dc89912c5227c83fb447792103279364e13dd452'] dependencies = [ From ee688d204233cdc44783555b3b03edcf930f48e8 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 8 Jul 2021 13:40:15 +0200 Subject: [PATCH 1242/2365] adding easyconfigs: MDAnalysis-1.1.1-foss-2020b.eb --- .../MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb new file mode 100644 index 0000000000..fb11a6330f --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb @@ -0,0 +1,51 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '1.1.1' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Biopython', '1.78'), + ('networkx', '2.5'), + ('tqdm', '4.60.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('GridDataFormats', '0.5.0', { + 'modulename': 'gridData', + 'checksums': ['f317ed60708de22d1b2a76ce89a00f722d903291b1055ff1018d441870c39d69'], + }), + ('gsd', '2.4.2', { + 'checksums': ['fa2ed62da3eb2cbfea02a22dadc1d84e80c16d874535de4bace6941c6d805851'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('mmtf-python', '1.1.2', { + 'modulename': 'mmtf', + 'checksums': ['a5caa7fcd2c1eaa16638b5b1da2d3276cbd3ed3513f0c2322957912003b6a8df'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + (name, version, { + 'modulename': 'MDAnalysis', + 'checksums': ['edfd5a8ac6cbaa8d02f505ac3e68d5a1866644a2d392a8f20e279c43e0886253'], + }), +] + +moduleclass = 'bio' From f591ee44b60ca87e5c1ee5448da79ab019edf9de Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sat, 10 Jul 2021 10:23:12 +0200 Subject: [PATCH 1243/2365] MDAnalysis: tqdm is adapted to foss 2020b requirements --- .../easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb index fb11a6330f..62cbd2a419 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb @@ -18,7 +18,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('Biopython', '1.78'), ('networkx', '2.5'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ] use_pip = True From c66c3f503737cac0d947989091be7c2668a9316a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Jul 2021 13:33:46 +0100 Subject: [PATCH 1244/2365] patch out __asm__ use in ctffind to avoid build failure on ppc64le --- .../easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb index e011de44ed..234319daa1 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb @@ -18,7 +18,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5'] +patches = ['%(name)s-%(version)s_asm-fix.patch'] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch +] dependencies = [ ('zlib', '1.2.11'), From eb75c4ff20f6702cd41f07253f0bc9d9f7966e90 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Jul 2021 13:43:50 +0100 Subject: [PATCH 1245/2365] Disable building man pages in Gdk-Pixbuf --- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb index 2d4114f968..84d0566473 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb @@ -34,7 +34,7 @@ dependencies = [ ] configopts = "--buildtype=release --default-library=both " -configopts += "-Dgio_sniffing=false -Dgir=true " +configopts += "-Dgio_sniffing=false -Dgir=true -Dman=false " sanity_check_paths = { 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], From 0d96a5bbbda149f2f04505b7e525b2d0292da508 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 12 Jul 2021 11:13:29 +0200 Subject: [PATCH 1246/2365] adding easyconfigs: lwgrp-1.0.3-gompi-2020b.eb --- .../l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb diff --git a/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb new file mode 100644 index 0000000000..10d0197ebd --- /dev/null +++ b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb @@ -0,0 +1,36 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'lwgrp' +version = '1.0.3' + +homepage = 'https://github.com/LLNL/lwgrp' +description = """The light-weight group library defines data structures and collective operations to +group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators +when the overhead of communicator creation is too costly. For example, certain sorting algorithms +recursively divide processes into subgroups as the sort algorithm progresses. These groups may be +different with each invocation, so that it is inefficient to create and destroy communicators during +the sort routine.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['650ab50d53f9af94d1c0dc0f8feb17b6692a8e1f01f9b6effafbb8a822f10eb7'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['share/%(name)s'], +} + +moduleclass = 'lib' From 541487bb82710d24156b2d934ebdd25f36b917a1 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 13 Jul 2021 09:40:14 +0200 Subject: [PATCH 1247/2365] {bio}[gompi/2020b] barrnap --- .../b/barrnap/barrnap-0.9-gompi-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2020b.eb diff --git a/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2020b.eb b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2020b.eb new file mode 100644 index 0000000000..42ca6abb5e --- /dev/null +++ b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'barrnap' +version = '0.9' + +homepage = 'https://github.com/tseemann/barrnap' +description = "Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes." + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://github.com/tseemann/barrnap/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['36c27cd4350531d98b3b2fb7d294a2d35c15b7365771476456d7873ba33cce15'] + +dependencies = [ + ('Perl', '5.32.0'), + ('HMMER', '3.3.2'), + ('BEDTools', '2.30.0'), +] + +sanity_check_paths = { + 'files': ['bin/barrnap'], + 'dirs': [], +} + +sanity_check_commands = ["barrnap --help"] + +moduleclass = 'bio' From 2f3ea52c66b3521c0957d9e611eac37aa4946096 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 13 Jul 2021 11:06:08 +0200 Subject: [PATCH 1248/2365] prokka needs Bio-Search-hmmer, but it is not part of BioPerl>1.7.3 --- .../Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb | 28 +++++++++++++++++++ .../p/prokka/prokka-1.14.5-gompi-2020b.eb | 1 + 2 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..ae7154fd3d --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.32.0'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/auto'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb index 28077ad116..0ba029a4f1 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -23,6 +23,7 @@ dependencies = [ ('BioPerl', '1.7.8'), ('BLAST+', '2.11.0'), ('Java', '11', '', True), + ('Bio-SearchIO-hmmer', '1.7.3'), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', From b59d0dce38beb8ae0150c49161bcf5aed0709411 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 13 Jul 2021 11:36:09 +0200 Subject: [PATCH 1249/2365] {bio}[{foss,fosscuda}/2020b] mhcnuggets 2.3 --- .../m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb | 28 +++++++++++++++++++ .../mhcnuggets-2.3-fosscuda-2020b.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb new file mode 100644 index 0000000000..25f8d885bd --- /dev/null +++ b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'mhcnuggets' +version = '2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/KarchinLab/mhcnuggets' +description = 'MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II.' + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'KarchinLab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5b0a8771e851e5d47c5f06c5b4a4ace218660c837b5bb527d8fa087d6dd55906'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('Keras', '2.4.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..4da712bc5d --- /dev/null +++ b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'mhcnuggets' +version = '2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/KarchinLab/mhcnuggets' +description = 'MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II.' + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +github_account = 'KarchinLab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5b0a8771e851e5d47c5f06c5b4a4ace218660c837b5bb527d8fa087d6dd55906'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('Keras', '2.4.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 05d87daec012d6a67598c6edc67c4cad639028d7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 13 Jul 2021 12:02:28 +0200 Subject: [PATCH 1250/2365] remove versionsuffix --- easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb | 1 - .../easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb index 25f8d885bd..e03e3bf731 100644 --- a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'mhcnuggets' version = '2.3' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/KarchinLab/mhcnuggets' description = 'MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II.' diff --git a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb index 4da712bc5d..7bca8c2f08 100644 --- a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'mhcnuggets' version = '2.3' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/KarchinLab/mhcnuggets' description = 'MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II.' From 9dc891af2692044369f146f852df92480d9a361c Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Tue, 13 Jul 2021 15:01:15 +0100 Subject: [PATCH 1251/2365] Suppress h5py's dependency management By default h5py's setup.py has a setup_requires for the minimum supported version of numpy (older then the one in SciPy-bundle, in some cases) based on the python interpretor version, resulting in pip attempting to fetch it during the install phase. As the dependency is already managed through easy_build, and h5py's install_requires is for any version newer than the minimum version, this change suppresses the setup_requires (using the mechanism provided by h2py for "downstream packgers - e.g. Linux distros"). --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb index 140b138358..ed2fe2ae89 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb @@ -26,6 +26,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 1a8b170bffee6d0af23e9234dccc56e89d258b97 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Tue, 13 Jul 2021 15:06:09 +0100 Subject: [PATCH 1252/2365] Suppress h5py's dependency management By default h5py's setup.py has a setup_requires for the minimum supported version of numpy (older then the one in SciPy-bundle, in some cases) based on the python interpretor version, resulting in pip attempting to fetch it during the install phase. As the dependency is already managed through easy_build, and h5py's install_requires is for any version newer than the minimum version, this change suppresses the setup_requires (using the mechanism provided by h2py for "downstream packgers - e.g. Linux distros"). --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb index 59473c4bdb..0124eaaa1e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb @@ -26,6 +26,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From a4678e460cecf0956028bf56cd40b81062e3d47e Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Tue, 13 Jul 2021 15:06:31 +0100 Subject: [PATCH 1253/2365] Suppress h5py's dependency management By default h5py's setup.py has a setup_requires for the minimum supported version of numpy (older then the one in SciPy-bundle, in some cases) based on the python interpretor version, resulting in pip attempting to fetch it during the install phase. As the dependency is already managed through easy_build, and h5py's install_requires is for any version newer than the minimum version, this change suppresses the setup_requires (using the mechanism provided by h2py for "downstream packgers - e.g. Linux distros"). --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb index 591338dd64..7e0797f278 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb @@ -26,6 +26,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 1a42eafeb0dfedce35795181741afb922c954950 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Tue, 13 Jul 2021 15:07:04 +0100 Subject: [PATCH 1254/2365] Suppress h5py's dependency management By default h5py's setup.py has a setup_requires for the minimum supported version of numpy (older then the one in SciPy-bundle, in some cases) based on the python interpretor version, resulting in pip attempting to fetch it during the install phase. As the dependency is already managed through easy_build, and h5py's install_requires is for any version newer than the minimum version, this change suppresses the setup_requires (using the mechanism provided by h2py for "downstream packgers - e.g. Linux distros"). --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb index f6bb27ac98..e53dea9b4b 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb @@ -26,6 +26,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 92264fb5115b687716a4ed919a26fd55bb0fb4b8 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 13 Jul 2021 18:04:33 +0200 Subject: [PATCH 1255/2365] adding easyconfigs: dtcmp-1.1.2-gompi-2020b.eb --- .../d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb diff --git a/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb new file mode 100644 index 0000000000..e2c9c89b8c --- /dev/null +++ b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb @@ -0,0 +1,39 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'dtcmp' +version = '1.1.2' + +homepage = 'https://github.com/LLNL/dtcmp' +description = """The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined +comparison operations to compare the values of two items which can be arbitrary MPI datatypes. +Using these comparison operations, the library provides various routines for manipulating data, +which may be distributed over the processes of an MPI communicator.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2187897220ef6cf1be753110adcd1b78571eb8f9386d90a835b79a3f9c60f18a'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('lwgrp', '1.0.3'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-lwgrp=$EBROOTLWGRP' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README.md'], + 'dirs': [] +} + +moduleclass = 'lib' From a355cb24ed1be0593261529da7071bdcd8369b8b Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:35:01 +0100 Subject: [PATCH 1256/2365] Comment explaining H5PY_SETUP_REQUIRES=0 --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb index ed2fe2ae89..b072b43d3b 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb @@ -26,6 +26,9 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 4ed8831efc66995826fd119a11037567def23893 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:35:29 +0100 Subject: [PATCH 1257/2365] Comment explaining H5PY_SETUP_REQUIRES=0 --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb index 0124eaaa1e..4110e34cc9 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb @@ -26,6 +26,9 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From a0d7c023e5fdbfa9f946fe9b43a2aad301c1ba37 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:35:48 +0100 Subject: [PATCH 1258/2365] Comment explaining H5PY_SETUP_REQUIRES=0 --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb index 7e0797f278..039b2bc3ae 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb @@ -26,6 +26,9 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 621a43219e728b01d1a67084768cc3bbf272e0af Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:36:06 +0100 Subject: [PATCH 1259/2365] Comment explaining H5PY_SETUP_REQUIRES=0 --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb index e53dea9b4b..87ef29ddce 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb @@ -26,6 +26,9 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 85d6ddd8514d298ec8ed7c17014d9300b04a587c Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:38:11 +0100 Subject: [PATCH 1260/2365] Missing word in comment --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb index b072b43d3b..3d23598929 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb @@ -27,7 +27,7 @@ sanity_pip_check = True download_dep_fail = True # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 -# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# without this environment variable, pip will fetch the minimum numpy version h5py supports during intall, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' From 5c69696f382f46807dd1df2d49f66e748461bc11 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:38:35 +0100 Subject: [PATCH 1261/2365] Missing word in comment --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb index 4110e34cc9..2ccf55fe6a 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb @@ -27,7 +27,7 @@ sanity_pip_check = True download_dep_fail = True # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 -# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' From 7ac21d630cf716291a1f1420d9d2ccd45000ca94 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:38:56 +0100 Subject: [PATCH 1262/2365] Missing word in comment --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb index 039b2bc3ae..ab4a302e17 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb @@ -27,7 +27,7 @@ sanity_pip_check = True download_dep_fail = True # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 -# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' From 968125119113b32247335d61ef1efecafd4d1d2a Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:39:14 +0100 Subject: [PATCH 1263/2365] Missing word in comment --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb index 87ef29ddce..f8dce1b3d7 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb @@ -27,7 +27,7 @@ sanity_pip_check = True download_dep_fail = True # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 -# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' From a6117048402662de93251b1bdc4752400d2547e1 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 14 Jul 2021 18:49:57 +0200 Subject: [PATCH 1264/2365] adding easyconfigs: libcircle-0.3-gompi-2020b.eb --- .../l/libcircle/libcircle-0.3-gompi-2020b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020b.eb diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020b.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020b.eb new file mode 100644 index 0000000000..7044e9c9fe --- /dev/null +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020b.eb @@ -0,0 +1,37 @@ +## +# Authors: +# * Petar Forai +# * Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'libcircle' +version = '0.3' + +homepage = 'https://github.com/hpc/libcircle/' + +description = """ + An API to provide an efficient distributed queue on a cluster. libcircle is an + API for distributing embarrassingly parallel workloads using self-stabilization. +""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://github.com/hpc/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' From d981c8af4e296d856c01289747c22a3015c2e87e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 14 Jul 2021 20:27:07 +0200 Subject: [PATCH 1265/2365] remove platform spec subdir from sanity check --- .../b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb index ae7154fd3d..b740298019 100644 --- a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb @@ -22,7 +22,7 @@ options = {'modulename': 'Bio::SearchIO::hmmer3'} sanity_check_paths = { 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/auto'], + 'dirs': [''], } moduleclass = 'bio' From e5d9eaaae20e6d23cbbb145483eec6095f4c21bd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 14 Jul 2021 20:28:37 +0200 Subject: [PATCH 1266/2365] remove platform spec subdir from sanity check v2 --- .../b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb index b740298019..124e6f8875 100644 --- a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb @@ -22,7 +22,7 @@ options = {'modulename': 'Bio::SearchIO::hmmer3'} sanity_check_paths = { 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], - 'dirs': [''], + 'dirs': [], } moduleclass = 'bio' From cd26a0c6ee93d0dd1abee525dbe0e1b6fed4f605 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 15 Jul 2021 13:59:59 +0200 Subject: [PATCH 1267/2365] adding easyconfigs: torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb --- ...text-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb new file mode 100644 index 0000000000..05a3968437 --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.9.1' +local_pytorch_version = '1.8.1' +local_python_suffix = '-Python-%(pyver)s' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +# The tarball of the final v0.9.1 release is labelled as a release candidate +# see https://github.com/pytorch/text/releases/tag/v0.9.1-rc1 +local_tarball_version = '%(version)s-rc1' + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%s.tar.gz' % local_tarball_version] +checksums = ['336397dfae5587e5dbdd2235020acb86f46af36c1c75b47186c67d0b19acee12'] + +builddependencies = [ + ('RE2', '2021-06-01'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SentencePiece', '0.1.96'), + ('tqdm', '4.56.2'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.1.5'), +] + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/BuildExtension/d' setup.py &&" + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 919748256f9ff6111d38b0a3e174b0201027cc7e Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 15 Jul 2021 15:28:25 +0200 Subject: [PATCH 1268/2365] adding easyconfigs: Scalasca-2.6-gompic-2020b.eb --- .../s/Scalasca/Scalasca-2.6-gompic-2020b.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompic-2020b.eb diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompic-2020b.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompic-2020b.eb new file mode 100644 index 0000000000..6896e705ca --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompic-2020b.eb @@ -0,0 +1,52 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Scalasca' +version = '2.6' + +homepage = 'https://www.scalasca.org/' +description = """ + Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The + analysis identifies potential performance bottlenecks -- in particular + those concerning communication and synchronization -- and offers guidance + in exploring their causes. +""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3f9cb1d58f3e25090a39da777bae8ca2769fd10cbd6dfb9a4887d873ee2441e'] + +builddependencies = [ + ('CubeWriter', '4.6'), +] + +dependencies = [ + ('CubeGUI', '4.6'), + ('CubeLib', '4.6'), + ('OTF2', '2.3'), + ('Score-P', '7.0'), +] + +sanity_check_paths = { + 'files': ['bin/scalasca', 'lib/libpearl.replay.a'], + 'dirs': [], +} + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scalasca/patterns'} + +moduleclass = 'perf' From d910adba36e6191ccc5bed63d790365afdd9a7e7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 16 Jul 2021 13:56:04 +0100 Subject: [PATCH 1269/2365] Add PCAmatchR to recent R --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 ++ .../easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 ++ .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 ++ .../easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 ++ .../easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 28 ++++++++----------- .../easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 ++ 6 files changed, 27 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 4217885745..ba996e728c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2882,6 +2882,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index d988cd20cc..e745b17b3e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2892,6 +2892,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 1f05e7f1af..b221d6c94b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2918,6 +2918,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index f56ea3e03b..be354b8bf2 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2923,6 +2923,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index b6cddf6bee..417a6fa52c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -770,7 +770,7 @@ exts_list = [ ('memoise', '2.0.0', { 'checksums': ['ff9ae3a1a95ad6271d98e6eca016768b790e44bd613356b8e86b685aefd9ecaf'], }), - ('bit64', '4.0.5', { + ('bit64', version, { 'checksums': ['25df6826ea5e93241c4874cad4fa8dadc87a40f4ff74c9107aa12a9e033e1578'], }), ('blob', '1.2.1', { @@ -1740,7 +1740,7 @@ exts_list = [ 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], 'checksums': [ 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz - '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch ], }), ('diveRsity', '1.9.90', { @@ -2160,8 +2160,7 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', - 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], + 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], @@ -2222,13 +2221,12 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.1', { 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], @@ -2342,8 +2340,7 @@ exts_list = [ 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], }), ('rda', '1.0.2-2.1', { - 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', - 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], }), ('sampling', '2.9', { 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], @@ -2442,9 +2439,9 @@ exts_list = [ 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], }), ('V8', '3.4.0', { - 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], - 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], }), ('rstan', '2.21.2', { 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], @@ -2696,13 +2693,9 @@ exts_list = [ 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), ('gWidgets2tcltk', '1.0-6', { - 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... 'modulename': False, + 'preinstallopts': "xvfb-run ", + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], }), ('mgsub', '1.7.2', { 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], @@ -2927,6 +2920,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index ad61d8b44d..8262ab1509 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2938,6 +2938,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From fe5b0a49e76b3276224652891db28d9e1e65719b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 16 Jul 2021 14:21:50 +0100 Subject: [PATCH 1270/2365] Include recent changes to R-4.0.5 --- .../easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 27 ++++++++++++------- 1 file changed, 17 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 417a6fa52c..2492b2ca6c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -770,7 +770,7 @@ exts_list = [ ('memoise', '2.0.0', { 'checksums': ['ff9ae3a1a95ad6271d98e6eca016768b790e44bd613356b8e86b685aefd9ecaf'], }), - ('bit64', version, { + ('bit64', '4.0.5', { 'checksums': ['25df6826ea5e93241c4874cad4fa8dadc87a40f4ff74c9107aa12a9e033e1578'], }), ('blob', '1.2.1', { @@ -1740,7 +1740,7 @@ exts_list = [ 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], 'checksums': [ 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz - '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, ], }), ('diveRsity', '1.9.90', { @@ -2160,7 +2160,8 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], @@ -2221,12 +2222,13 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.1', { 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], @@ -2340,7 +2342,8 @@ exts_list = [ 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.9', { 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], @@ -2439,9 +2442,9 @@ exts_list = [ 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], }), ('V8', '3.4.0', { - 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', - 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', }), ('rstan', '2.21.2', { 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], @@ -2693,9 +2696,13 @@ exts_list = [ 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), ('gWidgets2tcltk', '1.0-6', { - 'modulename': False, - 'preinstallopts': "xvfb-run ", 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, }), ('mgsub', '1.7.2', { 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], @@ -2920,7 +2927,7 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), - ('PCAmatchR', '0.3.0', { + ('PCAmatchR', '0.3.0', { 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], }), ] From d5113bc434c467761431ea2ac272fbd8446623bf Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 16 Jul 2021 14:50:38 +0100 Subject: [PATCH 1271/2365] Fix bad indent in R-4.0.5 --- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 2492b2ca6c..d80f499a0b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2927,7 +2927,7 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), - ('PCAmatchR', '0.3.0', { + ('PCAmatchR', '0.3.0', { 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], }), ] From 17c205dbb72d46bac6d0e82ad4570e405bc83015 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 16 Jul 2021 15:46:02 +0200 Subject: [PATCH 1272/2365] Avoid dependency on system GTK+ in GTK+ themes --- .../g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb index daf5522a2c..9eaad73eab 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} builddependencies = [ ('binutils', '2.35'), + ('Autotools', '20200321'), ('GObject-Introspection', '1.66.1'), ('gettext', '0.21'), ('pkg-config', '0.29.2'), @@ -40,18 +41,24 @@ default_component_specs = { } components = [ + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], }), ('adwaita-icon-theme', '3.38.0', { + 'preconfigopts': 'autoreconf -f -i && ', 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97'], - }), - (name, version, { - 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], }), ] From cc7aa41f1971e09616b0bbcff7991da0427f509d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 16 Jul 2021 16:33:15 +0200 Subject: [PATCH 1273/2365] {bio}[foss/2020b] Qualimap 2.2.1 --- .../Qualimap-2.2.1-foss-2020b-R-4.0.3.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..4b25f9686c --- /dev/null +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'Qualimap' +version = '2.2.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://qualimap.bioinfo.cipf.es/' +description = """Qualimap 2 is a platform-independent application written in Java and R that provides both + a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of + alignment sequencing data and its derivatives like feature counts.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads/'] +sources = ['qualimap_v%(version)s.zip'] +checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] + +dependencies = [ + ('Java', '11', '', True), + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': ['qualimap'], + 'dirs': [], +} + +sanity_check_commands = ["qualimap --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 29862533d35053f3968411694367649dc437a46c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 16 Jul 2021 21:19:26 +0200 Subject: [PATCH 1274/2365] Add hal9001 module to R v4 --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 6 ++++++ 6 files changed, 36 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 4217885745..79690927e5 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2882,6 +2882,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index d988cd20cc..115fc7be07 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2892,6 +2892,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 1f05e7f1af..8723c64f4e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2918,6 +2918,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index f56ea3e03b..bfe7e12665 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2923,6 +2923,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index b6cddf6bee..2e7c455697 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2927,6 +2927,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index ad61d8b44d..3ea4c22b46 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2938,6 +2938,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From 7e320985388632cc56fcd232c75624fdb0d0a8ef Mon Sep 17 00:00:00 2001 From: Sassy Date: Sat, 17 Jul 2021 21:05:36 +0000 Subject: [PATCH 1275/2365] OpenMM update to 7.5.1 required for alphafold --- .../o/OpenMM/OpenMM-7.5.1-foss-2020b.eb | 58 ++++++++++++++++ .../o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb | 66 +++++++++++++++++++ 2 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb new file mode 100644 index 0000000000..15672d7342 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb @@ -0,0 +1,58 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.1' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +separate_build_dir = True + +dependencies = [ + ('FFTW', '3.3.8'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SWIG', '4.0.2'), +] + +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..5f6aeae351 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb @@ -0,0 +1,66 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.1' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_path_to_nvcc.patch'] +checksums = [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # 7.5.1.tar.gz + '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SWIG', '4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 3a4447503d3ea5507d0e46bfe709f617b4435260 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 20 Jul 2021 16:55:31 +0200 Subject: [PATCH 1276/2365] Add TensorFlow patch to fix crash on shutdown --- .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 5e6c23ac57..bafbef6444 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -163,6 +163,7 @@ exts_list = [ 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', ], 'checksums': [ @@ -187,6 +188,8 @@ exts_list = [ '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', ], From dd3d4c1e07bbbe295d0fc99583ff862d91395f71 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 20 Jul 2021 13:55:09 +0200 Subject: [PATCH 1277/2365] adding easyconfigs: PySide2-5.14.2.3-GCCcore-10.2.0.eb --- .../PySide2-5.14.2.3-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dcc75de0c8 --- /dev/null +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PySide2' +version = '5.14.2.3' + +homepage = "https://pypi.python.org/pypi/%(name)s/" +description = """PySide2 is the official Python module from the Qt for Python project, + which provides access to the complete Qt 5.12+ framework.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://download.qt.io/official_releases/QtForPython/%(namelower)s/%(name)s-%(version)s-src/'] +sources = ['pyside-setup-opensource-src-%(version)s.tar.xz'] +checksums = ['032de309505c78ba52c225aaf5fd717b8d87ae863aa7cee8ba58ba6141c59022'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Sphinx', '3.5.2'), + ('Clang', '11.0.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Qt5', '5.14.2'), +] + +preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' +prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' +preinstallopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' + +options = {'modulename': 'PySide2'} + +moduleclass = 'devel' From 024b1782a70f17c1e03c14b0968873cb2be915c5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 21 Jul 2021 15:23:41 +0200 Subject: [PATCH 1278/2365] Explicitly specify use of pip and pip sanity checking for PySide2 --- .../easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb index dcc75de0c8..3ec394a440 100644 --- a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -24,6 +24,9 @@ dependencies = [ ('Qt5', '5.14.2'), ] +use_pip = True +sanity_pip_check = True + preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' preinstallopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' From 246545e61643a0a78b8badfb0104fa0df0eb8ce5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 21 Jul 2021 15:40:11 +0200 Subject: [PATCH 1279/2365] Explicitly prevent downloading pip dependencies for PySide2 --- .../easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb index 3ec394a440..f69741b3ee 100644 --- a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -26,6 +26,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' From 377f3063c594c0e94741fd05da42f2d273e1ea9b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 22 Jul 2021 12:04:34 +0200 Subject: [PATCH 1280/2365] adding easyconfigs: libdeflate-1.7-GCCcore-10.2.0.eb, libRmath-4.1.0-GCCcore-10.2.0.eb, LIBSVM-3.25-GCCcore-10.2.0.eb, TCLAP-1.2.4-GCCcore-10.2.0.eb, vt-0.57721-GCC-10.2.0.eb and patches: vt-0.57721_avoid-implicit-conversion.patch, vt-0.57721_fail-on-test-error.patch, vt-0.57721_fix-Rmath-includes.patch, vt-0.57721_update_htsutils.patch, vt-0.57721_use-external-libs.patch --- .../l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb | 38 ++++++++++ .../libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb | 53 ++++++++++++++ .../libdeflate-1.7-GCCcore-10.2.0.eb | 38 ++++++++++ .../t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb | 32 +++++++++ .../easyconfigs/v/vt/vt-0.57721-GCC-10.2.0.eb | 72 +++++++++++++++++++ 5 files changed, 233 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..54bac051fb --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.25' + +homepage = 'https://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'cjlin1' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%s.tar.gz' % version.replace('.', '')] +patches = ['LIBSVM-3.23_shared_lib.patch'] +checksums = [ + '1f587ec0df6fd422dfe50f942f8836ac179b0723b768fe9d2fabdfd1601a0963', # v325.tar.gz + 'c0ede89365949644f5d7f11382a3f176fd76317c7f5ae5769226ff7c3a801fe6', # LIBSVM-3.23_shared_lib.patch +] + +dependencies = [('binutils', '2.35')] + +local_bins = ['svm-%s' % x for x in ['predict', 'scale', 'train']] + +files_to_copy = [ + (local_bins, 'bin'), + (['svm.o'], 'lib'), + (['libsvm*'], 'lib'), + (['svm.h'], 'include/libsvm'), + 'tools' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + ['lib/libsvm.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1f09fb058e --- /dev/null +++ b/easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# Updated: Denis Kristak (INUITS) +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'libRmath' +version = '4.1.0' + +homepage = 'https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library' +description = """The routines supporting the distribution and special functions in R and a few others are declared + in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = ['R-%(version)s.tar.gz'] +checksums = ['e8e68959d7282ca147360fc9644ada9bd161bab781bab14d33b8999a95182781'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('cURL', '7.72.0'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('PCRE2', '10.35'), +] + +parallel = 1 + +start_dir = 'src/nmath/standalone' + +preconfigopts = 'cd %(builddir)s/R-%(version)s && ' +configopts = '--with-readline=no --with-recommended-packages=no --with-x=no' + +postinstallcmds = ["cp -r %(builddir)s/R-%(version)s/src/include/R_ext %(installdir)s/include/"] + +runtest = 'check' + +sanity_check_paths = { + 'files': ["lib/libRmath.%s" % SHLIB_EXT, "lib/libRmath.a", + "lib/pkgconfig/libRmath.pc", + "include/Rmath.h"], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c517a5b337 --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.7' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a5e6a0a9ab69f40f0f59332106532ca76918977a974e7004977a9498e3f11350'] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b2e44cb235 --- /dev/null +++ b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'TCLAP' +version = '1.2.4' + +homepage = 'http://tclap.sourceforge.net/' +description = """TCLAP is a small, flexible library that provides a simple interface for defining and accessing +command line arguments. It was intially inspired by the user friendly CLAP libary.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['634c5b59dbb1ccbc9d6a5f6de494a257e29a3f59dcb6fc30445ff39b45188574'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -i -f && " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/tclap/CmdLine.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.2.0.eb new file mode 100644 index 0000000000..f5b37df4b6 --- /dev/null +++ b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.2.0.eb @@ -0,0 +1,72 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) + +easyblock = 'MakeCp' + +name = 'vt' +version = '0.57721' + +homepage = 'https://genome.sph.umich.edu/wiki/Vt' +description = """A tool set for short variant discovery in genetic sequence data.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'atks' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-0.57721_use-external-libs.patch', + '%(name)s-0.57721_fix-Rmath-includes.patch', + '%(name)s-0.57721_avoid-implicit-conversion.patch', + '%(name)s-0.57721_fail-on-test-error.patch', + '%(name)s-0.57721_update_htsutils.patch', +] +checksums = [ + '8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17', # 0.57721.tar.gz + '5a31713ae7c5febf850eec294dbba45b6b240d832cb94bdfe9ee695fd13e45bb', # vt-0.57721_use-external-libs.patch + '663525f5180a66d8817f271a69de1884576e2414d46b7ba93029d78f71d5b14c', # vt-0.57721_fix-Rmath-includes.patch + '56d874d5c7d488761f25afb4ee3717c88dfd959ed76efb75a8531b8428d30ccd', # vt-0.57721_avoid-implicit-conversion.patch + '4146282eb6ec852485f5a16e647da9c3b210450ceb5519b9b4a98bc52124469a', # vt-0.57721_fail-on-test-error.patch + '1c170b7ba2a4d392830f64392075ff75bbbc29137fe9f2922aeb7345e2ab6298', # vt-0.57721_update_htsutils.patch +] + +# checksums = [ +# '8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17', # 0.57721.tar.gz +# '5a31713ae7c5febf850eec294dbba45b6b240d832cb94bdfe9ee695fd13e45bb', # vt-0.57721_use-external-libs.patch +# '663525f5180a66d8817f271a69de1884576e2414d46b7ba93029d78f71d5b14c', # vt-0.57721_fix-Rmath-includes.patch +# '56d874d5c7d488761f25afb4ee3717c88dfd959ed76efb75a8531b8428d30ccd', # vt-0.57721_avoid-implicit-conversion.patch +# 'ba2cfc24a88a4291b2da634db49e18199c379eb95d3b3acac59556bc68c292df', # vt-0.57721_update-faidx.patch +# '4146282eb6ec852485f5a16e647da9c3b210450ceb5519b9b4a98bc52124469a', # vt-0.57721_fail-on-test-error.patch +# ] + +builddependencies = [ + ('binutils', '2.35'), + ('TCLAP', '1.2.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.72.0'), + ('PCRE', '8.44'), + ('PCRE2', '10.35'), + ('libdeflate', '1.7'), + ('libRmath', '4.1.0'), + ('LIBSVM', '3.25'), + ('HTSlib', '1.12'), +] + +runtest = 'test' + +files_to_copy = [ + (['vt'], 'bin'), + (['*.h'], 'include/vt'), + 'test', 'README.md', 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/vt'], + 'dirs': [], +} + +moduleclass = 'bio' From b9cfcabfa2bdf07746ac872f535e787ce146b3bc Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 22 Jul 2021 12:11:51 +0200 Subject: [PATCH 1281/2365] adding easyconfigs: vcflib-1.0.2-GCC-10.2.0.eb, fsom-20141119-GCCcore-10.2.0.eb, intervaltree-0.1-GCCcore-10.2.0.eb, fastahack-1.0.0-GCCcore-10.2.0.eb and patches: vcflib-1.0.2_use-external-deps.patch, fsom-20141119_build-libs.patch, fsom-20141119_fix-abs-overload.patch, fastahack-1.0.0_build-libs.patch --- .../fastahack-1.0.0-GCCcore-10.2.0.eb | 32 ++++++++++ .../f/fsom/fsom-20141119-GCCcore-10.2.0.eb | 34 +++++++++++ .../intervaltree-0.1-GCCcore-10.2.0.eb | 32 ++++++++++ .../v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 60 +++++++++++++++++++ 4 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..73aaa73c4a --- /dev/null +++ b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'fastahack' +version = '1.0.0' + +homepage = 'https://github.com/ekg/fastahack' +description = """Utilities for indexing and sequence extraction from FASTA files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.0.0_build-libs.patch'] +checksums = [ + 'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae', # v1.0.0.tar.gz + '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4', # fastahack-1.0.0_build-libs.patch +] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..eac8d686cd --- /dev/null +++ b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'fsom' +version = '20141119' +local_commit = 'a6ef318' + +homepage = 'https://github.com/ekg/fsom' +description = """A tiny C library for managing SOM (Self-Organizing Maps) neural networks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [ + '%(name)s-20141119_build-libs.patch', + '%(name)s-20141119_fix-abs-overload.patch' +] + + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfsom.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bdf771c099 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'intervaltree' +version = '0.1' + +homepage = 'https://github.com/ekg/intervaltree' +description = """An interval tree can be used to efficiently find a set of numeric intervals + overlapping or containing another interval. This library provides a basic implementation of an + interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307'] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +preinstallopts = 'DESTDIR="" PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/interval_tree_test', 'include/intervaltree/IntervalTree.h'], + 'dirs': [], +} +sanity_check_commands = ["interval_tree_test"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..1b77b9cb61 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -0,0 +1,60 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.2' +# versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/vcflib/vcflib' +description = """vcflib provides methods to manipulate and interpret sequence variation as it can be + described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended + to concisely describe reference-indexed genetic variations between individuals.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['vcflib-1.0.2_use-external-deps.patch'] +checksums = [ + 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz + '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.12'), + ('tabixpp', '1.1.0'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20141119'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f -regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" +preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" +preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" +preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" +preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +sanity_check_paths = { + 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["vcfremap"] + +moduleclass = 'bio' From 777bed9b35162c888e8d796db2ff5c0689b23efb Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 22 Jul 2021 12:17:42 +0200 Subject: [PATCH 1282/2365] adding easyconfigs: any2fasta-0.4.2-GCCcore-10.2.0.eb, filevercmp-20191210-GCCcore-10.2.0.eb, freebayes-1.3.5-GCC-10.2.0.eb, multichoose-1.0.3-GCCcore-10.2.0.eb, samclip-0.4.0-GCCcore-10.2.0.eb and patches: filevercmp-20191210_build-libs.patch --- .../any2fasta-0.4.2-GCCcore-10.2.0.eb | 34 +++++++++++++++ .../filevercmp-20191210-GCCcore-10.2.0.eb | 30 +++++++++++++ .../f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb | 43 +++++++++++++++++++ .../multichoose-1.0.3-GCCcore-10.2.0.eb | 26 +++++++++++ .../s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb | 27 ++++++++++++ 5 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4b16b010fe --- /dev/null +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'any2fasta' +version = '0.4.2' + +homepage = 'https://github.com/tseemann/any2fasta' +description = "Convert various sequence formats to FASTA" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# https://github.com/tseemann/any2fasta +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] + +dependencies = [('Perl', '5.32.0')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['any2fasta'], + 'dirs': [], +} + +sanity_check_commands = [ + 'any2fasta -h', + 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2ce8759f9a --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'filevercmp' +version = '20191210' +local_commit = 'df20dcc' + +homepage = 'https://github.com/ekg/filevercmp' +description = """filevercmp function as in sort --version-sort.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20191210_build-libs.patch'] + + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'DESTDIR="" PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb new file mode 100644 index 0000000000..4f981788db --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'freebayes' +version = '1.3.5' + +homepage = 'https://github.com/freebayes/freebayes' +description = "Bayesian haplotype-based genetic polymorphism discovery and genotyping." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/freebayes', + 'repo_name': 'freebayes', + 'tag': 'v1.3.5', + 'recursive': True, + }, +}] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), +] + +dependencies = [ + ('parallel', '20210322'), + ('VCFtools', '0.1.16'), +] + +configopts = "--buildtype debug" + +postinstallcmds = ['cp %(builddir)s/freebayes/scripts/* %(installdir)s/'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['bin/freebayes', 'bin/bamleftalign', 'freebayes-parallel'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..423504cb40 --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'multichoose' +version = '1.0.3' + +homepage = 'https://github.com/ekg/multichoose' +description = """generate multiset combinations (n multichoose k).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877'] + +builddependencies = [('binutils', '2.35')] + +local_bins = [name, 'multipermute'] +files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/multichoose')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..52eb3f5c23 --- /dev/null +++ b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'samclip' +version = '0.4.0' + +homepage = 'https://github.com/tseemann/samclip' +description = """Filter SAM file for soft and hard clipped alignments.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127'] + +dependencies = [('Perl', '5.32.0')] + +sanity_check_paths = { + 'files': [name], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From fcdfac3a89e451a0adf4f82b038d4b88dd5d2361 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 22 Jul 2021 12:26:36 +0200 Subject: [PATCH 1283/2365] update --- .../smithwaterman-20160702-GCCcore-10.2.0.eb | 34 +++++++++++++ .../s/snippy/snippy-4.6.0-GCC-10.2.0.eb | 49 +++++++++++++++++++ .../snp-sites-2.5.1-GCCcore-10.2.0.eb | 37 ++++++++++++++ .../w/wgsim/wgsim-20111017-GCC-10.2.0.eb | 32 ++++++++++++ 4 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..65ec48867c --- /dev/null +++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'smithwaterman' +version = '20160702' +local_commit = '2610e25' + +homepage = 'https://github.com/ekg/smithwaterman' +description = """smith-waterman-gotoh alignment algorithm.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20160702_build-shared-lib.patch'] +checksums = [ + '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz + '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..b27c7c5455 --- /dev/null +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'Tarball' + +name = 'snippy' +version = '4.6.0' + +homepage = 'https://github.com/tseemann/snippy' +description = "Rapid haploid variant calling and core genome alignment" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/tseemann/snippy/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7264e3819e249387effd3eba170ff49404b1cf7347dfa25944866f5aeb6b11c3'] + +dependencies = [ + ('Perl', '5.32.0'), + ('BioPerl', '1.7.8'), + ('BWA', '0.7.17'), + ('BCFtools', '1.12'), + ('BEDTools', '2.30.0'), + ('SAMtools', '1.11'), + ('parallel', '20210322'), + ('minimap2', '2.18'), + ('vcflib', '1.0.2'), + ('vt', '0.57721'), + ('snpEff', '5.0', '-Java-13', True), + ('samclip', '0.4.0'), + ('seqtk', '1.3'), + ('snp-sites', '2.5.1'), + ('any2fasta', '0.4.2'), + ('wgsim', '20111017'), + ('freebayes', '1.3.5'), # todo freebayes-parallel +] + +# remove included binaries for required dependencies +postinstallcmds = ["rm -r %(installdir)s/binaries"] + +sanity_check_paths = { + 'files': ['bin/snippy', 'perl5/Snippy/Version.pm'], + 'dirs': ['etc'], +} + +sanity_check_commands = [ + "snippy --version", + "snippy --check", + "snippy --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d21942b053 --- /dev/null +++ b/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'snp-sites' +version = '2.5.1' + +homepage = 'https://sanger-pathogens.github.io/snp-sites/' +description = """Finds SNP sites from a multi-FASTA alignment file.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'sanger-pathogens' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['913f79302e5d3127aea382756abc9ffeb05e26ce00022f43a6ea16a55cdd7a7e'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), + ('binutils', '2.35'), + ('Check', '0.15.2'), +] + +dependencies = [('zlib', '1.2.11')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/snp-sites'], + 'dirs': [], +} +sanity_check_commands = ["snp-sites -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb new file mode 100644 index 0000000000..de520d35fa --- /dev/null +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'wgsim' +version = '20111017' +local_commit = 'a12da3375ff3b51a5594d4b6fa35591173ecc229' + +homepage = 'https://github.com/lh3/wgsim/' +description = """Wgsim is a small tool for simulating sequence reads from a reference genome.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = [ + ('wgsim-%(version)s_add_makefile.patch', 1) +] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +files_to_copy = [(["wgsim"], 'bin')] + +sanity_check_commands = [("%(name)s -h 2>&1 | grep 'Program: wgsim (short read simulator)'")] + +sanity_check_paths = { + 'files': ['bin/wgsim'], + 'dirs': [], +} + +moduleclass = 'bio' From fdf6f985b5812031e262b2762ec11d7fa857414d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 22 Jul 2021 14:03:07 +0200 Subject: [PATCH 1284/2365] Optimise PySide2/5.14.2.3 EB file --- .../p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb index f69741b3ee..4d1fe0c1f1 100644 --- a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -14,8 +14,8 @@ sources = ['pyside-setup-opensource-src-%(version)s.tar.xz'] checksums = ['032de309505c78ba52c225aaf5fd717b8d87ae863aa7cee8ba58ba6141c59022'] builddependencies = [ + ('binutils', '2.35'), ('CMake', '3.18.4'), - ('Sphinx', '3.5.2'), ('Clang', '11.0.1'), ] @@ -24,13 +24,17 @@ dependencies = [ ('Qt5', '5.14.2'), ] -use_pip = True +use_pip = False sanity_pip_check = True download_dep_fail = True preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' + prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' +buildcmd = 'build --parallel=16' + preinstallopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' +install_target = 'install --parallel=16' options = {'modulename': 'PySide2'} From f8ec7a7d5a304be021461170078a33843f5849bb Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 23 Jul 2021 11:35:41 +0200 Subject: [PATCH 1285/2365] added checksums --- .../easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb index eac8d686cd..a298d8f099 100644 --- a/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb @@ -17,7 +17,11 @@ patches = [ '%(name)s-20141119_build-libs.patch', '%(name)s-20141119_fix-abs-overload.patch' ] - +checksums = [ + '832ec7d0aff53e04fdb8bbaa5be2177de362afac6ed58a59a97abb7eef29cb60', # a6ef318.tar.gz + 'a6349a6462473f011260074eca6ad9826e3c6aeb20674b696c5848d10610cdd7', # fsom-20141119_build-libs.patch + '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639', # fsom-20141119_fix-abs-overload.patch +] builddependencies = [('binutils', '2.35')] From 01fa2f8e1716dd87223d76a160820da857374c1f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 23 Jul 2021 11:36:44 +0200 Subject: [PATCH 1286/2365] added checksums --- .../f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb | 5 ++++- .../easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb | 1 + 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb index 2ce8759f9a..a1ba056e29 100644 --- a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb @@ -14,7 +14,10 @@ github_account = 'ekg' source_urls = [GITHUB_SOURCE] sources = ['%s.tar.gz' % local_commit] patches = ['%(name)s-20191210_build-libs.patch'] - +checksums = [ + '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz + 'f0145a1590b555288d5c4560a58bf6976a7605ef949f9071d45e7afb815b540c', # filevercmp-20191210_build-libs.patch +] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb index 4f981788db..7889e193d7 100644 --- a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb @@ -17,6 +17,7 @@ sources = [{ 'recursive': True, }, }] +checksums = ['b614a44cb53a164ab8579d75c8eb6fc17415a502628aeeb12b42218893a10278'] builddependencies = [ ('binutils', '2.35'), From ba13e8685097957b370908aa5d09d46841649095 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 23 Jul 2021 11:38:44 +0200 Subject: [PATCH 1287/2365] added checksums --- easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb index de520d35fa..f7361ba8bb 100644 --- a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -15,6 +15,10 @@ sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_TAR patches = [ ('wgsim-%(version)s_add_makefile.patch', 1) ] +checksums = [ + 'e1e6bff5c084e4494023505206ae3e0b0f5a315c9f7390b2f347c370c7f36533', # wgsim-20111017.tar.gz + '81b61c6cceaa4a05e9ee12976dede0df1639f9504ded11e7099cbd1f932c6c9d', # wgsim-20111017_add_makefile.patch +] dependencies = [('zlib', '1.2.11')] From 3bfbe8dbe6f8dbcce515a84046faed91e7194395 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 23 Jul 2021 14:38:00 +0200 Subject: [PATCH 1288/2365] adding easyconfigs: AOCC-3.1.0-GCCcore-10.2.0.eb, AOCC-3.1.0-GCCcore-10.3.0.eb --- .../a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3d7d1d725e --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'AOCC' +version = '3.1.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['1948104a430506fe5e445c0c796d6956109e7cc9fc0a1e32c9f1285cfd566d0c'] + +clangversion = '12.0.0' + +dependencies = [ + ('binutils', '2.35'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +moduleclass = 'compiler' From 87466d9e8450a9da40944c05455ded8734f8c3be Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 23 Jul 2021 18:19:23 +0100 Subject: [PATCH 1289/2365] adding easyconfigs: GDCM-3.0.8-GCCcore-9.3.0.eb, GDCM-3.0.8-GCCcore-10.2.0.eb --- .../g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9386c09091 --- /dev/null +++ b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'GDCM' +version = '3.0.8' + +homepage = 'https://sourceforge.net/projects/gdcm' +description = "Grassroots DICOM: Cross-platform DICOM implementation" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['33077958ec2fb43361cd4e2889dc901cc4d45c30b7f134950fc57ecd4f0637e1'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = "-DGDCM_BUILD_DOCBOOK_MANPAGES=0" + +sanity_check_paths = { + 'files': ['lib/libgdcmCommon.a', 'lib/libgdcmDICT.a'], + 'dirs': ['include/gdcm-%(version_major_minor)s', 'lib/gdcm-%(version_major_minor)s'], +} + +moduleclass = 'tools' From 6dbfb6a736fa35530f6bca79b6743b22e6353a34 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 23 Jul 2021 12:32:03 -0700 Subject: [PATCH 1290/2365] {bio}[GCC/10.2.0] Jellyfish 2.3.0 --- .../j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..116f07001d --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.3.0' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e195b7cf7ba42a90e5e112c0ed27894cd7ac864476dc5fb45ab169f5b930ea5a'] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, +# they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' From 29f0c59ef2bf66862831156987077ba5f4a85697 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 23 Jul 2021 14:51:26 -0700 Subject: [PATCH 1291/2365] moved down to GCC --- .../m/Metal/Metal-2020-05-05-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb new file mode 100644 index 0000000000..67bd18df24 --- /dev/null +++ b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'Metal' +version = '2020-05-05' + +homepage = 'http://csg.sph.umich.edu/abecasis/Metal/' +description = """Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large + datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/statgen/METAL/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['0ffa2419ca2ab43766e7e6e8c97822c8ce1f5b6233fb5f992d1b1be1955fede7'] + +builddependencies = [('CMake', '3.18.4')] +dependencies = [('zlib', '1.2.11')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin && ' + + 'cp %(builddir)s/easybuild_obj/bin/metal %(installdir)s/bin' +] + +sanity_check_paths = { + 'files': ['bin/metal'], + 'dirs': [''], +} + +sanity_check_commands = ['%(namelower)s /dev/null'] + +moduleclass = 'bio' From 7add6f80836e62b30ccfba2f737992df0628f230 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Jul 2021 10:57:36 +0100 Subject: [PATCH 1292/2365] adding easyconfigs: FBPIC-0.20.3-fosscuda-2020b.eb, pyFFTW-0.12.0-fosscuda-2020b.eb --- .../f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb | 40 +++++++++++++++++++ .../p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb | 24 +++++++++++ 2 files changed, 64 insertions(+) create mode 100755 easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb create mode 100755 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb new file mode 100755 index 0000000000..03490cd20d --- /dev/null +++ b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb @@ -0,0 +1,40 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'FBPIC' +version = '0.20.3' + +homepage = "https://fbpic.github.io/" +description = """FBPIC (Fourier-Bessel Particle-In-Cell) is a Particle-In-Cell (PIC) code for relativistic plasma + physics. It is especially well-suited for physical simulations of laser-wakefield acceleration and + plasma-wakefield acceleration.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('CuPy', '8.5.0'), + ('h5py', '3.1.0'), + ('numba', '0.53.1'), + ('pyFFTW', '0.12.0'), + ('SciPy-bundle', '2020.11'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('picmistandard', '0.0.14', { + 'checksums': ['8f83b25b281fc0309a0c4f75c7605afd5fa0ef4df3b3ac115069478c119bc8c3'], + }), + ('periodictable', '1.6.0', { + 'checksums': ['52e925220005c20e97601e7b04ad6cebc271680947ab9adcbb1a796ddbaa0f23'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'use_pip_extras': 'picmi', + 'checksums': ['967d7f087861679467eab31d4b3b12e823a539b1161a1b5f9054e3578a7e000f'], + }), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb new file mode 100755 index 0000000000..6572216ac3 --- /dev/null +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pyFFTW' +version = '0.12.0' + +homepage = 'https://github.com/pyFFTW/pyFFTW' +description = """A pythonic wrapper around FFTW, the FFT library, presenting a unified interface + for all the supported transforms.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['60988e823ca75808a26fd79d88dbae1de3699e72a293f812aa4534f8a0a58cb0'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('FFTW', '3.3.8'), +] + +download_dep_fail = True +use_pip = True + +moduleclass = 'lib' From b5190241fd944d944c0f1635325f8b90c92d76c9 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Jul 2021 11:07:31 +0100 Subject: [PATCH 1293/2365] enable sanity_pip_check in pyFFTW --- easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb index 6572216ac3..bff68e6702 100755 --- a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb @@ -20,5 +20,6 @@ dependencies = [ download_dep_fail = True use_pip = True +sanity_pip_check = True moduleclass = 'lib' From a5145329c11cda408e7cd40ff5ac3f8bda53ad27 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Jul 2021 11:19:15 +0100 Subject: [PATCH 1294/2365] numba multi-variant deps --- easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb index 03490cd20d..676751bc2c 100755 --- a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb @@ -15,7 +15,7 @@ dependencies = [ ('Python', '3.8.6'), ('CuPy', '8.5.0'), ('h5py', '3.1.0'), - ('numba', '0.53.1'), + ('numba', '0.52.0'), ('pyFFTW', '0.12.0'), ('SciPy-bundle', '2020.11'), ] From 50d43ea62c4adf462ebc902a8e37c2ce9e4aa6be Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Jul 2021 11:28:27 +0100 Subject: [PATCH 1295/2365] revert numba change in FBPIC --- easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb index 676751bc2c..03490cd20d 100755 --- a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb @@ -15,7 +15,7 @@ dependencies = [ ('Python', '3.8.6'), ('CuPy', '8.5.0'), ('h5py', '3.1.0'), - ('numba', '0.52.0'), + ('numba', '0.53.1'), ('pyFFTW', '0.12.0'), ('SciPy-bundle', '2020.11'), ] From 9172f3c7e5c70900043e9897dedae42ee0b552b5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Jul 2021 12:32:35 +0100 Subject: [PATCH 1296/2365] allow for non-x86_64 in postinstallcmds for CuPy --- easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb index 498590b96e..7a92cacfd6 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb @@ -24,7 +24,7 @@ exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} postinstallcmds = [ # req for sanity check on build nodes without libcuda.so. # will be removed my patched __init__.py at sanity check import. - 'cp $EBROOTCUDA/./targets/x86_64-linux/lib/stubs/libcuda.* %(installdir)s/lib && ls %(installdir)s/lib' + 'cp $EBROOTCUDA/./targets/*-linux/lib/stubs/libcuda.* %(installdir)s/lib && ls %(installdir)s/lib' ] exts_list = [ ('fastrlock', '0.5', { From d9188dc276a23e866991a74975390e520a5f0c17 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 26 Jul 2021 10:57:43 +0200 Subject: [PATCH 1297/2365] AOCC: Adds EULA --- easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb index 3d7d1d725e..de0d6d8e54 100644 --- a/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb @@ -11,6 +11,8 @@ description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0 # already specified as the toolchain. toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +# By downloading, you accept the AOCC Compiler EULA (https://developer.amd.com/aocc-compiler-eula/) +# accept_eula = True source_urls = ['http://developer.amd.com/wordpress/media/files/'] sources = ['aocc-compiler-%(version)s.tar'] checksums = ['1948104a430506fe5e445c0c796d6956109e7cc9fc0a1e32c9f1285cfd566d0c'] From 436215e77e61724394a2971cc6df2f2b7168bad8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 26 Jul 2021 16:39:56 +0200 Subject: [PATCH 1298/2365] adding easyconfigs: DROP-1.1.0-foss-2020b-R-4.0.3.eb --- .../d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..014ae7c311 --- /dev/null +++ b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'DROP' +version = '1.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://gagneurlab-drop.readthedocs.io' +description = "Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), + ('tMAE', '1.0.0', '-R-%(rver)s'), + ('Java', '11', '', True), + ('GATK', '4.2.0.0', '-Java-%(javaver)s'), + ('Graphviz', '2.47.0', '-Java-%(javaver)s'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('snakemake', '6.1.0'), + ('wget', '1.20.3'), + ('HTSlib', '1.11'), # for tabix + ('SAMtools', '1.11'), + ('BCFtools', '1.11'), + ('Pandoc', '2.13', '', True), +] + +exts_list = [ + ('wbuild', '1.8.0', { + 'checksums': ['3088d3fcbc71106464f20e3546a73df400dc03d17f11e70bdb15d35d7e6c5a7e'], + }), + ('click-log', '0.3.2', { + 'checksums': ['16fd1ca3fc6b16c98cea63acf1ab474ea8e676849dc669d86afafb0ed7003124'], + }), + ('graphviz', '0.17', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['ef6e2c5deb9cdcc0c7eece1d89625fd07b0f2208ea2bcb483520907ddf8b4e12'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('about', '5.2', { + 'checksums': ['4a318ad1dcf6e9355b8ae18195c707d26413782b57ac5c740cc696b44350c959'], + }), + ('plumbum', '1.7.0', { + 'checksums': ['317744342c755319907c773cc87c3a30adaa3a41b0d34c0ce02d9d1904922dce'], + }), + ('pandoc', version, { + 'checksums': ['374f1791151b084e7aac17feeadf43b0c08f0ed39c666a907040f4ee18016b73'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/gagneurlab/drop/archive'], + 'checksums': ['705693610480aa319cec51c2c3118a8f96d2a781c85f9f1d7393e3cd3408d253'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/drop'], + 'dirs': [], +} + +sanity_check_commands = ['drop --help'] + +moduleclass = 'bio' From 548b33821c4f6e07e28ca30502f9a7f544093fc4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 27 Jul 2021 11:19:33 +0100 Subject: [PATCH 1299/2365] adding easyconfigs: QTLtools-1.3.1-foss-2020b.eb --- .../q/QTLtools/QTLtools-1.3.1-foss-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb new file mode 100644 index 0000000000..12a9ff928b --- /dev/null +++ b/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb @@ -0,0 +1,43 @@ +# Easyconfig for QTLtools +# Author: Caspar van Leeuwen +# SURFsara, Amsterdam, The Netherlands + +easyblock = 'MakeCp' + +name = 'QTLtools' +version = '1.3.1' + +homepage = "https://qtltools.github.io/qtltools/" +description = """QTLtools is a tool set for molecular QTL discovery and analysis. +It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) +in few easy-to-perform steps.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://qtltools.github.io/qtltools/binaries/'] +sources = ['QTLtools_%(version)s_source.tar.gz'] +checksums = ['8d812145a210fe96ae31590423a0eab6bf9e3f46b33a62c8b04b0d428bcfed8d'] + +dependencies = [ + ('GSL', '2.6'), + ('bzip2', '1.0.8'), + ('Boost', '1.74.0'), + ('Rmath', '4.0.4'), + ('HTSlib', '1.12'), + ('imkl', '2020.4.304'), +] + +# Overwrite CXX, CXXFLAG, LIB_FLAGS and LIB_FILES build options from the default makefile +# since the default makefile uses hard-coded compiler & library paths +buildopts = 'CXX="$CXX -std=c++0x" CXXFLAG="$CXXFLAGS" LIB_FILES="" ' +buildopts += 'LIB_FLAGS="-lz -lgsl -lmkl -lbz2 -lm -lpthread -lRmath -lhts -lboost_iostreams -lboost_program_options"' +buildopts += ' RMATH_INC=$EBROOTRMAT/include HTSLD_INC=$EBROOTHTSLIB/include BOOST_INC=$EBROOTBOOST/include' + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/QTLtools'], + 'dirs': [] +} + +moduleclass = 'bio' From 1af69c83e342586a904127c512d3705998e71e6d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 27 Jul 2021 11:33:09 +0100 Subject: [PATCH 1300/2365] Use the older HTSlib for 2020b in common with other ECs --- easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb index 12a9ff928b..e71d826080 100644 --- a/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('Boost', '1.74.0'), ('Rmath', '4.0.4'), - ('HTSlib', '1.12'), + ('HTSlib', '1.11'), ('imkl', '2020.4.304'), ] From 98043a96d08a06e15f4fdf468dd27e68679ec654 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 27 Jul 2021 15:58:54 +0200 Subject: [PATCH 1301/2365] adding easyconfigs: BLIS-3.0.1-GCCcore-10.2.0-amd.eb --- .../b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb new file mode 100644 index 0000000000..58742db0fc --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '3.0.1' +versionsuffix = '-amd' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' +description = """AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/amd/blis/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +# Build Serial and multithreaded library +configopts = ['--enable-cblas --enable-shared CC="$CC" auto', + '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto'] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT, + 'lib/libblis-mt.a', 'lib/libblis-mt.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' From 0ea677d16c0346dd5242e4eae3dfa21c0e7a2cb9 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 21 Jul 2021 15:16:26 +0200 Subject: [PATCH 1302/2365] adding easyconfigs: VisPy-0.6.6-foss-2020b.eb, VisPy-0.6.6-intel-2020b.eb --- .../v/VisPy/VisPy-0.6.6-foss-2020b.eb | 34 +++++++++++++++++++ .../v/VisPy/VisPy-0.6.6-intel-2020b.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb create mode 100644 easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb diff --git a/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb new file mode 100644 index 0000000000..8bdc452acc --- /dev/null +++ b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'VisPy' +version = '0.6.6' + +homepage = 'https://vispy.org' +description = """VisPy is a high-performance interactive 2D/3D data visualization library + leveraging the computational power of modern Graphics Processing Units (GPUs) through the + OpenGL library to display very large datasets.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyQt5', '5.15.1'), +] + +use_pip = True + +exts_list = [ + ('freetype_py', '2.2.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-2.2.0.zip'], + 'checksums': ['cf43716bc5246cd54a64b2238b942e8dc80b79eda92f814c720286fa6fab387a'], + }), + ('vispy', version, { + 'checksums': ['6f3c4d00be9e6761c046d520a86693d78a0925d47eeb2fc095e95dac776f74ee'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb new file mode 100644 index 0000000000..6ae981a021 --- /dev/null +++ b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'VisPy' +version = '0.6.6' + +homepage = 'https://vispy.org' +description = """VisPy is a high-performance interactive 2D/3D data visualization library + leveraging the computational power of modern Graphics Processing Units (GPUs) through the + OpenGL library to display very large datasets.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyQt5', '5.15.1'), +] + +use_pip = True + +exts_list = [ + ('freetype_py', '2.2.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-2.2.0.zip'], + 'checksums': ['cf43716bc5246cd54a64b2238b942e8dc80b79eda92f814c720286fa6fab387a'], + }), + ('vispy', version, { + 'checksums': ['6f3c4d00be9e6761c046d520a86693d78a0925d47eeb2fc095e95dac776f74ee'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From 79c4f906c63e4ade9d0da259e8816bd35e9b3260 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 29 Jul 2021 14:41:06 +0200 Subject: [PATCH 1303/2365] {bio}[foss/2020b] nanopolish 0.13.3 --- .../nanopolish-0.13.3-foss-2020b.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb new file mode 100644 index 0000000000..ffba642eb4 --- /dev/null +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -0,0 +1,52 @@ +easyblock = 'MakeCp' + +name = 'nanopolish' +version = '0.13.3' + +homepage = 'https://github.com/jts/nanopolish' +description = "Software package for signal-level analysis of Oxford Nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://github.com/jts/nanopolish/archive/', + 'https://github.com/mateidavid/fast5/archive/', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.6.5.tar.gz', 'filename': 'fast5-v0.6.5.tar.gz'}, +] +checksums = [ + 'eac02b7db76f223375e246fa361a0a4fbf74021b9094573e5324fd7f75743d55', # nanopolish-0.13.3.tar.gz + 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz +] + +builddependencies = [('Eigen', '3.3.7', '', True)] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('Pysam', '0.16.0.1'), + ('HDF5', '1.10.7'), + ('HTSlib', '1.11'), + ('minimap2', '2.18'), +] + +prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " +buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall" + +runtest = 'test ' + buildopts + +files_to_copy = [(['nanopolish'], 'bin'), 'scripts'] + +postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"] + +sanity_check_paths = { + 'files': ['bin/nanopolish'], + 'dirs': ['scripts'], +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From b10764527f05d81a67f6de8de194e6b9ef52a390 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 29 Jul 2021 16:31:41 +0100 Subject: [PATCH 1304/2365] adding easyconfigs: Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb and patches: Qt5Webkit-5.212.0-alpha4_bison3.7.patch --- ...Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0fff752203 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb @@ -0,0 +1,56 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeNinja' + +name = 'Qt5Webkit' +# Qt5 > 5.9 required at least version 5.212.0 +# At the time of writing the latest version was 5.212.0-alpha3 +version = '5.212.0-alpha4' + +homepage = 'https://github.com/qt/qtwebkit' +description = "Qt Port of WebKit. WebKit is an open source web browser engine." +docurls = ['https://github.com/qt/qtwebkit/blob/dev/README'] + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/qtwebkit/qtwebkit/releases/download/qtwebkit-%(version)s/'] +sources = ['qtwebkit-%(version)s.tar.xz'] +patches = ['%(name)s-%(version)s_bison3.7.patch'] +checksums = [ + '9ca126da9273664dd23a3ccd0c9bebceb7bb534bddd743db31caf6a5a6d4a9e6', # qtwebkit-5.212.0-alpha4.tar.xz + '34f37b53ee0bc31c63ce85ebd1ae95543a8ba28483e387b20efd50574bd813be', # Qt5Webkit-5.212.0-alpha4_bison3.7.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.10.1'), + ('Python', '3.8.6'), + ('Ruby', '2.7.2'), +] + +dependencies = [ + ('Qt5', '5.14.2'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('ICU', '67.1'), + ('libxslt', '1.1.34'), + ('libjpeg-turbo', '2.0.5'), +] + +configopts = "-G Ninja -DPORT=Qt -DCMAKE_BUILD_TYPE=Release -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " + +sanity_check_paths = { + 'files': [ + 'lib64/libQt5WebKit.%s' % SHLIB_EXT, + 'lib64/libQt5WebKitWidgets.%s' % SHLIB_EXT, + ], + 'dirs': ['include/QtWebKit', 'include/QtWebKitWidgets'], +} + +moduleclass = 'devel' From 299a7862219f37ef276650b1acea9fac0ea652c7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 30 Jul 2021 00:35:06 +0200 Subject: [PATCH 1305/2365] use CMakeMakeCp easyblock in Metal v2020-05-05 --- .../m/Metal/Metal-2020-05-05-GCC-10.2.0.eb | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb index 67bd18df24..5d713d8d11 100644 --- a/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakeMakeCp' name = 'Metal' version = '2020-05-05' @@ -16,20 +16,13 @@ checksums = ['0ffa2419ca2ab43766e7e6e8c97822c8ce1f5b6233fb5f992d1b1be1955fede7'] builddependencies = [('CMake', '3.18.4')] dependencies = [('zlib', '1.2.11')] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=Release' - -postinstallcmds = [ - 'mkdir -p %(installdir)s/bin && ' + - 'cp %(builddir)s/easybuild_obj/bin/metal %(installdir)s/bin' -] +files_to_copy = [(['metal/metal'], 'bin')] sanity_check_paths = { 'files': ['bin/metal'], 'dirs': [''], } -sanity_check_commands = ['%(namelower)s /dev/null'] +sanity_check_commands = ['%(namelower)s'] moduleclass = 'bio' From 9bdf6b4609e60c45a2ef1368a77d8e363f63ac85 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 30 Jul 2021 15:38:47 +0100 Subject: [PATCH 1306/2365] Rename NINJA to TWL-NINJA to avoid nameclash --- .../TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb b/easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb new file mode 100644 index 0000000000..7a2314cce7 --- /dev/null +++ b/easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb @@ -0,0 +1,28 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'TWL-NINJA' +version = '0.97-cluster_only' + +homepage = 'https://github.com/TravisWheelerLab/NINJA' +description = "Nearly Infinite Neighbor Joining Application." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'cstd': 'gnu++11', 'openmp': True, 'opt': True} + +source_urls = ['https://github.com/TravisWheelerLab/NINJA/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['b9b948c698efc3838e63817f732ead35c08debe1c0ae36b5c74df7d26ca4c4b6'] + +start_dir = 'NINJA' +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +files_to_copy = [(['NINJA/Ninja'], 'bin'), 'NINJA/README', 'README.md', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/Ninja'], + 'dirs': [], +} + +moduleclass = 'bio' From 914c026174066628dc4578f28d54105629cd57db Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 30 Jul 2021 15:44:49 +0100 Subject: [PATCH 1307/2365] use renamed TWL-NINJA NINJA renamed to TWL-NINJA in #13529 --- .../r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb index 44ec3867af..97c902e910 100644 --- a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb @@ -25,7 +25,7 @@ dependencies = [ ('MAFFT', '7.475', '-with-extensions'), ('GenomeTools', '1.6.1'), # for LTRHarvest ('LTR_retriever', '2.9.0'), - ('NINJA', '0.97-cluster_only'), + ('TWL-NINJA', '0.97-cluster_only'), ] exts_defaultclass = 'PerlModule' From f0efb15ff696c3ecab85e5019abaaafee28f3f79 Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 30 Jul 2021 15:05:39 +0000 Subject: [PATCH 1308/2365] Some suggested tidy up, name changed to kalign, current.tar.gz renamed to kalign-2.0.4.tar.gz --- .../k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb | 28 ++++++++++++++++ .../k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb | 32 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dd1f62fb09 --- /dev/null +++ b/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'Kalign' +version = '2.0.4' + +homepage = 'https://msa.sbc.su.se/cgi-bin/msa.cgi' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://msa.sbc.su.se/downloads/kalign/'] +sources = [{'filename': SOURCELOWER_TAR_GZ, 'download_filename': 'current.tar.gz'}] +checksums = ['8cf20ac4e1807dc642e7ffba8f42a117313beccaee4f87c5555d53a2eeac4cbb'] # kalign.tar.gz + +builddependencies = [('binutils', '2.35')] + +install_cmd = "mkdir %(installdir)s/bin && cp kalign %(installdir)s/bin" + +sanity_check_paths = { + 'files': ['bin/kalign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..61e06fe157 --- /dev/null +++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'Kalign' +version = '3.3.1' + +homepage = 'https://github.com/TimoLassmann/kalign' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f10acf9a3fa15deabbc0304e7c14efa25cea39108318c9f02b47257de2d7390'] # 3.3.1.tar.gz + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Autotools', '20200321'), +] + +configure_cmd_prefix = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/kchaos', 'bin/kalign'], + 'dirs': [], +} + +moduleclass = 'bio' From a028dc5e700ee14b2f9285907c64415f139fa62b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 31 Jul 2021 02:04:25 +0200 Subject: [PATCH 1309/2365] remove leftover comment in vcflib-1.0.2-GCC-10.2.0.eb --- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 1b77b9cb61..734f106ab1 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -4,7 +4,6 @@ easyblock = 'CMakeMake' name = 'vcflib' version = '1.0.2' -# versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/vcflib/vcflib' description = """vcflib provides methods to manipulate and interpret sequence variation as it can be From e2397c9477cf1aca489bf929d678d9f33f5442b9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 31 Jul 2021 02:09:38 +0200 Subject: [PATCH 1310/2365] adding easyconfig filevercmp-20191210-GCCcore-10.2.0.eb --- .../filevercmp-20191210-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a1ba056e29 --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'filevercmp' +version = '20191210' +local_commit = 'df20dcc' + +homepage = 'https://github.com/ekg/filevercmp' +description = """filevercmp function as in sort --version-sort.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20191210_build-libs.patch'] +checksums = [ + '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz + 'f0145a1590b555288d5c4560a58bf6976a7605ef949f9071d45e7afb815b540c', # filevercmp-20191210_build-libs.patch +] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'DESTDIR="" PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From dcaee995b0527ce3594f6d866a97cd10ef4ee061 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 31 Jul 2021 02:11:06 +0200 Subject: [PATCH 1311/2365] adding easyconfig multichoose-1.0.3-GCCcore-10.2.0.eb --- .../multichoose-1.0.3-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..423504cb40 --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'multichoose' +version = '1.0.3' + +homepage = 'https://github.com/ekg/multichoose' +description = """generate multiset combinations (n multichoose k).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877'] + +builddependencies = [('binutils', '2.35')] + +local_bins = [name, 'multipermute'] +files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/multichoose')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +moduleclass = 'bio' From b272ca6c70ebb55676c6105d07f0a4ea163b10f9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 31 Jul 2021 02:11:53 +0200 Subject: [PATCH 1312/2365] adding easyconfig smithwaterman-20160702-GCCcore-10.2.0.eb --- .../smithwaterman-20160702-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..65ec48867c --- /dev/null +++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'smithwaterman' +version = '20160702' +local_commit = '2610e25' + +homepage = 'https://github.com/ekg/smithwaterman' +description = """smith-waterman-gotoh alignment algorithm.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20160702_build-shared-lib.patch'] +checksums = [ + '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz + '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' From 6948802438182f4eaad6610529e6e153695df57b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 31 Jul 2021 02:23:33 +0200 Subject: [PATCH 1313/2365] update checksum of filevercmp-20191210_build-libs.patch --- .../f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb index a1ba056e29..5aafc94550 100644 --- a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ sources = ['%s.tar.gz' % local_commit] patches = ['%(name)s-20191210_build-libs.patch'] checksums = [ '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz - 'f0145a1590b555288d5c4560a58bf6976a7605ef949f9071d45e7afb815b540c', # filevercmp-20191210_build-libs.patch + '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f', # filevercmp-20191210_build-libs.patch ] builddependencies = [('binutils', '2.35')] From 058c0bf7fa4c9ac48fa6b1adf6756f3ba2e81ae4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 1 Aug 2021 00:07:49 +0200 Subject: [PATCH 1314/2365] add missing dependencies and fix build of freebayes-1.3.5-GCC-10.2.0.eb --- .../f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb | 50 +++++++++++++------ 1 file changed, 35 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb index 7889e193d7..f57fb4074b 100644 --- a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb @@ -8,37 +8,57 @@ description = "Bayesian haplotype-based genetic polymorphism discovery and genot toolchain = {'name': 'GCC', 'version': '10.2.0'} -sources = [{ - 'filename': SOURCE_TAR_GZ, - 'git_config': { - 'url': 'https://github.com/freebayes', - 'repo_name': 'freebayes', - 'tag': 'v1.3.5', - 'recursive': True, - }, -}] -checksums = ['b614a44cb53a164ab8579d75c8eb6fc17415a502628aeeb12b42218893a10278'] +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['freebayes-1.3.5_fix-meson-build.patch'] +checksums = [ + 'af195a8c54b742d01af5a7e1fd1781a89290d726b310216c83e78c650d7aee49', # v1.3.5.tar.gz + 'c408bda1092d6f72d14eb22ab842e12ba27f52be35d82e3a33506e64e04077d8', # freebayes-1.3.5_fix-meson-build.patch +] builddependencies = [ ('binutils', '2.35'), + ('CMake', '3.18.4'), ('Meson', '0.55.3'), ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), ] dependencies = [ ('parallel', '20210322'), ('VCFtools', '0.1.16'), + ('vcflib', '1.0.2'), + ('SeqLib', '1.2.0'), + ('fastahack', '1.0.0'), + ('intervaltree', '0.1'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), ] -configopts = "--buildtype debug" +# freebayes expects intervaltree headers in its source directory +local_intervaltree_path = '%(builddir)s/%(name)s-%(version)s/intervaltree' +preconfigopts = "mv %(i)s %(i)s.orig && " % {'i': local_intervaltree_path} +preconfigopts += "ln -s $EBROOTINTERVALTREE/include/intervaltree %(i)s && " % {'i': local_intervaltree_path} +# workaround for direct includes of multichoose headers +preconfigopts += 'CPPFLAGS="-I${EBROOTMULTICHOOSE}/include/multichoose ${CPPFLAGS}" ' +# add missing linker flags for fastahack and smithwaterman +preconfigopts += 'LDFLAGS="-lsw -lfastahack ${LDFLAGS}"' -postinstallcmds = ['cp %(builddir)s/freebayes/scripts/* %(installdir)s/'] +configopts = "--buildtype release" -modextrapaths = {'PATH': ['']} +postinstallcmds = [ + # add extra scripts + "cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s/", + # only make freebayes-parallel directly executable + "cd %(installdir)s/bin && ln -s ../scripts/freebayes-parallel", +] sanity_check_paths = { - 'files': ['bin/freebayes', 'bin/bamleftalign', 'freebayes-parallel'], - 'dirs': [], + 'files': ['bin/freebayes', 'bin/bamleftalign', 'bin/freebayes-parallel'], + 'dirs': ['scripts'], } +sanity_check_commands = ["freebayes --help"] + moduleclass = 'bio' From a8c1ba732c4ab862cfca40b922b654046f4e1329 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 1 Aug 2021 00:09:10 +0200 Subject: [PATCH 1315/2365] upgrade dependency on HTSlib to v1.12 --- easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb index 04dec16e82..faf8ac8607 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ dependencies = [ ('Perl', '5.32.0'), - ('HTSlib', '1.11'), + ('HTSlib', '1.12'), ('zlib', '1.2.11'), ] From fff517ea26eb5b93a366b912efbfb74ff2af51d6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 1 Aug 2021 00:10:25 +0200 Subject: [PATCH 1316/2365] adding easyconfigs: SeqLib-1.2.0-GCC-10.2.0.eb, fermi-lite-20190320-GCCcore-10.2.0.eb, SSW-1.1-GCCcore-10.2.0.eb --- .../fermi-lite-20190320-GCCcore-10.2.0.eb | 46 +++++++++++++++++ .../s/SSW/SSW-1.1-GCCcore-10.2.0.eb | 48 ++++++++++++++++++ .../s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb | 49 +++++++++++++++++++ 3 files changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5f7b29effc --- /dev/null +++ b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'fermi-lite' +version = '20190320' +local_commit = 'b499514' + +homepage = 'https://github.com/lh3/fermi-lite' +description = """Standalone C library for assembling Illumina short reads in small regions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [ + '%(name)s-20190320_avoid-bwa-namespace-conflict.patch', + '%(name)s-20190320_build-shared-lib.patch', +] +checksums = [ + 'ea1230e298b8e7193a996b5aceeff7fea44ef00852b0b87d4fcb504bdca0e712', # b499514.tar.gz + # fermi-lite-20190320_avoid-bwa-namespace-conflict.patch + '27600733f1cea8b1d1503b1a67b9d41526e907c1b6321313ff51194e166c1842', + '43398559fbb3910d6d3d1a41af3fb16bf8f26bd7cc34176dfc9a068a551c3f50', # fermi-lite-20190320_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +prebuildopts = 'CFLAGS="$CFLAGS -fcommon"' + +files_to_copy = [ + (['fml-asm'], 'bin'), + (['*.a', '*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/fml'), + 'test', +] + +sanity_check_paths = { + 'files': ['bin/fml-asm', 'lib/libfml.a', 'lib/libfml.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..915ce0d1e9 --- /dev/null +++ b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'SSW' +version = '1.1' + +homepage = 'https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library' +description = """SSW is a fast implementation of the Smith-Waterman algorithm, which uses the + Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the + instruction level. SSW library provides an API that can be flexibly used by programs written in + C, C++ and other languages. We also provide a software that can do protein and genome alignment + directly. Current version of our implementation is ~50 times faster than an ordinary + Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path + (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and + location heuristically. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1_build-cpp-lib.patch'] +checksums = [ + 'cdbc20740daeb188ed39413ea5ff9ae4cf72c4d7ccff1d2de2cac0446d64d99f', # v1.1.tar.gz + 'fe0d1f536ecd526dda8879b2f41b62c3c82b39d236f023ee735c1c18d584f06a', # SSW-1.1_build-cpp-lib.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +buildopts = 'default' + +files_to_copy = [ + (['ssw_test'], 'bin'), + (['*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/ssw'), +] + +sanity_check_paths = { + 'files': ['bin/ssw_test', 'lib/libssw.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..507c2fec11 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb @@ -0,0 +1,49 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'SeqLib' +version = '1.2.0' + +homepage = 'https://github.com/walaj/SeqLib' +description = """C++ interface to HTSlib, BWA-MEM and Fermi.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'walaj' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version_major_minor)s.0_avoid-bwa-fml-namespace-conflict.patch', + '%(name)s-%(version_major_minor)s.0_use-external-deps.patch', +] +checksums = [ + '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz + # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch + '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', + '8a90edf72f95a52c61e4aed62a9a951bbd56f7c668dec326f2d3836f76b0f71d', # SeqLib-1.2.0_use-external-deps.patch +] + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), + ('JsonCpp', '1.9.4'), + ('BWA', '0.7.17'), + ('HTSlib', '1.12'), + ('fermi-lite', '20190320'), + ('SSW', '1.1'), + ('PCRE', '8.44'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/seqtools', 'lib/libseqlib.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["seqtools"] + +moduleclass = 'bio' From 892083263f493420a82819551ec942bfb253b144 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 1 Aug 2021 00:36:01 +0200 Subject: [PATCH 1317/2365] removing easyconfigs from PR: any2fasta-0.4.2-GCCcore-10.2.0.eb, samclip-0.4.0-GCCcore-10.2.0.eb, filevercmp-20191210-GCCcore-10.2.0.eb --- .../any2fasta-0.4.2-GCCcore-10.2.0.eb | 34 ------------------- .../filevercmp-20191210-GCCcore-10.2.0.eb | 33 ------------------ .../s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb | 27 --------------- 3 files changed, 94 deletions(-) delete mode 100644 easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb deleted file mode 100644 index 4b16b010fe..0000000000 --- a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'Tarball' - -name = 'any2fasta' -version = '0.4.2' - -homepage = 'https://github.com/tseemann/any2fasta' -description = "Convert various sequence formats to FASTA" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -# https://github.com/tseemann/any2fasta -github_account = 'tseemann' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.zip'] -checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] - -dependencies = [('Perl', '5.32.0')] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['any2fasta'], - 'dirs': [], -} - -sanity_check_commands = [ - 'any2fasta -h', - 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb deleted file mode 100644 index a1ba056e29..0000000000 --- a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -# Updated: Denis Kristak (INUITS) -easyblock = 'ConfigureMake' - -name = 'filevercmp' -version = '20191210' -local_commit = 'df20dcc' - -homepage = 'https://github.com/ekg/filevercmp' -description = """filevercmp function as in sort --version-sort.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -github_account = 'ekg' -source_urls = [GITHUB_SOURCE] -sources = ['%s.tar.gz' % local_commit] -patches = ['%(name)s-20191210_build-libs.patch'] -checksums = [ - '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz - 'f0145a1590b555288d5c4560a58bf6976a7605ef949f9071d45e7afb815b540c', # filevercmp-20191210_build-libs.patch -] - -builddependencies = [('binutils', '2.35')] - -skipsteps = ['configure'] - -installopts = 'DESTDIR="" PREFIX=%(installdir)s ' - -sanity_check_paths = { - 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb deleted file mode 100644 index 52eb3f5c23..0000000000 --- a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'Tarball' - -name = 'samclip' -version = '0.4.0' - -homepage = 'https://github.com/tseemann/samclip' -description = """Filter SAM file for soft and hard clipped alignments.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -github_account = 'tseemann' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127'] - -dependencies = [('Perl', '5.32.0')] - -sanity_check_paths = { - 'files': [name], - 'dirs': [], -} - -sanity_check_commands = ["%(name)s --help"] - -modextrapaths = {'PATH': ''} - -moduleclass = 'bio' From e1086ae20391169857bb5f40c606160556ee16e7 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 2 Aug 2021 10:03:30 +0200 Subject: [PATCH 1318/2365] moving samclip and anytofasta to final (SNIPPY) PR --- .../any2fasta-0.4.2-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ .../s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb | 30 ++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1ba03ee613 --- /dev/null +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Author: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'any2fasta' +version = '0.4.2' + +homepage = 'https://github.com/tseemann/any2fasta' +description = "Convert various sequence formats to FASTA" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# https://github.com/tseemann/any2fasta +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] + +dependencies = [('Perl', '5.32.0')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['any2fasta'], + 'dirs': [], +} + +sanity_check_commands = [ + 'any2fasta -h', + 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..372ab575da --- /dev/null +++ b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# Author: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'samclip' +version = '0.4.0' + +homepage = 'https://github.com/tseemann/samclip' +description = """Filter SAM file for soft and hard clipped alignments.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127'] + +dependencies = [('Perl', '5.32.0')] + +sanity_check_paths = { + 'files': [name], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 7d412422aa76594b02b4d59f078582ea357704b6 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 2 Aug 2021 11:26:44 +0200 Subject: [PATCH 1319/2365] add VBZ compress capability (for fast5 files) --- .../easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb index ffba642eb4..d0a19258d2 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -31,6 +31,7 @@ dependencies = [ ('HDF5', '1.10.7'), ('HTSlib', '1.11'), ('minimap2', '2.18'), + ('vbz_compression', '1.0.1'), ] prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " From e30b159a65183af89bb9596e1afe0eba1adb0e08 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 2 Aug 2021 13:33:51 +0200 Subject: [PATCH 1320/2365] vbz_c -> VBZ_C and use SHLIB_EXT --- .../easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb index d0a19258d2..84295cb17e 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -31,7 +31,7 @@ dependencies = [ ('HDF5', '1.10.7'), ('HTSlib', '1.11'), ('minimap2', '2.18'), - ('vbz_compression', '1.0.1'), + ('VBZ_Compression', '1.0.1'), ] prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " From bbc98009b441086639450da871f0383acdcead85 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 2 Aug 2021 11:49:11 +0000 Subject: [PATCH 1321/2365] Header corrected, toolchain downgraded to gompi, sanity check improved by adding more relevant files, toolchainoptions removed --- .../h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb new file mode 100644 index 0000000000..d59bb692b1 --- /dev/null +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -0,0 +1,52 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Updated to use gompi-2020b toolchain: +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'HH-suite' +version = '3.3.0' + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """The HH-suite is an open-source software package +for sensitive protein sequence searching based on the pairwise +alignment of hidden Markov models (HMMs).""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +separate_build_dir = True + +_binaries = [ + 'hhalign', 'hhalign_mpi', 'hhalign_omp', + 'hhblits', 'hhblits_mpi', 'hhblits_omp', + 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp', + 'hhmake', 'hhfilter', 'hhconsensus', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries], + 'dirs': ['data', 'scripts'] +} + +moduleclass = 'bio' From ae90708289b4d20e516bbd5fff686530e77fe93a Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Mon, 2 Aug 2021 09:25:34 -0400 Subject: [PATCH 1322/2365] Fix p7zip path issues (Issue #13540) --- .../p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb index 7da7616f42..14596aee0f 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -22,12 +22,19 @@ prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' files_to_copy = [ - (['bin/7z', 'bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), - (['bin/7z.%s' % SHLIB_EXT, 'bin/Codecs'], 'libexec'), + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.%s' % SHLIB_EXT, 'bin/Codecs'], 'libexec'), # 7z requires 7z.so plugin in same directory +] + +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask ] sanity_check_paths = { - 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z.%s' % SHLIB_EXT], + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.%s' % SHLIB_EXT], 'dirs': ['libexec/Codecs'], } From 167a73df4fcbec15ed0651d71600bed6082733ae Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 2 Aug 2021 17:05:25 +0200 Subject: [PATCH 1323/2365] VBZ_C -> VBZ-C --- .../nanopolish-0.13.3-foss-2020b.eb | 2 +- .../VBZ-Compression-1.0.1-gompi-2020b.eb | 43 +++++++++++++++++++ 2 files changed, 44 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.1-gompi-2020b.eb diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb index 84295cb17e..d7aeb4c75d 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -31,7 +31,7 @@ dependencies = [ ('HDF5', '1.10.7'), ('HTSlib', '1.11'), ('minimap2', '2.18'), - ('VBZ_Compression', '1.0.1'), + ('VBZ-Compression', '1.0.1'), ] prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " diff --git a/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.1-gompi-2020b.eb b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.1-gompi-2020b.eb new file mode 100644 index 0000000000..09c6e077ce --- /dev/null +++ b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.1-gompi-2020b.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'VBZ-Compression' +version = '1.0.1' + +homepage = 'https://github.com/nanoporetech/vbz_compression' +description = "VBZ compression HDF5 plugin for nanopolish" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = [ + 'https://github.com/nanoporetech/vbz_compression/archive', + 'https://github.com/lemire/streamvbyte/archive', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'}, +] +checksums = [ + '3c140fb4f60f8451db68768457c59b10aadba4c33f1b1a1eadb4439345b68192', # VBZ-Compression-1.0.1.tar.gz + '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc', # streamvbyte-v0.4.1.tar.gz +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('HDF5', '1.10.7'), + ('zstd', '1.4.5'), +] + +preconfigopts = "rmdir %(builddir)s/vbz_compression*/third_party/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte-* %(builddir)s/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte %(builddir)s/vbz_compression*/third_party/. && " +configopts = "-DENABLE_CONAN=OFF -DENABLE_PERF_TESTING=OFF -DENABLE_PYTHON=OFF " + +sanity_check_paths = { + 'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'HDF5_PLUGIN_PATH': 'hdf5/lib/plugin/'} + +moduleclass = 'lib' From ba5239b03dfc4e3adc4f22a8d41f2bf144f9daff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Aug 2021 18:11:45 +0200 Subject: [PATCH 1324/2365] add cobalt extension for recent R 4.0.x and 4.1.0 easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 +++ 6 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 8e1e2c5b93..df5788a6eb 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2891,6 +2891,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index cb0dff7a4d..2154e87ccb 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2901,6 +2901,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 9b77a35e2f..3d0bffd502 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2927,6 +2927,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index dec33c7779..e7e51b34c7 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2932,6 +2932,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index e0d0501d05..8a52c5c7c8 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2936,6 +2936,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 4a7563f2d6..d60bd6ae02 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2947,6 +2947,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From b1a4ea564e61af1896f1080c895a9596e0f9e9c8 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 2 Aug 2021 18:01:38 +0000 Subject: [PATCH 1325/2365] Patch file removed, patch version set to 7.5.0 in OpenMM-7.5.1-fosscuda-2020b.eb --- easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb index 5f6aeae351..439ac03341 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb @@ -18,7 +18,7 @@ toolchainopts = {'opt': True} source_urls = ['https://github.com/openmm/openmm/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix_path_to_nvcc.patch'] +patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] checksums = [ 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # 7.5.1.tar.gz '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch From dc9a8dac78f95e43385d8c1e66228e4ccd624809 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Tue, 3 Aug 2021 12:29:19 +1000 Subject: [PATCH 1326/2365] Create almosthere-2.0.2-GCCcore-10.2.0.eb Update to new major release and new GCC --- .../almosthere-2.0.2-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..70063cf416 --- /dev/null +++ b/easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'almosthere' +version = '2.0.2' + +homepage = 'https://github.com/horta/almosthere' +description = """Progress indicator C library. +ATHR is a simple yet powerful progress indicator library that works on Windows, +Linux, and macOS. It is non-blocking as the progress update is done via a +dedicated, lightweight thread, as to not impair the performance of the calling program.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'horta' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b50ff32f5f1aa213589c81118e7312bd5e0f5a3d0a72ace499595a1f0bbff42f'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libathr.a', 'lib/libathr.%s' % SHLIB_EXT, 'include/athr/athr.h'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'tools' From f088a5f29f5b264b3c51fc69d56287ba203c13ae Mon Sep 17 00:00:00 2001 From: jedokaplan Date: Tue, 3 Aug 2021 14:20:26 +0800 Subject: [PATCH 1327/2365] adding easyconfigs: PyQt5-5.15.4-GCCcore-10.2.0.eb --- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb | 99 +++++++++++++++++++ 1 file changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b04ed87846 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb @@ -0,0 +1,99 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.4' + +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.35')] +dependencies = [ + ('Python', '3.8.6'), + ('Qt5', '5.14.2'), + ('Qt5Webkit', '5.212.0-alpha4') +] + +default_easyblock = 'PythonPackage' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +local_sipver = '5.5.0' + +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + + ('PyQt-builder', '1.10.3', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['6ade47445b7d8c08eb96e91ebda5f8b3494b3e7a9da2be343b9d0704419cb5c7'], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + + ('PyQt5_sip', '12.9.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], + 'easyblock': 'Binary', + 'start_dir': '%(name)s-%(version)s', + 'skipsteps': ['configure', 'build'], + 'install_cmd': local_setup_env + local_pyqt5_sip_install, + }), + + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip-wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip-wheel --help", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From e32bd9d7584d1d394aca6571c2c51549573a24c4 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Tue, 3 Aug 2021 16:40:32 +1000 Subject: [PATCH 1328/2365] Create bgen-4.1.3-GCCcore-10.2.0.eb New major version, new toolchain, new sanity checks. --- .../b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..460afd5c0d --- /dev/null +++ b/easybuild/easyconfigs/b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'bgen' +version = '4.1.3' + +homepage = 'https://github.com/limix/bgen' +description = "A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'limix' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7e2da4831b631cb18e16bbe2b645f08c9b325fb4eb2f53615fcdeec2a75bbd35'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zstd', '1.4.5'), + ('almosthere', '2.0.2'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libbgen.a', 'include/bgen/bgen.h'], + 'dirs': [], +} + +moduleclass = 'bio' From 08fe3c5aa9a287c47445bb3ca8cb1942f090fbe7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Aug 2021 10:15:31 +0200 Subject: [PATCH 1329/2365] add CBPS extension for recent R 4.0.x and 4.1.0 easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 +++ 6 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index df5788a6eb..9eb85d1c0d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2894,6 +2894,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 2154e87ccb..2b8973c846 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2904,6 +2904,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 3d0bffd502..cf3cce3824 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2930,6 +2930,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index e7e51b34c7..99facf4817 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2935,6 +2935,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 8a52c5c7c8..f9a6bf3629 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2939,6 +2939,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index d60bd6ae02..ef355408f9 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2950,6 +2950,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From 9faf67c98eb2ffb40df66d2afa612f905ec49ca4 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Tue, 3 Aug 2021 11:12:25 +0200 Subject: [PATCH 1330/2365] patch so that MaxBin2 uses the EB provided Perl and not the system Perl --- easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb index 65c321a169..523aa09a5e 100644 --- a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] +patches = ['MaxBin-2.2.7_fix_perl_shebang.patch'] +checksums = [ + 'cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e', # src + 'f966952e7bb910b24687001c89dd1667318346911db964438b8e726ca3415913', # MaxBin-2.2.7_fix_perl_shebang.patch +] builddependencies = [('binutils', '2.35')] From 2870b0a59a24d1686fbbcbf8855451fd11a56e90 Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Tue, 3 Aug 2021 11:08:13 -0400 Subject: [PATCH 1331/2365] add sanity check to address path issue --- easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb index 14596aee0f..d0abc3db27 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -41,6 +41,7 @@ sanity_check_paths = { sanity_check_commands = [ '7z --help', '7z x || test $? -gt 0', + "! 7z i | grep -q \"Can't load\"", ] moduleclass = 'tools' From a06d33015365489f80e4104b0c81c375efe89116 Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Tue, 3 Aug 2021 11:38:34 -0400 Subject: [PATCH 1332/2365] add spaces to fix parsing issue --- easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb index d0abc3db27..8c1b293c37 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -41,7 +41,7 @@ sanity_check_paths = { sanity_check_commands = [ '7z --help', '7z x || test $? -gt 0', - "! 7z i | grep -q \"Can't load\"", + "! 7z i | grep -q \"Can't load\" ", ] moduleclass = 'tools' From a3934b60c5b486a98d2b07b42d4407f6227b910b Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 3 Aug 2021 19:22:33 +0000 Subject: [PATCH 1333/2365] Moved Autotools to builddep --- .../easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb index 61e06fe157..aeeec32aa8 100644 --- a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb @@ -16,9 +16,8 @@ source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['7f10acf9a3fa15deabbc0304e7c14efa25cea39108318c9f02b47257de2d7390'] # 3.3.1.tar.gz -builddependencies = [('binutils', '2.35')] - -dependencies = [ +builddependencies = [ + ('binutils', '2.35'), ('Autotools', '20200321'), ] From 189858fe74d872496a6e639ea5ccc83639a84d64 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Aug 2021 21:36:41 +0200 Subject: [PATCH 1334/2365] add SBdecomp extension for recent R 4.0.x and 4.1.0 easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 +++ 6 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 9eb85d1c0d..3f73cf6e80 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2897,6 +2897,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 2b8973c846..25bfe94116 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2907,6 +2907,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index cf3cce3824..600336ef2a 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2933,6 +2933,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 99facf4817..6410c41672 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2938,6 +2938,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index f9a6bf3629..9d7859add8 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2942,6 +2942,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index ef355408f9..044bfdd295 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2953,6 +2953,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From d2994c4687c729628f34585009082adfee0aad7f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 4 Aug 2021 00:35:46 +0200 Subject: [PATCH 1335/2365] Add missing zlib dependency to libarchive --- .../l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb index 8c373a125e..7214c3ae94 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb @@ -19,6 +19,10 @@ checksums = ['ee1e749213c108cb60d53147f18c31a73d6717d7e3d2481c157e1b34c881ea39'] builddependencies = [ ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), ('XZ', '5.2.5'), ] From 87e66e699efb273cc14bc4183fc0de2b2fffa6ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 4 Aug 2021 00:43:56 +0200 Subject: [PATCH 1336/2365] Fix pkgconfig version in patch for bzip 1.0.8 --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb index ec886cad08..4e0873a1c5 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb @@ -14,10 +14,10 @@ toolchainopts = {'pic': True} source_urls = ['https://sourceware.org/pub/%(name)s/'] sources = [SOURCE_TAR_GZ] -patches = ['bzip2-1.0.6-pkgconfig.patch'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] checksums = [ 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz - '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch ] builddependencies = [ From 270aeaf58477220b9cd7652a17fd1efa9813c6c1 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Wed, 4 Aug 2021 15:30:31 +1000 Subject: [PATCH 1337/2365] Create CharLS-2.2.0-GCCcore-10.2.0.eb New minor version, new GCCcore --- .../c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..afad4ef356 --- /dev/null +++ b/easybuild/easyconfigs/c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CharLS' +version = '2.2.0' + +homepage = 'https://github.com/team-charls/charls' +description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image +compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 +compression ratios.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/team-charls/charls/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e1d7dd70cd9d6d46de5abbf22278dc8169707995a21e8bf705f5746c04c76891'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libcharls.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 95cc33ff48d2a9eaf042e5f26228d9782f93906a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 4 Aug 2021 11:35:49 +0200 Subject: [PATCH 1338/2365] adding easyconfigs: coverage-5.5-GCCcore-10.2.0.eb --- .../c/coverage/coverage-5.5-GCCcore-10.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b619a1c1c2 --- /dev/null +++ b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'coverage' +version = '5.5' + +homepage = 'https://coverage.readthedocs.io' +description = """ Coverage.py is a tool for measuring code coverage of Python programs. + It monitors your program, noting which parts of the code have been executed, + then analyzes the source to identify code that could have been executed but was not. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ebe78fe9a0e874362175b02371bdfbee64d8edc42a044253ddf4ee7d3c15212c'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True + +sanity_check_paths = { + 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'tools' From 37e911f591da9655d9b9f5a62a3934c3b85d501f Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Wed, 4 Aug 2021 12:53:17 +0200 Subject: [PATCH 1339/2365] use fix_perl_shebang for function --- .../easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb index 523aa09a5e..535fd62d21 100644 --- a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb @@ -12,11 +12,7 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['MaxBin-2.2.7_fix_perl_shebang.patch'] -checksums = [ - 'cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e', # src - 'f966952e7bb910b24687001c89dd1667318346911db964438b8e726ca3415913', # MaxBin-2.2.7_fix_perl_shebang.patch -] +checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] builddependencies = [('binutils', '2.35')] @@ -32,6 +28,8 @@ prebuildopts = "cd src && " files_to_copy = ['*'] +fix_perl_shebang_for = ['run_MaxBin.pl'] + sanity_check_paths = { 'files': ['run_MaxBin.pl', 'src/MaxBin'], 'dirs': [], From 8f40f46606c47e1f4d2699eadd83b072d10ed0a1 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Thu, 5 Aug 2021 14:13:28 +1000 Subject: [PATCH 1340/2365] Create FreeImage-3.18.0-GCCcore-10.2.0.eb Update to GCCcore 10.2.0 and binutils 2.35 --- .../FreeImage-3.18.0-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6953a03baf --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FreeImage' +version = '3.18.0' + +homepage = 'http://freeimage.sourceforge.net' +description = """FreeImage is an Open Source library project for developers who would like to support popular graphics +image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to +use, fast, multithreading safe.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(name)s%s.zip' % ''.join(version.split('.'))] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip + '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # FreeImage-3.18.0-fix-makefile.patch +] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +buildopts = ['', '-f Makefile.fip'] +installopts = [ + 'INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib', + '-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib' +] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['include/FreeImage.h', 'include/FreeImagePlus.h', 'lib/libfreeimage.a', 'lib/libfreeimage.%s' % SHLIB_EXT, + 'lib/libfreeimageplus.a', 'lib/libfreeimageplus.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' From a9cd28ff3bd49a267a58611b25f9a750de3c7ef7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 10:02:06 +0200 Subject: [PATCH 1341/2365] Arrow: Remove superflous CMAKE_BUILD_TYPE --- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 5ab6551adb..8fbcaf8468 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -40,7 +40,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" # also install Python bindings diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index d5c0491c4c..ee3c044110 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -36,7 +36,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" # also install Python bindings From 963b81502eb9a9dfc7de7783bfc57764d382557f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 10:38:20 +0200 Subject: [PATCH 1342/2365] MMseqs2: Use build_type instead of configopts --- easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb index 876e969d18..2ea322fa29 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb @@ -19,7 +19,6 @@ dependencies = [('bzip2', '1.0.8')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' sanity_check_paths = { 'files': ['bin/mmseqs'], From 38ca5974f1bfbdc5090e33eac9f5b5da4360c8fb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 10:56:20 +0200 Subject: [PATCH 1343/2365] MMseqs2: Remove superflous cfg option --- .../easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb index 2ea322fa29..0e1cf8f454 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb @@ -17,9 +17,6 @@ builddependencies = [('CMake', '3.18.4')] dependencies = [('bzip2', '1.0.8')] -separate_build_dir = True - - sanity_check_paths = { 'files': ['bin/mmseqs'], 'dirs': [], From 6103e043523bd1a4f15e385cdd27d1b7989a0041 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 5 Aug 2021 15:50:46 +0000 Subject: [PATCH 1344/2365] Add upstream GCC patch to avoid spurious FPE on avx512 (affects UCX) --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 65f6fc7c6c..4ce3d1f4b9 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -36,6 +36,7 @@ patches = [ 'GCCcore-10.2.0_fix-has-include-Fortran.patch', 'GCCcore-10.2.0_fix-ice-on-arm.patch', 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz @@ -52,6 +53,7 @@ checksums = [ '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278', # GCCcore-10.2.0_fix-ice-on-arm.patch # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch ] builddependencies = [ From b76af13d082ffed292584b328624b7c061e88efe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Aug 2021 17:52:42 +0200 Subject: [PATCH 1345/2365] rename goatools to GOATOOLS (to use official software name) --- .../g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb new file mode 100644 index 0000000000..fd0085761c --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb @@ -0,0 +1,71 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.1.6' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2020b'} + +# extra downloaded files are needed acc. to docs: https://github.com/tanghaibao/goatools#installation +sources = [ + {'source_urls': ['https://github.com/tanghaibao/goatools/archive/'], + 'filename': 'v%(version)s.tar.gz'}, + {'source_urls': ['http://geneontology.org/ontology/'], + 'filename': 'go-basic.obo', 'extract_cmd': 'cp %s %(builddir)s'}, + {'source_urls': ['http://www.geneontology.org/ontology/subsets/'], + 'filename': 'goslim_generic.obo', 'extract_cmd': 'cp %s %(builddir)s'}] +checksums = [ + '41222308c2bc34eefd3292326a61bc215bd32831b4b2652eff00b1b8e3fcf8c6', # v1.1.6.tar.gz + '57bd37b4301a7a6be65da033c8e812698e62fd0f12a30e18cf9e3cfeed238702', # go-basic.obo + '161ccdabf702faee796335939858772703f5e05a2ccb0400a4cab481f41136d9', # goslim_generic.obo +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('XlsxWriter', '1.4.0'), + ('statsmodels', '0.12.1'), + ('pydot', '1.4.2'), +] +download_dep_fail = True + +preinstallopts = "sed -i 's/==[0-9]*.[0-9]*.[0-9]*//g' requirements.txt && " +# wget was here only to download some src files which we download via sources +preinstallopts += "sed -i 's/wget//g' requirements.txt && " + +local_go_path = "%(installdir)s/bin/goafiles" + + +local_data_dir = '%(builddir)s/%(name)s-%(version)s/data/*' +# copy downloaded GOA files into dedicated folder for user and to bin/ for sanity_check +postinstallcmds = ["mkdir %s" % local_go_path, + "cp %%(builddir)s/go-basic.obo %s" % local_go_path, + "cp %%(builddir)s/goslim_generic.obo %s" % local_go_path, + "cp %(builddir)s/go-basic.obo %(installdir)s/bin/", + "cp %(builddir)s/goslim_generic.obo %(installdir)s/bin/", + "mkdir %%(installdir)s/bin/data && cp -r %s %%(installdir)s/bin/data" % local_data_dir] + +# making sure user knows about downloaded files +modextravars = {'GOAFILES': local_go_path} +modloadmsg = """\n GOATOOLS: Downloaded files from "geneontology.org" are accessible in a directory behind a variable \ +$GOAFILES.\n You need to have them in a directory from which you run goatools commands.""" + +use_pip = True + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['bin/data'], +} + +# example from https://github.com/tanghaibao/goatools#find-go-enrichment-of-genes-under-study +local_cmd = "cd %(installdir)s/bin && find_enrichment.py --pval=0.05\ + --indent data/study data/population data/association && cd -" +sanity_check_commands = [local_cmd] + +sanity_pip_check = True + +moduleclass = 'bio' From 3b365c8ac421ba09870e56444fbb851594bb65fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Aug 2021 18:41:38 +0200 Subject: [PATCH 1346/2365] don't include unversioned go-basic.odo and goslin_generic.odo files in GOATOOLS installation --- .../g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb | 53 ++++++------------- 1 file changed, 17 insertions(+), 36 deletions(-) diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb index fd0085761c..18701693a4 100644 --- a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb @@ -10,19 +10,11 @@ description = "A Python library for Gene Ontology analyses" toolchain = {'name': 'foss', 'version': '2020b'} -# extra downloaded files are needed acc. to docs: https://github.com/tanghaibao/goatools#installation -sources = [ - {'source_urls': ['https://github.com/tanghaibao/goatools/archive/'], - 'filename': 'v%(version)s.tar.gz'}, - {'source_urls': ['http://geneontology.org/ontology/'], - 'filename': 'go-basic.obo', 'extract_cmd': 'cp %s %(builddir)s'}, - {'source_urls': ['http://www.geneontology.org/ontology/subsets/'], - 'filename': 'goslim_generic.obo', 'extract_cmd': 'cp %s %(builddir)s'}] -checksums = [ - '41222308c2bc34eefd3292326a61bc215bd32831b4b2652eff00b1b8e3fcf8c6', # v1.1.6.tar.gz - '57bd37b4301a7a6be65da033c8e812698e62fd0f12a30e18cf9e3cfeed238702', # go-basic.obo - '161ccdabf702faee796335939858772703f5e05a2ccb0400a4cab481f41136d9', # goslim_generic.obo -] +source_urls = ['https://github.com/tanghaibao/goatools/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['41222308c2bc34eefd3292326a61bc215bd32831b4b2652eff00b1b8e3fcf8c6'] + +builddependencies = [('cURL', '7.72.0')] dependencies = [ ('Python', '3.8.6'), @@ -31,40 +23,29 @@ dependencies = [ ('statsmodels', '0.12.1'), ('pydot', '1.4.2'), ] + download_dep_fail = True +use_pip = True preinstallopts = "sed -i 's/==[0-9]*.[0-9]*.[0-9]*//g' requirements.txt && " # wget was here only to download some src files which we download via sources preinstallopts += "sed -i 's/wget//g' requirements.txt && " -local_go_path = "%(installdir)s/bin/goafiles" - - -local_data_dir = '%(builddir)s/%(name)s-%(version)s/data/*' -# copy downloaded GOA files into dedicated folder for user and to bin/ for sanity_check -postinstallcmds = ["mkdir %s" % local_go_path, - "cp %%(builddir)s/go-basic.obo %s" % local_go_path, - "cp %%(builddir)s/goslim_generic.obo %s" % local_go_path, - "cp %(builddir)s/go-basic.obo %(installdir)s/bin/", - "cp %(builddir)s/goslim_generic.obo %(installdir)s/bin/", - "mkdir %%(installdir)s/bin/data && cp -r %s %%(installdir)s/bin/data" % local_data_dir] - -# making sure user knows about downloaded files -modextravars = {'GOAFILES': local_go_path} -modloadmsg = """\n GOATOOLS: Downloaded files from "geneontology.org" are accessible in a directory behind a variable \ -$GOAFILES.\n You need to have them in a directory from which you run goatools commands.""" - -use_pip = True +local_data_dir = '%(builddir)s/%(namelower)s-%(version)s/data/*' +postinstallcmds = ["mkdir %%(installdir)s/data && cp -r %s %%(installdir)s/data" % local_data_dir] sanity_check_paths = { 'files': ['bin/find_enrichment.py'], - 'dirs': ['bin/data'], + 'dirs': ['data'], } -# example from https://github.com/tanghaibao/goatools#find-go-enrichment-of-genes-under-study -local_cmd = "cd %(installdir)s/bin && find_enrichment.py --pval=0.05\ - --indent data/study data/population data/association && cd -" -sanity_check_commands = [local_cmd] +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] sanity_pip_check = True From e1922b75bba03505045d3d700f9c480d081b8e5c Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 5 Aug 2021 19:39:25 +0000 Subject: [PATCH 1347/2365] Perl suffix and separate_build_dir = True removed --- .../h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 23 ++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index d59bb692b1..6e6f5b7ed6 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -32,10 +32,11 @@ checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] builddependencies = [ ('CMake', '3.18.4'), - ('Doxygen', '1.8.20'), ] -separate_build_dir = True +dependencies = [ + ('Perl', '5.32.0'), +] _binaries = [ 'hhalign', 'hhalign_mpi', 'hhalign_omp', @@ -44,9 +45,25 @@ _binaries = [ 'hhmake', 'hhfilter', 'hhconsensus', ] +_scriptfiles = [ + 'a3m.py', 'check_a3m.py', 'cif2fasta.py', 'ffindex.py', 'get_a3m_size.py', + 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +] + +_perlfiles = [ + 'addss.pl', 'create_profile_from_hmmer.pl', 'hhmakemodel.pl', + 'mergeali.pl', 'multithread.pl', 'pdb2fasta.pl', 'pdbfilter.pl', + 'reformat.pl', 'renumberpdb.pl', 'splitfasta.pl', +] + +fix_perl_shebang_for = ['scripts/%s' % z for z in _perlfiles] + sanity_check_paths = { - 'files': ['bin/%s' % x for x in _binaries], + 'files': ['bin/%s' % x for x in _binaries] + + ['scripts/%s' % y for y in _scriptfiles], 'dirs': ['data', 'scripts'] } +modextrapaths = {'PATH': 'scripts'} + moduleclass = 'bio' From c2fd46c11466e022d0300999a14d4430a25f63ce Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Fri, 6 Aug 2021 14:04:24 +1000 Subject: [PATCH 1348/2365] Create gflags-2.2.2-GCCcore-10.2.0.eb New compiler, binutils, CMake --- .../g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..958caa83e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' From 77f0ae5077a0324b73f9fe02fbf1759626b01918 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Fri, 6 Aug 2021 14:14:11 +1000 Subject: [PATCH 1349/2365] Create glog-0.5.0-GCCcore-10.2.0.eb Update version, toolchain, builddependencies, dependencies --- .../g/glog/glog-0.5.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/glog/glog-0.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/glog/glog-0.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/glog/glog-0.5.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d6dded4986 --- /dev/null +++ b/easybuild/easyconfigs/g/glog/glog-0.5.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'glog' +version = '0.5.0' + +homepage = 'https://github.com/google/glog' +description = "A C++ implementation of the Google logging module." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/google/glog/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['eede71f28371bf39aa69b45de23b329d37214016e2055269b3b5e7cfd40b59f5'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('gflags', '2.2.2'), + ('libunwind', '1.4.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['include/glog/logging.h', 'include/glog/raw_logging.h', 'lib/libglog.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From fdadcc72bfb7e9ee3c6c32aa24fd4d2cdcb1eff9 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 6 Aug 2021 19:49:56 +0200 Subject: [PATCH 1350/2365] using snippys prebuilt snpEff binary --- easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb index b27c7c5455..5f23968bf1 100644 --- a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb @@ -23,17 +23,15 @@ dependencies = [ ('minimap2', '2.18'), ('vcflib', '1.0.2'), ('vt', '0.57721'), - ('snpEff', '5.0', '-Java-13', True), ('samclip', '0.4.0'), ('seqtk', '1.3'), ('snp-sites', '2.5.1'), ('any2fasta', '0.4.2'), ('wgsim', '20111017'), - ('freebayes', '1.3.5'), # todo freebayes-parallel + ('freebayes', '1.3.5') ] -# remove included binaries for required dependencies -postinstallcmds = ["rm -r %(installdir)s/binaries"] +modextrapaths = {'PATH': 'binaries/noarch'} sanity_check_paths = { 'files': ['bin/snippy', 'perl5/Snippy/Version.pm'], From e341bc3e45238f678c07d335039a6aedc83ae9d4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Aug 2021 23:12:13 +0200 Subject: [PATCH 1351/2365] update checksum of wgsim v20111017 --- easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb index f7361ba8bb..fc3409253c 100644 --- a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -16,7 +16,7 @@ patches = [ ('wgsim-%(version)s_add_makefile.patch', 1) ] checksums = [ - 'e1e6bff5c084e4494023505206ae3e0b0f5a315c9f7390b2f347c370c7f36533', # wgsim-20111017.tar.gz + '1180fdd1d66691da5634e8c98b78c4742d0faf10042f35c2d17d26844d550f1c', # wgsim-20111017.tar.gz '81b61c6cceaa4a05e9ee12976dede0df1639f9504ded11e7099cbd1f932c6c9d', # wgsim-20111017_add_makefile.patch ] From 55a461d77b07b3eb1757ea5d650d2bc515d78b37 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Aug 2021 23:26:29 +0200 Subject: [PATCH 1352/2365] use CmdCp easyblock for wgsim v20111017 --- .../w/wgsim/wgsim-20111017-GCC-10.2.0.eb | 26 ++++++++----------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb index fc3409253c..718a1bb0cb 100644 --- a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -1,36 +1,32 @@ -easyblock = 'MakeCp' +easyblock = 'CmdCp' name = 'wgsim' version = '20111017' local_commit = 'a12da3375ff3b51a5594d4b6fa35591173ecc229' homepage = 'https://github.com/lh3/wgsim/' -description = """Wgsim is a small tool for simulating sequence reads from a reference genome.""" +description = "Wgsim is a small tool for simulating sequence reads from a reference genome." toolchain = {'name': 'GCC', 'version': '10.2.0'} github_account = 'lh3' source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = [ - ('wgsim-%(version)s_add_makefile.patch', 1) -] -checksums = [ - '1180fdd1d66691da5634e8c98b78c4742d0faf10042f35c2d17d26844d550f1c', # wgsim-20111017.tar.gz - '81b61c6cceaa4a05e9ee12976dede0df1639f9504ded11e7099cbd1f932c6c9d', # wgsim-20111017_add_makefile.patch -] - -dependencies = [('zlib', '1.2.11')] +sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_ZIP}] +checksums = ['1180fdd1d66691da5634e8c98b78c4742d0faf10042f35c2d17d26844d550f1c'] -buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' +dependencies = [ + ('zlib', '1.2.11'), +] -files_to_copy = [(["wgsim"], 'bin')] +cmds_map = [('.*', "$CC $CFLAGS -o %(name)s %(name)s.c $LDFLAGS -lz -lm")] -sanity_check_commands = [("%(name)s -h 2>&1 | grep 'Program: wgsim (short read simulator)'")] +files_to_copy = [(['wgsim'], 'bin')] sanity_check_paths = { 'files': ['bin/wgsim'], 'dirs': [], } +sanity_check_commands = ["wgsim -h 2>&1 | grep 'Program: wgsim (short read simulator)'"] + moduleclass = 'bio' From ff2dd2a1eada901e31275d264d82ac5011369b75 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Aug 2021 23:28:03 +0200 Subject: [PATCH 1353/2365] add wgsim_eval.pl to installation of wgsim --- easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb index 718a1bb0cb..4fc09775ac 100644 --- a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -16,14 +16,15 @@ checksums = ['1180fdd1d66691da5634e8c98b78c4742d0faf10042f35c2d17d26844d550f1c'] dependencies = [ ('zlib', '1.2.11'), + ('Perl', '5.32.0'), ] cmds_map = [('.*', "$CC $CFLAGS -o %(name)s %(name)s.c $LDFLAGS -lz -lm")] -files_to_copy = [(['wgsim'], 'bin')] +files_to_copy = [(['wgsim', 'wgsim_eval.pl'], 'bin')] sanity_check_paths = { - 'files': ['bin/wgsim'], + 'files': ['bin/wgsim', 'bin/wgsim_eval.pl'], 'dirs': [], } From d4b620e3427d89d96cebd4382f261c1de2623471 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Aug 2021 23:29:33 +0200 Subject: [PATCH 1354/2365] restore original attribution in any2fasta v0.4.2 --- .../easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb index 1ba03ee613..52f8445081 100644 --- a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb @@ -1,4 +1,5 @@ -# Author: Denis Kristak (INUITS) +# Author: Pavel Grochal (INUITS) +# Updated by: Denis Kristak (INUITS) # License: GPLv2 easyblock = 'Tarball' From 14e285aa015a2d22e9afa82a3f1180ea9b982e16 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Aug 2021 23:55:35 +0200 Subject: [PATCH 1355/2365] add dependency on snpEff v5.0e to snippy v4.6.0 --- .../s/snippy/snippy-4.6.0-GCC-10.2.0.eb | 5 ++- .../snpEff-5.0e-GCCcore-10.2.0-Java-13.eb | 35 +++++++++++++++++++ 2 files changed, 37 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb diff --git a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb index 5f23968bf1..ac4d831cb4 100644 --- a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb @@ -26,16 +26,15 @@ dependencies = [ ('samclip', '0.4.0'), ('seqtk', '1.3'), ('snp-sites', '2.5.1'), + ('snpEff', '5.0e', '-Java-13'), ('any2fasta', '0.4.2'), ('wgsim', '20111017'), ('freebayes', '1.3.5') ] -modextrapaths = {'PATH': 'binaries/noarch'} - sanity_check_paths = { 'files': ['bin/snippy', 'perl5/Snippy/Version.pm'], - 'dirs': ['etc'], + 'dirs': ['etc', 'test'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb new file mode 100644 index 0000000000..cfde903143 --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.0e' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d'] + +dependencies = [ + ('Java', '13', '', True), + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 70778f27294f09c55b0c4571875548a0e584f617 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 7 Aug 2021 19:37:37 +0200 Subject: [PATCH 1356/2365] adding easyconfigs: FORD-6.1.1-GCCcore-10.2.0.eb --- .../f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f51c81c928 --- /dev/null +++ b/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'FORD' +version = '6.1.1' + +homepage = 'https://github.com/Fortran-FOSS-Programmers/ford/wiki' +description = 'FORD is an automatic documentation generator for modern Fortran programs' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Graphviz', '2.47.0', '-Java-11'), + ('BeautifulSoup', '4.9.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('graphviz', '0.17', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['ef6e2c5deb9cdcc0c7eece1d89625fd07b0f2208ea2bcb483520907ddf8b4e12'], + }), + ('MarkupSafe', '2.0.1', { + 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], + }), + ('Jinja2', '3.0.1', { + 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], + }), + ('Pygments', '2.9.0', { + 'checksums': ['a18f47b506a429f6f4b9df81bb02beab9ca21d0a5fee38ed15aef65f0545519f'], + }), + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('markdown-include', '0.6.0', { + 'checksums': ['6f5d680e36f7780c7f0f61dca53ca581bd50d1b56137ddcd6353efafa0c3e4a2'], + }), + ('md-environ', '0.1.0', { + 'checksums': ['fe3c2a255af523d6f522831c699336cd71f9d543714067d93206ed35836f1793'], + }), + ('toposort', '1.6', { + 'checksums': ['a7428f56ef844f5055bb9e9e44b343983773ae6dce0fe5b101e08e27ffbd50ac'], + }), + ('tqdm', '4.62.0', { + 'checksums': ['3642d483b558eec80d3c831e23953582c34d7e4540db86d9e5ed9dad238dabc6'], + }), + (name, version, { + 'checksums': ['6c107316ecee48f174316f0deffa9e6407dabca414845b9fa66f4313341da9ac'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ford'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' From 8d3733d65b9e128cb37993c1bb47584202bf521e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 7 Aug 2021 19:46:19 +0200 Subject: [PATCH 1357/2365] Tidy up EB file for coverage v5.5 for GCCcore/10.2.0 --- easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb index b619a1c1c2..441df135ab 100644 --- a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb @@ -10,7 +10,6 @@ description = """ Coverage.py is a tool for measuring code coverage of Python pr toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ebe78fe9a0e874362175b02371bdfbee64d8edc42a044253ddf4ee7d3c15212c'] @@ -23,6 +22,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], From e5ab1a56f5fefde8310491450c9885a2bcf8a028 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 9 Aug 2021 09:46:52 +0200 Subject: [PATCH 1358/2365] Update and rename openstackclient-5.5.0-GCCcore-10.2.0.eb to OpenStackClient-5.5.0-GCCcore-10.2.0.eb rename to OpenStackClient --- .../OpenStackClient-5.5.0-GCCcore-10.2.0.eb | 133 ++++++++++++++++++ 1 file changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b013362d2e --- /dev/null +++ b/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -0,0 +1,133 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/08 +easyblock = 'PythonBundle' + +name = 'OpenStackClient' +version = '5.5.0' + +homepage = 'https://docs.openstack.org/python-openstackclient/latest/' +description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the +command set for Compute, Identity, Image, Network, Object Store and Block +Storage APIs together in a single shell with a uniform command structure.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), +] +builddependencies = [('binutils', '2.35')] + +exts_default_options = { + 'use_pip': True, +} +exts_list = [ + ('pbr', '5.6.0', { + 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('cmd2', '2.1.2', { + 'checksums': ['25dbb2e9847aaa686a8a21e84e3d101db8b79f5cb992e044fc54210ab8c0ad41'], + }), + ('charset-normalizer', '2.0.4', { + 'checksums': ['f23667ebe1084be45f6ae0538e4a5a865206544097e4e8bbcacf42cd02a348f3'], + }), + ('jsonpointer', '2.1', { + 'checksums': ['5a34b698db1eb79ceac454159d3f7c12a451a91f6334a4f638454327b7a89962'], + }), + ('cliff', '3.8.0', { + 'checksums': ['8dd215d0a84c9a3ab2fa2aa700849f4e7b786639f66caa0ad4108c85dca95a7c'], + }), + ('openstacksdk', '0.58.0', { + 'modulename': 'openstack', + 'checksums': ['d8368d1728f686114213d22cc8e3eef71629fae1424b2ad2c5d22a7b9a04a278'], + }), + ('stevedore', '3.3.0', { + 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], + }), + ('dogpile.cache', '1.1.3', { + 'checksums': ['6f0bcf97c73bfec1a7bf14e5a248488cee00c2d494bf63f3789ea6d95a57c1cf'], + }), + ('prettytable', '0.7.2', { + 'checksums': ['2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('jsonpatch', '1.32', { + 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + ('os-service-types', '1.7.0', { + 'checksums': ['31800299a82239363995b91f1ebf9106ac7758542a1e4ef6dc737a5932878c6c'], + }), + ('requestsexceptions', '1.4.0', { + 'checksums': ['b095cbc77618f066d459a02b137b020c37da9f46d9b057704019c9f77dba3065'], + }), + ('requests', '2.26.0', { + 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], + }), + ('osc-lib', '2.4.1', { + 'checksums': ['257ef0cda902664605a850a858172306acb2b08b0e7e32d7a5b4f12dc6bc56c5'], + }), + ('keystoneauth1', '4.3.1', { + 'checksums': ['93605430a6d1424f31659bc5685e9dc1be9a6254e88c99f00cffc0a60c648a64'], + }), + ('debtcollector', '2.2.0', { + 'checksums': ['787981f4d235841bf6eb0467e23057fb1ac7ee24047c32028a8498b9128b6829'], + }), + ('oslo.i18n', '5.0.1', { + 'modulename': 'oslo_i18n', + 'checksums': ['3484b71e30f75c437523302d1151c291caf4098928269ceec65ce535456e035b'], + }), + ('oslo.utils', '4.9.2', { + 'modulename': 'oslo_utils', + 'checksums': ['20db285734ff6c3b50d5a6afcb2790ade0c7ba02fbc876feed43733f2c41a5c9'], + }), + ('oslo.serialization', '4.1.0', { + 'modulename': 'oslo_serialization', + 'checksums': ['cecc7794df806c85cb70dbd6c2b3af19bc68047ad29e3c6442be90a0a4de5379'], + }), + ('oslo.config', '8.7.1', { + 'modulename': 'oslo_config', + 'checksums': ['a0c346d778cdc8870ab945e438bea251b5f45fae05d6d99dfe4953cca2277b60'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('iso8601', '0.1.16', { + 'checksums': ['36532f77cc800594e8f16641edae7f1baf7932f05d8e508545b95fc53c6dc85b'], + }), + ('python-novaclient', '17.5.0', { + 'modulename': 'novaclient', + 'checksums': ['7aa0fe9a74b1336e56c2f7965f14e04bad29dbfbd7ba41dcb7b364f94c9bee7f'], + }), + ('python-keystoneclient', '4.2.0', { + 'modulename': 'keystoneclient', + 'checksums': ['0248426e483b95de395086482c077d48e45990d3b1a3e334b2ec8b2e108f5a8a'], + }), + ('python-cinderclient', '8.0.0', { + 'modulename': 'cinderclient', + 'checksums': ['4ced8c562064ab73f757d91d26846faaf1fc1c82f1fee5597e24df3d1ffcf116'], + }), + ('python-openstackclient', version, { + 'modulename': 'openstackclient', + 'checksums': ['8d40491374172f9375ce1642ac2230b1cbb5a564320edbcc2a9ebe857fd9a880'], + }), +] + +sanity_pip_check = True +enhance_sanity_check = True +sanity_check_commands = ['openstack -h'] + +sanity_check_paths = { + 'files': ['bin/openstack'], + 'dirs': ["bin", 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' From ea12e2a33128bcd52ac099b41c515d710fe000fa Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 9 Aug 2021 10:20:30 +0200 Subject: [PATCH 1359/2365] rename to OpenStackClient --- .../OpenStackClient-5.5.0-GCCcore-10.2.0.eb | 133 ++++++++++++++++++ 1 file changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b013362d2e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -0,0 +1,133 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/08 +easyblock = 'PythonBundle' + +name = 'OpenStackClient' +version = '5.5.0' + +homepage = 'https://docs.openstack.org/python-openstackclient/latest/' +description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the +command set for Compute, Identity, Image, Network, Object Store and Block +Storage APIs together in a single shell with a uniform command structure.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), +] +builddependencies = [('binutils', '2.35')] + +exts_default_options = { + 'use_pip': True, +} +exts_list = [ + ('pbr', '5.6.0', { + 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('cmd2', '2.1.2', { + 'checksums': ['25dbb2e9847aaa686a8a21e84e3d101db8b79f5cb992e044fc54210ab8c0ad41'], + }), + ('charset-normalizer', '2.0.4', { + 'checksums': ['f23667ebe1084be45f6ae0538e4a5a865206544097e4e8bbcacf42cd02a348f3'], + }), + ('jsonpointer', '2.1', { + 'checksums': ['5a34b698db1eb79ceac454159d3f7c12a451a91f6334a4f638454327b7a89962'], + }), + ('cliff', '3.8.0', { + 'checksums': ['8dd215d0a84c9a3ab2fa2aa700849f4e7b786639f66caa0ad4108c85dca95a7c'], + }), + ('openstacksdk', '0.58.0', { + 'modulename': 'openstack', + 'checksums': ['d8368d1728f686114213d22cc8e3eef71629fae1424b2ad2c5d22a7b9a04a278'], + }), + ('stevedore', '3.3.0', { + 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], + }), + ('dogpile.cache', '1.1.3', { + 'checksums': ['6f0bcf97c73bfec1a7bf14e5a248488cee00c2d494bf63f3789ea6d95a57c1cf'], + }), + ('prettytable', '0.7.2', { + 'checksums': ['2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('jsonpatch', '1.32', { + 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + ('os-service-types', '1.7.0', { + 'checksums': ['31800299a82239363995b91f1ebf9106ac7758542a1e4ef6dc737a5932878c6c'], + }), + ('requestsexceptions', '1.4.0', { + 'checksums': ['b095cbc77618f066d459a02b137b020c37da9f46d9b057704019c9f77dba3065'], + }), + ('requests', '2.26.0', { + 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], + }), + ('osc-lib', '2.4.1', { + 'checksums': ['257ef0cda902664605a850a858172306acb2b08b0e7e32d7a5b4f12dc6bc56c5'], + }), + ('keystoneauth1', '4.3.1', { + 'checksums': ['93605430a6d1424f31659bc5685e9dc1be9a6254e88c99f00cffc0a60c648a64'], + }), + ('debtcollector', '2.2.0', { + 'checksums': ['787981f4d235841bf6eb0467e23057fb1ac7ee24047c32028a8498b9128b6829'], + }), + ('oslo.i18n', '5.0.1', { + 'modulename': 'oslo_i18n', + 'checksums': ['3484b71e30f75c437523302d1151c291caf4098928269ceec65ce535456e035b'], + }), + ('oslo.utils', '4.9.2', { + 'modulename': 'oslo_utils', + 'checksums': ['20db285734ff6c3b50d5a6afcb2790ade0c7ba02fbc876feed43733f2c41a5c9'], + }), + ('oslo.serialization', '4.1.0', { + 'modulename': 'oslo_serialization', + 'checksums': ['cecc7794df806c85cb70dbd6c2b3af19bc68047ad29e3c6442be90a0a4de5379'], + }), + ('oslo.config', '8.7.1', { + 'modulename': 'oslo_config', + 'checksums': ['a0c346d778cdc8870ab945e438bea251b5f45fae05d6d99dfe4953cca2277b60'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('iso8601', '0.1.16', { + 'checksums': ['36532f77cc800594e8f16641edae7f1baf7932f05d8e508545b95fc53c6dc85b'], + }), + ('python-novaclient', '17.5.0', { + 'modulename': 'novaclient', + 'checksums': ['7aa0fe9a74b1336e56c2f7965f14e04bad29dbfbd7ba41dcb7b364f94c9bee7f'], + }), + ('python-keystoneclient', '4.2.0', { + 'modulename': 'keystoneclient', + 'checksums': ['0248426e483b95de395086482c077d48e45990d3b1a3e334b2ec8b2e108f5a8a'], + }), + ('python-cinderclient', '8.0.0', { + 'modulename': 'cinderclient', + 'checksums': ['4ced8c562064ab73f757d91d26846faaf1fc1c82f1fee5597e24df3d1ffcf116'], + }), + ('python-openstackclient', version, { + 'modulename': 'openstackclient', + 'checksums': ['8d40491374172f9375ce1642ac2230b1cbb5a564320edbcc2a9ebe857fd9a880'], + }), +] + +sanity_pip_check = True +enhance_sanity_check = True +sanity_check_commands = ['openstack -h'] + +sanity_check_paths = { + 'files': ['bin/openstack'], + 'dirs': ["bin", 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' From ae37e2dbd6c4f57b03efd400d51d35af20911c59 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 9 Aug 2021 10:22:52 +0200 Subject: [PATCH 1360/2365] Delete easybuild/easyconfigs/o/openstackclient directory --- .../OpenStackClient-5.5.0-GCCcore-10.2.0.eb | 133 ------------------ 1 file changed, 133 deletions(-) delete mode 100644 easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb deleted file mode 100644 index b013362d2e..0000000000 --- a/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb +++ /dev/null @@ -1,133 +0,0 @@ -# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/08 -easyblock = 'PythonBundle' - -name = 'OpenStackClient' -version = '5.5.0' - -homepage = 'https://docs.openstack.org/python-openstackclient/latest/' -description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the -command set for Compute, Identity, Image, Network, Object Store and Block -Storage APIs together in a single shell with a uniform command structure.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -dependencies = [ - ('Python', '3.8.6'), - ('PyYAML', '5.3.1'), -] -builddependencies = [('binutils', '2.35')] - -exts_default_options = { - 'use_pip': True, -} -exts_list = [ - ('pbr', '5.6.0', { - 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], - }), - ('pyperclip', '1.8.2', { - 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], - }), - ('cmd2', '2.1.2', { - 'checksums': ['25dbb2e9847aaa686a8a21e84e3d101db8b79f5cb992e044fc54210ab8c0ad41'], - }), - ('charset-normalizer', '2.0.4', { - 'checksums': ['f23667ebe1084be45f6ae0538e4a5a865206544097e4e8bbcacf42cd02a348f3'], - }), - ('jsonpointer', '2.1', { - 'checksums': ['5a34b698db1eb79ceac454159d3f7c12a451a91f6334a4f638454327b7a89962'], - }), - ('cliff', '3.8.0', { - 'checksums': ['8dd215d0a84c9a3ab2fa2aa700849f4e7b786639f66caa0ad4108c85dca95a7c'], - }), - ('openstacksdk', '0.58.0', { - 'modulename': 'openstack', - 'checksums': ['d8368d1728f686114213d22cc8e3eef71629fae1424b2ad2c5d22a7b9a04a278'], - }), - ('stevedore', '3.3.0', { - 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], - }), - ('dogpile.cache', '1.1.3', { - 'checksums': ['6f0bcf97c73bfec1a7bf14e5a248488cee00c2d494bf63f3789ea6d95a57c1cf'], - }), - ('prettytable', '0.7.2', { - 'checksums': ['2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9'], - }), - ('jmespath', '0.10.0', { - 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], - }), - ('jsonpatch', '1.32', { - 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], - }), - ('munch', '2.5.0', { - 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], - }), - ('os-service-types', '1.7.0', { - 'checksums': ['31800299a82239363995b91f1ebf9106ac7758542a1e4ef6dc737a5932878c6c'], - }), - ('requestsexceptions', '1.4.0', { - 'checksums': ['b095cbc77618f066d459a02b137b020c37da9f46d9b057704019c9f77dba3065'], - }), - ('requests', '2.26.0', { - 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], - }), - ('osc-lib', '2.4.1', { - 'checksums': ['257ef0cda902664605a850a858172306acb2b08b0e7e32d7a5b4f12dc6bc56c5'], - }), - ('keystoneauth1', '4.3.1', { - 'checksums': ['93605430a6d1424f31659bc5685e9dc1be9a6254e88c99f00cffc0a60c648a64'], - }), - ('debtcollector', '2.2.0', { - 'checksums': ['787981f4d235841bf6eb0467e23057fb1ac7ee24047c32028a8498b9128b6829'], - }), - ('oslo.i18n', '5.0.1', { - 'modulename': 'oslo_i18n', - 'checksums': ['3484b71e30f75c437523302d1151c291caf4098928269ceec65ce535456e035b'], - }), - ('oslo.utils', '4.9.2', { - 'modulename': 'oslo_utils', - 'checksums': ['20db285734ff6c3b50d5a6afcb2790ade0c7ba02fbc876feed43733f2c41a5c9'], - }), - ('oslo.serialization', '4.1.0', { - 'modulename': 'oslo_serialization', - 'checksums': ['cecc7794df806c85cb70dbd6c2b3af19bc68047ad29e3c6442be90a0a4de5379'], - }), - ('oslo.config', '8.7.1', { - 'modulename': 'oslo_config', - 'checksums': ['a0c346d778cdc8870ab945e438bea251b5f45fae05d6d99dfe4953cca2277b60'], - }), - ('rfc3986', '1.5.0', { - 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('iso8601', '0.1.16', { - 'checksums': ['36532f77cc800594e8f16641edae7f1baf7932f05d8e508545b95fc53c6dc85b'], - }), - ('python-novaclient', '17.5.0', { - 'modulename': 'novaclient', - 'checksums': ['7aa0fe9a74b1336e56c2f7965f14e04bad29dbfbd7ba41dcb7b364f94c9bee7f'], - }), - ('python-keystoneclient', '4.2.0', { - 'modulename': 'keystoneclient', - 'checksums': ['0248426e483b95de395086482c077d48e45990d3b1a3e334b2ec8b2e108f5a8a'], - }), - ('python-cinderclient', '8.0.0', { - 'modulename': 'cinderclient', - 'checksums': ['4ced8c562064ab73f757d91d26846faaf1fc1c82f1fee5597e24df3d1ffcf116'], - }), - ('python-openstackclient', version, { - 'modulename': 'openstackclient', - 'checksums': ['8d40491374172f9375ce1642ac2230b1cbb5a564320edbcc2a9ebe857fd9a880'], - }), -] - -sanity_pip_check = True -enhance_sanity_check = True -sanity_check_commands = ['openstack -h'] - -sanity_check_paths = { - 'files': ['bin/openstack'], - 'dirs': ["bin", 'lib/python%(pyshortver)s/site-packages'] -} - -moduleclass = 'tools' From 0237a0c41f643e46ae0a98df45b420e8332b98ca Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 9 Aug 2021 10:35:44 +0100 Subject: [PATCH 1361/2365] Create libtinfo symlinks in ncurses 6.2 --- .../easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb index a3839f2181..5044d91b4c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -28,6 +28,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", From 88fad7eea5eb540d4a483be6df61576f6dea33c6 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 9 Aug 2021 16:13:20 +0200 Subject: [PATCH 1362/2365] adding easyconfigs: torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb, torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb --- ...orchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb | 32 +++++++++++++++++++ ...info-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb create mode 100644 easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb diff --git a/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..0ba85a72a5 --- /dev/null +++ b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'torchinfo' +version = '1.5.2' +local_pytorch_version = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/TylerYep/torchinfo' +description = """" +Torchinfo provides information complementary to what is provided by print(your_model) in PyTorch, similar to +Tensorflow's model.summary() API to view the visualization of the model, which is helpful while debugging your network. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'TylerYep' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['25f076ab469f29a63dee5a048d39edf0f7a809a5d9e640dccd4174a349ea0143'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', local_pytorch_version), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..1b2083358f --- /dev/null +++ b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'torchinfo' +version = '1.5.2' +local_pytorch_version = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/TylerYep/torchinfo' +description = """" +Torchinfo provides information complementary to what is provided by print(your_model) in PyTorch, similar to +Tensorflow's model.summary() API to view the visualization of the model, which is helpful while debugging your network. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +github_account = 'TylerYep' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['25f076ab469f29a63dee5a048d39edf0f7a809a5d9e640dccd4174a349ea0143'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', local_pytorch_version), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From e06d5170e95badd1ea647153dacc84d85595ed80 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 9 Aug 2021 16:45:22 +0100 Subject: [PATCH 1363/2365] functions without return should be declared as void in ctffind --- .../easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb index 234319daa1..978e186cf1 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb @@ -18,10 +18,14 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] checksums = [ 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch ] dependencies = [ From 37967c11939ddc537f3fb8ac4f9064075ab37b35 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Tue, 10 Aug 2021 11:59:54 +1000 Subject: [PATCH 1364/2365] Create libffcall-2.4-GCCcore-10.2.0.eb New version, new compiler, new binutils --- .../libffcall/libffcall-2.4-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..60a3b0255b --- /dev/null +++ b/easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libffcall' +version = '2.4' + +homepage = 'https://www.gnu.org/software/libffcall/' + +description = """ + GNU Libffcall is a collection of four libraries which can be used to build + foreign function call interfaces in embedded interpreters +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8ef69921dbdc06bc5bb90513622637a7b83a71f31f5ba377be9d8fd8f57912c2'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['include/avcall.h', 'include/callback.h', 'include/trampoline.h', + 'include/vacall.h', 'lib/libavcall.a', 'lib/libcallback.a', + 'lib/libtrampoline.a', 'lib/libvacall.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'lib' From 633956239228f19f7d6902df56759fb6c6974d47 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 9 Aug 2021 16:45:22 +0100 Subject: [PATCH 1365/2365] functions without return should be declared as void in ctffind --- .../easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb index 234319daa1..978e186cf1 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb @@ -18,10 +18,14 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] checksums = [ 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch ] dependencies = [ From 5474e99c1444480a4f15e9d7bd8e8b1c8c787a5c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 Aug 2021 11:44:25 +0200 Subject: [PATCH 1366/2365] Add download_dep_file = True to coverage/5.5 for GCCcore/10.2.0 --- easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb index 441df135ab..9d69f0f5eb 100644 --- a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb @@ -23,6 +23,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True sanity_check_paths = { 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], From 2551e340fdabc5dd5e40db5cf3c141ac848d9525 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 Aug 2021 11:49:01 +0200 Subject: [PATCH 1367/2365] BeautifulSoup v4.9.3 for GCCcore/10.2.0 --- .../BeautifulSoup-4.9.3-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7d8438a884 --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.9.3' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35') +] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.2.1', { + 'checksums': ['052774848f448cf19c7e959adf5566904d525f33a3f8b6ba6f6f8f26ec7de0cc'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['84729e322ad1d5b4d25f805bfa05b902dd96450f43842c4e99067d5e1369eb25'], + }), +] + +moduleclass = 'data' From f96cff86a8c1f1c4acd70b43468fc6a92ebc0f8b Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Tue, 10 Aug 2021 13:50:14 +0200 Subject: [PATCH 1368/2365] adding easyconfigs: RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb --- .../RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb new file mode 100644 index 0000000000..a853e77a97 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb @@ -0,0 +1,38 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.12' +versionsuffix = '-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +moduleclass = 'bio' From 87d03fb2beb6b557fa584758b9f7bef5baee3cb4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 10 Aug 2021 16:20:52 +0100 Subject: [PATCH 1369/2365] Build with EGL --- .../easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb index 2bf072bd40..023da3d66a 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('Mesa', '20.2.1'), ] -configopts = '-Degl=no --libdir %(installdir)s/lib ' +configopts = '-Degl=yes --libdir %(installdir)s/lib ' sanity_check_paths = { 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + From f06a95d55fac2c0b0f3f37bf1b50cfe653f17fe9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 18:33:08 +0200 Subject: [PATCH 1370/2365] adding easyconfigs: netcdf4-python-1.5.5.1-foss-2020b.eb, netcdf4-python-1.5.7-foss-2021a.eb --- .../netcdf4-python-1.5.5.1-foss-2020b.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb new file mode 100644 index 0000000000..58f903e181 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.5.5.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('netCDF', '4.7.4'), + ('cURL', '7.72.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.4.1', { + 'checksums': ['7c55540bc164746c3c4f86a07c9c7b9ed4dfb0b0d988348ec63cec065c58766d'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'checksums': [ + 'd957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd', # netCDF4-1.5.5.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' From 1ab047e279e95435ca85a0acb467d88f0e162c95 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 18:43:23 +0200 Subject: [PATCH 1371/2365] adding easyconfigs: openpyxl-3.0.7-GCCcore-10.3.0.eb, openpyxl-3.0.7-GCCcore-10.2.0.eb --- .../openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0ce06b699c --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.0.7' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('lxml', '4.6.2'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['6456a3b472e1ef0facb1129f3c6ef00713cebf62e736cd7a75bcc3247432f251'], + }), +] + +moduleclass = 'data' From 948267b564276700432ab798c199d957677476a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 18:47:55 +0200 Subject: [PATCH 1372/2365] adding easyconfigs: pandapower-2.7.0-foss-2020b.eb --- .../pandapower/pandapower-2.7.0-foss-2020b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb new file mode 100644 index 0000000000..8aefe245c9 --- /dev/null +++ b/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pandapower' +version = '2.7.0' + +homepage = 'http://www.pandapower.org/' +description = """An easy to use open source tool for power system modeling, analysis and optimization with a high +degree of automation""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_ZIP] +checksums = ['abd64ade5bbaa107df2f5b69769ac7747c1190c7c8b7a03d83ef3a14da29f1cd'], + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), + ('XlsxWriter', '1.4.0'), + ('openpyxl', '3.0.7'), +] + +runtest = 'pytest' + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From d29fc8eb3fbccf37a9886989a8d768410544c1e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 19:52:01 +0200 Subject: [PATCH 1373/2365] adding easyconfigs: xarray-0.16.2-foss-2020b.eb --- .../x/xarray/xarray-0.16.2-foss-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb new file mode 100644 index 0000000000..e3caa965c4 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.16.2' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['38e8439d6c91bcd5b7c0fca349daf8e0643ac68850c987262d53526e9d7d01e4'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'data' From f8d3f8457bb9f06796fe5f3d1f45d5a8f70733df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 20:09:46 +0200 Subject: [PATCH 1374/2365] Drop extra comma --- .../easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb index 8aefe245c9..b7d9b8c920 100644 --- a/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb @@ -10,7 +10,7 @@ degree of automation""" toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCE_ZIP] -checksums = ['abd64ade5bbaa107df2f5b69769ac7747c1190c7c8b7a03d83ef3a14da29f1cd'], +checksums = ['abd64ade5bbaa107df2f5b69769ac7747c1190c7c8b7a03d83ef3a14da29f1cd'] dependencies = [ ('Python', '3.8.6'), From 303c75aa44e8dafff216aeb90ea555544c0013f1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 10 Aug 2021 19:13:02 +0100 Subject: [PATCH 1375/2365] Enhance sanity check --- .../easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb index 023da3d66a..a1bd6be54f 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb @@ -28,7 +28,8 @@ dependencies = [ configopts = '-Degl=yes --libdir %(installdir)s/lib ' sanity_check_paths = { - 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + ['lib/libepoxy.%s' % SHLIB_EXT], 'dirs': ['lib'] } From e2b713d9a819cce0b9b5bcc6972d67dbbea7ec3e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 23:28:04 +0200 Subject: [PATCH 1376/2365] adding easyconfigs: PYPOWER-5.1.15-foss-2020b.eb --- .../p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb b/easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb new file mode 100644 index 0000000000..966cf0a6e7 --- /dev/null +++ b/easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'PYPOWER' +version = '5.1.15' + +homepage = 'https://github.com/rwl/PYPOWER' +description = """PYPOWER is a power flow and Optimal Power Flow (OPF) solver. It is a port of MATPOWER to the Python +programming language.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d01e40f1850937e1a4e34ab3c7aa5c76006b23d4cc8a547818b26a808303c8a8'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From 876406c82364172593e59f6672415152558db43c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 23:42:27 +0200 Subject: [PATCH 1377/2365] adding easyconfigs: Shapely-1.8a1-GCC-10.2.0.eb --- .../s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb new file mode 100644 index 0000000000..cac4a8093f --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '1.8a1' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a748ab74c187060264e7ce838aaac30eead2a791bbea8cc3ab1dfc3cc0b4d067'] + +dependencies = [ + ('Python', '3.8.6'), + ('GEOS', '3.9.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From b69df1d9627903b236820a05967b69b3764f39bc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Aug 2021 01:06:42 +0200 Subject: [PATCH 1378/2365] adding easyconfigs: pyshp-2.1.3-GCCcore-10.2.0.eb --- .../p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2abf70d7bd --- /dev/null +++ b/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pyshp' +version = '2.1.3' + +homepage = 'https://github.com/GeospatialPython/pyshp' +description = """Pure Python read/write support for ESRI Shapefile format""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'GeospatialPython' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b9c5420a013ae04b81306d36435d42fb78d336a36dd18c31e1b365c18e319e05'] + +dependencies = [ + ('Python', '3.8.6'), + ('cURL', '7.72.0'), +] + +options = {'modulename': 'shapefile'} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From 96289aa4b5b12df141660fa88107c78dc6198ec7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Aug 2021 02:00:50 +0200 Subject: [PATCH 1379/2365] Fix binutils dep --- easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb index 2abf70d7bd..96e075cd30 100644 --- a/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb @@ -13,6 +13,10 @@ source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['b9c5420a013ae04b81306d36435d42fb78d336a36dd18c31e1b365c18e319e05'] +builddependencies = [ + ('binutils', '2.35'), +] + dependencies = [ ('Python', '3.8.6'), ('cURL', '7.72.0'), From 0761b5f10ceea27648861aeccf3801bcfd6bee1f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Aug 2021 02:13:46 +0200 Subject: [PATCH 1380/2365] adding easyconfigs: Clp-1.17.6-foss-2020b.eb, Cgl-0.60.3-foss-2020b.eb, Cbc-2.10.5-foss-2020b.eb, CoinUtils-2.11.4-GCCcore-10.2.0.eb, Osi-0.108.6-GCCcore-10.2.0.eb --- .../c/Cbc/Cbc-2.10.5-foss-2020b.eb | 63 +++++++++++++++++++ .../c/Cgl/Cgl-0.60.3-foss-2020b.eb | 50 +++++++++++++++ .../c/Clp/Clp-1.17.6-foss-2020b.eb | 55 ++++++++++++++++ .../CoinUtils-2.11.4-GCCcore-10.2.0.eb | 38 +++++++++++ .../o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb | 50 +++++++++++++++ 5 files changed, 256 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb new file mode 100644 index 0000000000..427e25ee82 --- /dev/null +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb @@ -0,0 +1,63 @@ +easyblock = "ConfigureMake" + +name = 'Cbc' +version = '2.10.5' + +homepage = "https://github.com/coin-or/Cbc" +description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming +solver written in C++. It can be used as a callable library or using a +stand-alone executable.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['da1a945648679b21ba56b454b81e939451dc7951d9beb3c3e14f18f64dde6972'] + +builddependencies = [ + ('Autotools', '20200321'), + ('Doxygen', '1.8.20'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.3.5', '-metis'), + ('CoinUtils', '2.11.4'), + ('Osi', '0.108.6'), + ('Clp', '1.17.6'), + ('Cgl', '0.60.3'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +# Disable GLPK, dependencies have to be built with it as well +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' +# Use Cgl from EB +configopts += '--with-cgl-lib="-lCgl" ' +configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb new file mode 100644 index 0000000000..e9e8533a7c --- /dev/null +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb @@ -0,0 +1,50 @@ +easyblock = "ConfigureMake" + +name = 'Cgl' +version = '0.60.3' + +homepage = "https://github.com/coin-or/Cgl" +description = """The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that +can be used with other COIN-OR packages that make use of cuts, such as, among +others, the linear solver Clp or the mixed integer linear programming solvers +Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or +communicate with a solver. It does not directly call a solver.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['cf11e3476d2182040cec412abb232d8bafa12ff5b619eca3b7b9ac1d220476c8'] + +builddependencies = [ + ('Autotools', '20200321'), + ('Doxygen', '1.8.20'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CoinUtils', '2.11.4'), + ('Osi', '0.108.6'), + ('Clp', '1.17.6'), +] + +# Use CoinUtils from EB +configopts = '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['lib/libCgl.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb new file mode 100644 index 0000000000..4a649579d2 --- /dev/null +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'Clp' +version = '1.17.6' + +homepage = "https://github.com/coin-or/Clp" +description = """Clp (Coin-or linear programming) is an open-source linear programming solver. +It is primarily meant to be used as a callable library, but a basic, +stand-alone executable version is also available.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['f9cfcdd3db23bbc2d18b562012a7e25b99a40e8ce72dc296bd46dddb2970e12a'] + +builddependencies = [ + ('Autotools', '20200321'), + ('Doxygen', '1.8.20'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.3.5', '-metis'), + ('CoinUtils', '2.11.4'), + ('Osi', '0.108.6'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +# Disable GLPK because Clp requires headers from its sources +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Osi from EB +configopts += '--with-osi-lib="-lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['Clp', 'ClpSolver', 'OsiClp']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ebc08762ad --- /dev/null +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = "ConfigureMake" + +name = 'CoinUtils' +version = '2.11.4' + +homepage = "https://github.com/coin-or/CoinUtils" +description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and +functions that are generally useful to more than one COIN-OR project.""" + + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['1b24f8f6057661b3225d24f4e671527f53bf13aff66e06cbbbd4f20cc7d31dce'] + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('Doxygen', '1.8.20'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/libCoinUtils.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6b7abcdbec --- /dev/null +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +easyblock = "ConfigureMake" + +name = 'Osi' +version = '0.108.6' + +homepage = "https://github.com/coin-or/Osi" +description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear +programming (LP) solver, along with derived classes for specific solvers. Many +applications may be able to use the Osi to insulate themselves from a specific +LP solver. That is, programs written to the OSI standard may be linked to any +solver with an OSI interface and should produce correct results. The OSI has +been significantly extended compared to its first incarnation. Currently, the +OSI supports linear programming solvers and has rudimentary support for integer +programming.""" + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['57ef3f0c97995bac647504aee0ed34d31f79033ece04cd2cb86b4645f0a552d8'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('Doxygen', '1.8.20'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CoinUtils', '2.11.4'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Disable GLPK because Osi requires GLPK<=4.48 +configopts = '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +sanity_check_paths = { + 'files': ['lib/libOsi.%s' % SHLIB_EXT, 'lib/libOsiCommonTests.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" From ca9210c68b6dbcac93ade6f8a2add83b8328f971 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Wed, 11 Aug 2021 16:22:30 +1000 Subject: [PATCH 1381/2365] Create shrinkwrap-1.1.0-GCCcore-10.2.0.eb New version, new compiler, new binutils, new dependencies etc. --- .../shrinkwrap-1.1.0-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a9387c69f6 --- /dev/null +++ b/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' + +name = 'shrinkwrap' +version = '1.1.0' + +homepage = "https://github.com/jonathonl/shrinkwrap" +description = """A std::streambuf wrapper for compression formats.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/jonathonl/shrinkwrap/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['833e85bdc41e7bf82a57f0fb52958795fb089f691981d2e3a2b68eee17128082'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('XZ', '5.2.5'), + ('zstd', '1.4.5'), +] + +sanity_check_paths = { + 'files': ['include/%%(name)s/%s.hpp' % i for i in ['gz', 'istream', 'xz', 'zstd']], + 'dirs': [], +} + +moduleclass = 'data' From 921a406b27eeeef4b6d977533039cae2b7105af7 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 11 Aug 2021 11:27:32 +0200 Subject: [PATCH 1382/2365] adding easyconfigs: imkl-2020.4.304-gompic-2020b.eb --- .../i/imkl/imkl-2020.4.304-gompic-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb new file mode 100644 index 0000000000..e07323d8ee --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb @@ -0,0 +1,26 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.4.304' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +moduleclass = 'numlib' From 5caa95ddd9ae1b4d02c25a17bb22b2f95a086422 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 11 Aug 2021 11:28:34 +0200 Subject: [PATCH 1383/2365] adding easyconfigs: PyTorch-1.9.0-fosscuda-2020b-imkl.eb --- .../PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 129 ++++++++++++++++++ 1 file changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb new file mode 100644 index 0000000000..feaef854fa --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -0,0 +1,129 @@ +name = 'PyTorch' +version = '1.9.0' +versionsuffix = '-imkl' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', + 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', + 'PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch', + 'PyTorch-1.9.0_fix-testnn-on-A100.patch', + 'PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', + 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', + 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', + 'PyTorch-1.9.0_skip-nccl-error-tests.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch + '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', + # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch + 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', + # PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch + 'edb180d6967c507c147400a64422ff4499bcd5519f9be8d332890c317359dbad', + '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch + # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch + '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', + '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + # PyTorch-1.9.0_increase-test-cuda-tolerance.patch + '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', + # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch + '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.9.0_skip-lstm-serialization-test.patch + '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', + '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('imkl', '2020.4.304'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + 'distributed/elastic/multiprocessing/api_test', + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From d84005326200193f4c03f84f2718e117c60576c8 Mon Sep 17 00:00:00 2001 From: spottho1 Date: Wed, 11 Aug 2021 11:43:01 +0200 Subject: [PATCH 1384/2365] adding easyconfigs: sklearn-som-1.1.0-foss-2020b.eb --- .../sklearn-som-1.1.0-foss-2020b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb new file mode 100644 index 0000000000..45bf357d16 --- /dev/null +++ b/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'sklearn-som' +version = '1.1.0' + +homepage = 'https://github.com/rileypsmith/sklearn-som' +description = """A simple, planar self-organizing map with methods similar to clustering methods in Scikit Learn.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9b8107f42dfbd68db0d1aa75dd2007be4e0136bf0af96da51513e295f76646d9'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/sklearn_som/som.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn_som'], +} + +sanity_check_commands = ['python -c "from sklearn_som.som import SOM"'] + +moduleclass = 'data' From b4cabf43730713a7fedf8a11f53d0c639d000f04 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 11 Aug 2021 12:01:32 +0200 Subject: [PATCH 1385/2365] Increase test timeouts for PyTorch 1.8.1 and 1.9.0 --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 2 +- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index 1d96d37ea3..b93b0e8242 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -48,7 +48,7 @@ checksums = [ '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', 'a8fcb63cf963dc743e8b0a96b966f18d8edde6a4e76365d6de56aa2c71ce6d3f', # PyTorch-1.8.1_fix-vsx-vector-functions.patch # PyTorch-1.8.1_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index b7c08cd300..95baaba3bc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -64,7 +64,7 @@ checksums = [ # PyTorch-1.8.1_honor_shared_cupti-setting.patch 'a6459fe544f9e2b61ab09ba54e8db5b294176ffdbf41c99e0d0b678e1e617b8f', # PyTorch-1.8.1_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch 'c3488fa24405eac6e2e36fbdf94e877bd39fd177e92fb3a0b6bbd5c8b7ddc7bc', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index d614502526..34f2218ba3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -43,7 +43,7 @@ checksums = [ # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', # PyTorch-1.8.1_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index ede9dfd996..0fc9595a1b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -53,7 +53,7 @@ checksums = [ # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', # PyTorch-1.8.1_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch From d36f3615d6b48cbdcdfbf899dd38a7ba64ba2915 Mon Sep 17 00:00:00 2001 From: spottho1 Date: Wed, 11 Aug 2021 13:01:02 +0200 Subject: [PATCH 1386/2365] add download_dep_fail --- .../easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb index 45bf357d16..75357f2279 100644 --- a/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb @@ -18,6 +18,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True sanity_check_paths = { 'files': ['lib/python%(pyshortver)s/site-packages/sklearn_som/som.py'], From 546f74c9218b1c4990ecb2108a4bb151cf358d47 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 11 Aug 2021 15:18:45 +0200 Subject: [PATCH 1387/2365] Linting and reference reasons for excluding tests. --- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index feaef854fa..b880ebaefd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -112,10 +112,13 @@ excluded_tests = { '': [ # Bad tests: https://github.com/pytorch/pytorch/issues/60260 'distributed/elastic/utils/distributed_test', - 'distributed/test_distributed_fork', - 'distributed/test_distributed_spawn', 'distributed/elastic/multiprocessing/api_test', - 'test_optim', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', ] From 571569c503d68245767c64ea89876bd31e084a61 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Aug 2021 15:48:20 +0200 Subject: [PATCH 1388/2365] Also build shared libs for MUMPS 5.3.5 --- .../m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb | 10 +++++++++- .../m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb | 10 +++++++++- 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb index ef32bdb818..c3b9ed471b 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb @@ -10,7 +10,15 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['http://mumps.enseeiht.fr/'] sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + 'e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4', # MUMPS_5.3.5.tar.gz + 'e39441eaf90191b5d967223e085b9fa9adbd4264c49f0dabdbf3c1a6685900fb', # MUMPS-5.3.5_shared-pord.patch + '3662a075d1eab1143409424278c63a1c198b6cd75572610b4bb17dd3d6f4d614', # MUMPS-5.3.5_shared-mumps.patch +] dependencies = [ ('SCOTCH', '6.1.0'), diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb index 162fb38b82..3e9e86cfe0 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -10,7 +10,15 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['http://mumps.enseeiht.fr/'] sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + 'e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4', # MUMPS_5.3.5.tar.gz + 'e39441eaf90191b5d967223e085b9fa9adbd4264c49f0dabdbf3c1a6685900fb', # MUMPS-5.3.5_shared-pord.patch + '3662a075d1eab1143409424278c63a1c198b6cd75572610b4bb17dd3d6f4d614', # MUMPS-5.3.5_shared-mumps.patch +] dependencies = [ ('SCOTCH', '6.1.0'), From 24401ceca596f69c6e0fe8b7a2080e7d3ba25d62 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 11 Aug 2021 16:48:23 +0100 Subject: [PATCH 1389/2365] adding easyconfigs: Cellpose-0.6.5-foss-2020b.eb, Cellpose-0.6.5-fosscuda-2020b.eb and patches: Cellpose-0.6.5_OpenCV.patch, Cellpose-0.6.5_PyQt5.patch --- .../c/Cellpose/Cellpose-0.6.5-foss-2020b.eb | 47 +++++++++++++++++++ .../Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb | 47 +++++++++++++++++++ 2 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb new file mode 100644 index 0000000000..b86e1d18a3 --- /dev/null +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb @@ -0,0 +1,47 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'Cellpose' +version = '0.6.5' + +homepage = "https://www.cellpose.org/" +description = """a generalist algorithm for cellular segmentation""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('numba', '0.53.1'), + ('OpenCV', '4.5.1', '-contrib'), + ('Python', '3.8.6'), + ('PyQt5', '5.15.1'), + ('PyQtGraph', '0.11.1'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('tifffile', '2021.8.8', { + 'checksums': ['8260f31c4700143e8374ff6cde5cef7fe54fc9b7313afe88329f407881901dc5'], + }), + (name, version, { + 'patches': [ + '%(name)s-%(version)s_OpenCV.patch', + '%(name)s-%(version)s_PyQt5.patch', + ], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'use_pip_extras': 'gui', + 'checksums': [ + '19aafedfe5723285f270ad55e7947fbd828abff943a13216a8205809e41fb870', # cellpose-0.6.5.tar.gz + 'b8fd5bece5b5ea66ce41a08f0468fe5785dd4b07cc281eac08a19dd38e3ef410', # Cellpose-0.6.5_OpenCV.patch + '97fc96189993127998fd1388228a4a1b52bbe15d7355162579259a795ebbd937', # Cellpose-0.6.5_PyQt5.patch + ], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..47616f4265 --- /dev/null +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb @@ -0,0 +1,47 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'Cellpose' +version = '0.6.5' + +homepage = "https://www.cellpose.org/" +description = """a generalist algorithm for cellular segmentation""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('numba', '0.53.1'), + ('OpenCV', '4.5.1', '-contrib'), + ('Python', '3.8.6'), + ('PyQt5', '5.15.1'), + ('PyQtGraph', '0.11.1'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('tifffile', '2021.8.8', { + 'checksums': ['8260f31c4700143e8374ff6cde5cef7fe54fc9b7313afe88329f407881901dc5'], + }), + (name, version, { + 'patches': [ + '%(name)s-%(version)s_OpenCV.patch', + '%(name)s-%(version)s_PyQt5.patch', + ], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'use_pip_extras': 'gui', + 'checksums': [ + '19aafedfe5723285f270ad55e7947fbd828abff943a13216a8205809e41fb870', # cellpose-0.6.5.tar.gz + 'b8fd5bece5b5ea66ce41a08f0468fe5785dd4b07cc281eac08a19dd38e3ef410', # Cellpose-0.6.5_OpenCV.patch + '97fc96189993127998fd1388228a4a1b52bbe15d7355162579259a795ebbd937', # Cellpose-0.6.5_PyQt5.patch + ], + }), +] + +moduleclass = 'bio' From 351626a0b14728d9a4bf8e1d326c7f2394c8d7ba Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 11 Aug 2021 18:26:14 +0200 Subject: [PATCH 1390/2365] Add CMake to tbb 2020.03 --- easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb index 3b9ad904fe..ee01f36685 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb @@ -12,7 +12,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['ebc4f6aa47972daed1f7bf71d100ae5bf6931c2e3144cf299c8cc7d041dca2f3'] builddependencies = [ - ('binutils', '2.35') + ('binutils', '2.35'), + ('CMake', '3.18.4'), ] moduleclass = 'lib' From 6bf8417f6264442f879f5b8df644930688e4c4f2 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Thu, 12 Aug 2021 15:58:55 +1000 Subject: [PATCH 1391/2365] Create libsigsegv-2.13-GCCcore-10.2.0.eb New version, new compiler, new binutils --- .../libsigsegv-2.13-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.13-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.13-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2f09752a34 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.13-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libsigsegv' +version = '2.13' + +homepage = 'https://www.gnu.org/software/libsigsegv/' + +description = "GNU libsigsegv is a library for handling page faults in user mode." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['be78ee4176b05f7c75ff03298d84874db90f4b6c9d5503f0da1226b3a3c48119'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['include/sigsegv.h', 'lib/libsigsegv.a', 'lib/libsigsegv.la'], + 'dirs': [], +} + +moduleclass = 'lib' From 9733060f74fd13834373f425ec109dfc4bb098de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 12:12:26 +0200 Subject: [PATCH 1392/2365] Revamp almost everything, add many more dependencies --- .../p/PyPSA/PyPSA-0.17.1-foss-2020b.eb | 49 +++++++++++++++++++ .../p/Pyomo/Pyomo-6.0.1-foss-2020b.eb | 38 ++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb new file mode 100644 index 0000000000..4a89af3e9d --- /dev/null +++ b/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'PyPSA' +version = '0.17.1' + +homepage = 'https://pypsa.readthedocs.io/' +description = """PyPSA is an open source toolbox for simulating and optimising modern power systems that include +features such as conventional generators with unit commitment, variable wind and solar generation, storage units, +coupling to other energy sectors, and mixed alternating and direct current networks. PyPSA is designed to scale +well with large networks and long time series.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pandapower', '2.7.0'), # Needed for some tests + ('PYPOWER', '5.1.15'), # Needed for some tests +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('networkx', '2.5'), + ('PyTables', '3.6.1'), + ('netcdf4-python', '1.5.5.1'), + ('xarray', '0.16.2'), + ('Pyomo', '6.0.1'), + ('Shapely', '1.8a1'), # for optional cartopy + ('PROJ', '7.2.1'), # for optional cartopy + ('pyshp', '2.1.3'), # for optional cartopy +] + +exts_list = [ + ('Cartopy', '0.19.0.post1', { + 'checksums': ['4b8b4773a98ed7009fe17d9b6ec87ac3ac62b7d14634d7768c190eadc647d576'], + }), + (name, version, { + # Single test fails, with no clear fix + 'runtest': "PYTHONPATH=.:$PYTHONPATH pytest --ignore=test/test_sclopf_scigrid.py ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['47811fc24b2daf663a2bb86749235e03e9988c7604a4d7fea48fbc8d9b4431c9'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb new file mode 100644 index 0000000000..d6de3792fc --- /dev/null +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Pyomo' +version = '6.0.1' + +homepage = 'https://www.pyomo.org/' +description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization + capabilities for formulating and analyzing optimization models. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('GLPK', '4.65'), # Optional solver backend + ('Cbc', '2.10.5'), # Optional solver backend +] + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('PyUtilib', '6.0.0', { + 'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'], + }), + (name, version, { + 'checksums': ['4b27bc917b12a6011e7eb3442a54619f0f42f1087d4defa14b903dd985fdbe7c'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['pyomo -h'] + +moduleclass = 'math' From c2e4ff2333c055929724a548cc3c3b4f01732dfa Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Thu, 12 Aug 2021 12:29:08 +0200 Subject: [PATCH 1393/2365] Updating checksum for the revised timeout patch as per #13700. --- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index b880ebaefd..a05a60e0fd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -54,7 +54,7 @@ checksums = [ # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', # PyTorch-1.8.1_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch From a243fcfa4dafe7a83c0f2e3dff70995cf878a430 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 13:04:04 +0200 Subject: [PATCH 1394/2365] adding easyconfigs: UShER-0.4.1-gompi-2020b.eb and patches: UShER-0.4.1_external-tbb.patch --- .../u/UShER/UShER-0.4.1-gompi-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb diff --git a/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb b/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb new file mode 100644 index 0000000000..2eabcf7163 --- /dev/null +++ b/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'UShER' +version = '0.4.1' + +homepage = 'https://github.com/yatisht/usher' +description = """UShER is now a package consisting of a family of programs for +rapid phylogenetic analyses, particularly suitable for the SARS-CoV-2 genomes.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'yatisht' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['UShER-%(version)s_external-tbb.patch'] +checksums = [ + '61acdeaec61f2b376704b4a519bba44b7cffdebf315f8126aba0a80ac3268b0e', # v0.4.1.tar.gz + 'a5b08fbf0ec65c3f548d794c2ad97b044ce536deab2f3362ad7f985a245bd677', # UShER-0.4.1_external-tbb.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] +dependencies = [ + ('tbb', '2020.3'), + ('protobuf', '3.14.0'), + ('MAFFT', '7.475', '-with-extensions'), + ('Boost', '1.74.0'), + ('Python', '3.8.6'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['usher', 'ripples', 'matOptimize', 'matUtils']], + 'dirs': [], +} + +sanity_check_commands = ['usher -h', 'ripples -h', 'matOptimize -h', 'matUtils -h'] + +moduleclass = 'bio' From 862e7684a53eae455ee139f722db385179bf0537 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Thu, 12 Aug 2021 22:02:31 +1000 Subject: [PATCH 1395/2365] Create MATIO-1.5.21-GCCcore-10.2.0.eb New version, new compiler, new binutils --- .../m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fcb5c5d763 --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'MATIO' +version = '1.5.21' + +homepage = 'https://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] +checksums = ['bf1808a20412534a7c9e69c6eb0d2612'] + +preconfigopts = 'chmod +x configure && ' + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 74fe24f79649d7c37deb410d594079c439c8edd2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 16:32:55 +0200 Subject: [PATCH 1396/2365] Fix typo --- easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb b/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb index 2eabcf7163..3c336471f3 100644 --- a/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb +++ b/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb @@ -31,8 +31,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/' + x for x in ['usher', 'ripples', 'matOptimize', 'matUtils']], - 'dirs': [], + 'files': ['bin/' + x for x in ['usher', 'ripples', 'matOptimize', 'matUtils']], + 'dirs': [], } sanity_check_commands = ['usher -h', 'ripples -h', 'matOptimize -h', 'matUtils -h'] From 0e8aef2bdfc945110f25e205e1a3ae99b59411cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Aug 2021 19:20:27 +0200 Subject: [PATCH 1397/2365] remove unused buildcmd from libgpuarray easyconfigs --- .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index 21aa4a17f7..d871b75c78 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -33,7 +33,6 @@ exts_default_options = { } exts_list = [ (name, version, { - 'buildcmd': 'build_ext', 'modulename': 'pygpu', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], From 0f04a4e0845d03467096dc9c8fdfeb2fcb35bae1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 21:01:30 +0200 Subject: [PATCH 1398/2365] add easyconfigs for pytest-xdist and pytest-benchmark build dependencies of jax --- .../pytest-benchmark-3.4.1-GCCcore-10.2.0.eb | 41 ++++++++++++ .../pytest-xdist-2.3.0-GCCcore-10.2.0.eb | 62 +++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fc22ef3468 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'pytest-benchmark' +version = '3.4.1' + +homepage = 'https://github.com/ionelmc/pytest-benchmark' +description = "A pytest fixture for benchmarking code." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True + +exts_list = [ + ('py-cpuinfo', '8.0.0', { + 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], + 'modulename': 'cpuinfo', + }), + (name, version, { + 'checksums': ['40e263f912de5a81d891619032983557d62a3d85843f9a9f30b98baea0cd7b47'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cpuinfo', 'bin/pytest-benchmark'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cpuinfo --help", + "pytest-benchmark --help", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..93631bf96c --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'pytest-xdist' +version = '2.3.0' + +homepage = 'https://github.com/pytest-dev/pytest-xdist' +description = """xdist: pytest distributed testing plugin + +The pytest-xdist plugin extends pytest with some unique test execution modes: + + * test run parallelization: if you have multiple CPUs or hosts you + can use those for a combined test run. This allows to speed up + development or to use special resources of remote machines. + + * --looponfail: run your tests repeatedly in a subprocess. After + each run pytest waits until a file in your project changes and + then re-runs the previously failing tests. This is repeated + until all tests pass after which again a full run is + performed. + + * Multi-Platform coverage: you can specify different Python + interpreters or different platforms and run tests in parallel on + all of them. + +Before running tests remotely, pytest efficiently “rsyncs” your +program source code to the remote place. All test results are reported +back and displayed to your local terminal. You may specify different +Python versions and interpreters.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('apipkg', '1.5', { + 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], + }), + ('execnet', '1.9.0', { + 'checksums': ['8f694f3ba9cc92cab508b152dcfe322153975c29bda272e2fd7f3f00f36e47c5'], + }), + ('pytest-forked', '1.3.0', { + 'checksums': ['6aa9ac7e00ad1a539c41bec6d21011332de671e938c7637378ec9710204e37ca'], + }), + (name, version, { + 'modulename': 'xdist', + 'checksums': ['e8ecde2f85d88fbcadb7d28cb33da0fa29bca5cf7d5967fa89fc0e97e5299ea5'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From a4faf7a5161291ada2d8af7558ae9dbc9363b217 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 21:02:13 +0200 Subject: [PATCH 1399/2365] update to jax 0.2.19 --- .../j/jax/jax-0.2.19-foss-2020b.eb | 113 ++++++++++++++++++ 1 file changed, 113 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb new file mode 100644 index 0000000000..1efc76bfb9 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -0,0 +1,113 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.2.19' +local_jaxlib_ver = '0.1.70' +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and +more""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('pytest-xdist', '2.3.0'), + ('pytest-benchmark', '3.4.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Cython', '0.29.22'), + ('flatbuffers-python', '1.12'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = '4039feeb743bc42cd0a3d8146ce63fc05d23eb8d' + +local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_commit + +local_jax_prebuildopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir + +local_jax_build_cmd = 'python build/build.py ' +local_jax_build_cmd += '--target_cpu_features=native ' +local_jax_build_cmd += '--bazel_startup_options="--output_user_root=%(builddir)s" ' +local_jax_build_cmd += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' +local_jax_build_cmd += '--bazel_options=--subcommands ' +local_jax_build_cmd += '--bazel_options=--jobs=%(parallel)s --bazel_options=--action_env=PYTHONPATH ' +local_jax_build_cmd += '--bazel_options=--action_env=EBPYTHONPREFIXES' + +use_pip = True + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('absl-py', '0.13.0', { + 'options': {'modulename': 'absl'}, + 'easyblock': 'PythonPackage', + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + 'use_pip': True, + }), + ('jaxlib', local_jaxlib_ver, { + 'easyblock': 'PythonPackage', + 'sources': [ + 'jaxlib-v%s.zip' % local_jaxlib_ver, + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib-%s_no-tensorflow-download.patch' % local_jaxlib_ver, 1), + ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../tensorflow-%s' % local_tf_commit), + ], + 'checksums': [ + # jaxlib-v0.1.70.zip + '1205b180de70c98899d842f75bb589599c10a3c7a1c6099475c3a7d39b2e44ac', + # tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d.tar.gz + '0f13410284b9186e436350e9617b3bed2d65f1dc1a220fd37ad9ef43c2035663', + # jaxlib-0.1.70_no-tensorflow-download.patch + '1496c6be9336fb563b997f8da83d690a9b3a0a6e29fdd87fac60409300a2fd95', + # TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d-build-env.patch + 'd067836b1d18d66a8c69fb3db311855c8a56c0106d42a11299a1733c385e9c22', + ], + 'start_dir': 'jax-jaxlib-v%s' % local_jaxlib_ver, + 'prebuildopts': local_jax_prebuildopts, + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, + 'buildcmd': local_jax_build_cmd, + 'install_src': 'dist/*.whl', + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'checksums': ['e55534680a05b6ced92dadde307bd3b2207efd1aaaec304e96197b00ad7560d3'], + }), +] + +# can't run tests in sanity check step, because build dependencies must be available +postinstallcmds = [ + "cd %%(builddir)s/jax-jaxlib-v%s && " + "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH " + "pytest -n auto tests" % local_jaxlib_ver, +] + +sanity_pip_check = True + +moduleclass = 'tools' From f08cc61f13d1bb9486e1a6ff79af6a2acb967574 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 13 Aug 2021 14:52:38 -0700 Subject: [PATCH 1400/2365] {bio}[GCC/10.2.0] RAxML-NG 1.0.3 --- .../r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..2eaf3ce90c --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb @@ -0,0 +1,46 @@ +# EasyBuild easyconfig +# +# Contributed from Fred Hutchinson Cancer Research Center, Seattle WA, US +# John Dey jfdey@fredhutch.org +# +easyblock = 'CMakeMake' + +name = 'RAxML-NG' +version = '1.0.3' + +homepage = 'https://github.com/amkozlov/raxml-ng' +description = """RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) + optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree + Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/amkozlov', + 'repo_name': '%(namelower)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [ + '3bee0fd77b18d273349190ea47719211474dc4de2261579a06faa12d4cdb8219', +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' + From 139d0f6875027b71a69f28904585648666a3a52d Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 13 Aug 2021 16:39:41 -0700 Subject: [PATCH 1401/2365] {math}[GCCcore 10.2.0] SpectrA 1.0.0 --- .../s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..49cc5f7278 --- /dev/null +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# +# Fred Hutchinson Cancer Research Center - Seattle - Washington - US +# https://www.fredhutch.org +# John Dey +# +easyblock = 'CMakeMake' + +name = 'SpectrA' +version = '1.0.0' + +homepage = 'https://spectralib.org/' +description = """Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ + library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/yixuan/spectra/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['45228b7d77b916b5384245eb13aa24bc994f3b0375013a8ba6b85adfd2dafd67'] + +builddependencies = [('CMake', '3.18.4')] +dependencies = [('Eigen', '3.3.8')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +sanity_check_paths = { + 'files': ['include/Spectra/SymEigsSolver.h'], + 'dirs': [''], +} + +moduleclass = 'math' From 38195fa18ec2465a13de293f594a9772c0a24767 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 06:38:57 +0200 Subject: [PATCH 1402/2365] adding easyconfigs: AlphaFold-2.0.0-foss-2020b.eb --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb new file mode 100644 index 0000000000..aa4d274464 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.0.0' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '3.7.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.5.0'), + ('Biopython', '1.78'), + ('jax', '0.2.19'), # also provides absl-py +] + +use_pip = True + +exts_list = [ + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + # source tarball on PyPI is missing requirements.txt, + # see https://github.com/deepmind/dm-haiku/issues/44 + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + 'modulename': 'haiku', + }), + ('dm-tree', '0.1.6', { + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + 'modulename': 'tree', + }), + ('websocket-client', '1.2.1', { + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + 'modulename': 'websocket', + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + # see https://github.com/google/ml_collections/issues/7 + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + (name, version, { + 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From b880699a9fb3207a551bab172e038a7f710f0fb5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 06:47:07 +0200 Subject: [PATCH 1403/2365] enhance sanity check for SpectrA, remove easyconfig parameters that are set by default for CMakeMake --- .../easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb index 49cc5f7278..8cb83e6444 100644 --- a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb @@ -20,15 +20,12 @@ sources = ['v%(version)s.tar.gz'] checksums = ['45228b7d77b916b5384245eb13aa24bc994f3b0375013a8ba6b85adfd2dafd67'] builddependencies = [('CMake', '3.18.4')] -dependencies = [('Eigen', '3.3.8')] - -separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +dependencies = [('Eigen', '3.3.8')] sanity_check_paths = { 'files': ['include/Spectra/SymEigsSolver.h'], - 'dirs': [''], + 'dirs': ['include/Spectra/LinAlg', 'share/spectra/cmake'], } moduleclass = 'math' From a49bb80bcbdbcba4f594f0ccf441ac198a03fcba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 07:23:17 +0200 Subject: [PATCH 1404/2365] fix trivial style issues in RAxML-NG 1.0.3 easyconfig --- .../r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb index 2eaf3ce90c..4d8a39740f 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb @@ -18,11 +18,11 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} sources = [{ 'filename': '%(name)s-%(version)s.tar.gz', 'git_config': { - 'url': 'https://github.com/amkozlov', - 'repo_name': '%(namelower)s', - 'tag': '%(version)s', - 'recursive': True, - 'keep_git_dir': True, + 'url': 'https://github.com/amkozlov', + 'repo_name': '%(namelower)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, } }] checksums = [ @@ -43,4 +43,3 @@ sanity_check_paths = { } moduleclass = 'bio' - From 80a8347db260b6676e5bc111af108dd5ba266942 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 07:27:05 +0200 Subject: [PATCH 1405/2365] don't use checksum in easyconfig for RAxML-NG 1.0.3, since git_config is used for sources --- easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb index 4d8a39740f..a29ce5a975 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb @@ -25,9 +25,7 @@ sources = [{ 'keep_git_dir': True, } }] -checksums = [ - '3bee0fd77b18d273349190ea47719211474dc4de2261579a06faa12d4cdb8219', -] +checksums = [None] builddependencies = [ ('CMake', '3.18.4'), From e68665d770c46435c4afb0852d420e01e9ea4d2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 07:54:36 +0200 Subject: [PATCH 1406/2365] add Perl build dependency to recent Clang easyconfigs --- easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb index 6a528a4897..a7ec71f94d 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb @@ -57,6 +57,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.18.4'), ('Python', '3.8.6'), + ('Perl', '5.32.0'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb index 037c1ef7f8..34cb362004 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb @@ -57,6 +57,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.18.4'), ('Python', '3.8.6'), + ('Perl', '5.32.0'), ('elfutils', '0.183'), ] From b581b952bc4d4eda4c35aa36e6f1ee22d21dd2e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 08:00:36 +0200 Subject: [PATCH 1407/2365] stick to TensorFlow 2.4.1 dependency for AlphaFold 2.0.0 with foss/2020b --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index aa4d274464..9fe9c5a44e 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('PyYAML', '5.3.1'), - ('TensorFlow', '2.5.0'), + ('TensorFlow', '2.4.1'), ('Biopython', '1.78'), ('jax', '0.2.19'), # also provides absl-py ] From 10c321d7764d71cf64bbb9b5b1a0a9066b67f427 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sat, 14 Aug 2021 20:02:27 +1000 Subject: [PATCH 1408/2365] Update MATIO-1.5.21-GCCcore-10.2.0.eb Fix checksum --- easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb index fcb5c5d763..c8a95327a3 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_ZIP] -checksums = ['bf1808a20412534a7c9e69c6eb0d2612'] +checksums = ['2ac1d5406e51f2bdfaa545a535d6dbf6347be89891a06323961d7a2acbf37be9'] preconfigopts = 'chmod +x configure && ' From 6a4fd45b38a1cb04c88795252f96f3c8d9acd314 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 15 Aug 2021 09:00:00 +0100 Subject: [PATCH 1409/2365] disable using system Valgrind in the json-c tests --- easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb index 3368d5ac78..150611776a 100644 --- a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb @@ -20,6 +20,8 @@ builddependencies = [ ('CMake', '3.18.4'), ] +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' runtest = 'test' sanity_check_paths = { From cd3d94a7e313ed093e64cda0de418e908da71802 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 09:32:29 +0200 Subject: [PATCH 1410/2365] add patch for AlphaFold to fix setup.py, add OpenMM and PDBFixer dependencies, also install scripts and 'alphafold' command --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 25 ++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 9fe9c5a44e..6da221ba1a 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -19,6 +19,8 @@ dependencies = [ ('PyYAML', '5.3.1'), ('TensorFlow', '2.4.1'), ('Biopython', '1.78'), + ('OpenMM', '7.5.1'), # for simtk + ('PDBFixer', '1.7'), ('jax', '0.2.19'), # also provides absl-py ] @@ -67,10 +69,31 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], 'sources': ['v%(version)s.tar.gz'], - 'checksums': ['78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2'], + 'patches': ['AlphaFold-%(version)s_fix-packages.patch'], + 'checksums': [ + '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + ], }), ] +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/AlphaFold/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/AlphaFold/alphafold-%(version)s/scripts %(installdir)s/", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/run_alphafold.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = ["alphafold --help"] + sanity_pip_check = True moduleclass = 'bio' From 61ed5b7209861334e3e828e27e0fc447cba34a1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 10:36:19 +0200 Subject: [PATCH 1411/2365] enhance sanity check for HH-suite 3.3.0 + add path to scripts subdirectory to $PERL5LIB --- .../h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 27 +++++++++---------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index 6e6f5b7ed6..1c6f7bec0d 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -45,25 +45,24 @@ _binaries = [ 'hhmake', 'hhfilter', 'hhconsensus', ] -_scriptfiles = [ - 'a3m.py', 'check_a3m.py', 'cif2fasta.py', 'ffindex.py', 'get_a3m_size.py', - 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', -] - -_perlfiles = [ - 'addss.pl', 'create_profile_from_hmmer.pl', 'hhmakemodel.pl', - 'mergeali.pl', 'multithread.pl', 'pdb2fasta.pl', 'pdbfilter.pl', - 'reformat.pl', 'renumberpdb.pl', 'splitfasta.pl', -] - -fix_perl_shebang_for = ['scripts/%s' % z for z in _perlfiles] +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] sanity_check_paths = { 'files': ['bin/%s' % x for x in _binaries] + - ['scripts/%s' % y for y in _scriptfiles], + ['scripts/ffindex.py', 'scripts/hh_reader.py', 'scripts/hhmakemodel.pl', 'scripts/splitfasta.pl'], 'dirs': ['data', 'scripts'] } -modextrapaths = {'PATH': 'scripts'} +sanity_check_commands = [ + "hhsearch -h", + "ffindex.py --help", + "hhmakemodel.pl 2>&1 | grep 'hhmakemodel.pl from HHsuite'", +] + +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} moduleclass = 'bio' From 04a5c4a4258e532357a13847c6a1895fc629f5d3 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 16 Aug 2021 09:26:31 +0000 Subject: [PATCH 1412/2365] Address suggested changes by Boegel --- .../h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index 6e6f5b7ed6..587b1efc8e 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -46,17 +46,10 @@ _binaries = [ ] _scriptfiles = [ - 'a3m.py', 'check_a3m.py', 'cif2fasta.py', 'ffindex.py', 'get_a3m_size.py', 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', ] -_perlfiles = [ - 'addss.pl', 'create_profile_from_hmmer.pl', 'hhmakemodel.pl', - 'mergeali.pl', 'multithread.pl', 'pdb2fasta.pl', 'pdbfilter.pl', - 'reformat.pl', 'renumberpdb.pl', 'splitfasta.pl', -] - -fix_perl_shebang_for = ['scripts/%s' % z for z in _perlfiles] +fix_perl_shebang_for = ['scripts/*pl'] sanity_check_paths = { 'files': ['bin/%s' % x for x in _binaries] + @@ -64,6 +57,9 @@ sanity_check_paths = { 'dirs': ['data', 'scripts'] } -modextrapaths = {'PATH': 'scripts'} +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} moduleclass = 'bio' From b2712a16ed2621cef573d10281206838a2510ece Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 11:34:21 +0200 Subject: [PATCH 1413/2365] add missing dependencies for AlphaFold + patch to pick up on them and take into account $ALPHAFOLD_DATA_DIR, fix sanity check command --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 6da221ba1a..af15e18801 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -20,6 +20,9 @@ dependencies = [ ('TensorFlow', '2.4.1'), ('Biopython', '1.78'), ('OpenMM', '7.5.1'), # for simtk + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), ('PDBFixer', '1.7'), ('jax', '0.2.19'), # also provides absl-py ] @@ -69,10 +72,14 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], 'sources': ['v%(version)s.tar.gz'], - 'patches': ['AlphaFold-%(version)s_fix-packages.patch'], + 'patches': [ + 'AlphaFold-%(version)s_fix-packages.patch', + 'AlphaFold-%(version)s_data-dep-paths.patch', + ], 'checksums': [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '5a1b17002273cc05a06541297b8017b1928063fe54cffe0b133fa4b39b5435ad', # AlphaFold-2.0.0_data-dep-paths.patch ], }), ] @@ -92,7 +99,7 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } -sanity_check_commands = ["alphafold --help"] +sanity_check_commands = ["alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'"] sanity_pip_check = True From e843e8bb9055e112489c3e303d464527543d2ee9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 11:49:08 +0200 Subject: [PATCH 1414/2365] avoid warnigns about non-default values for required options to run_alphafold.py script --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index af15e18801..9038dac8d5 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -79,7 +79,7 @@ exts_list = [ 'checksums': [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '5a1b17002273cc05a06541297b8017b1928063fe54cffe0b133fa4b39b5435ad', # AlphaFold-2.0.0_data-dep-paths.patch + '7e19d944934b8004e4ee114c94f580d899ac503f3147fc7746c960cc5ca18c0d', # AlphaFold-2.0.0_data-dep-paths.patch ], }), ] From 85d483353ff6577977df4ce250f0ef56fe4fb1ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 11:52:30 +0200 Subject: [PATCH 1415/2365] fix default value for template_mmcif_dir based on \ALPHAFOLD_DATA_DIR --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 9038dac8d5..cab8b7153a 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -79,7 +79,7 @@ exts_list = [ 'checksums': [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '7e19d944934b8004e4ee114c94f580d899ac503f3147fc7746c960cc5ca18c0d', # AlphaFold-2.0.0_data-dep-paths.patch + '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch ], }), ] From b0cc68597a6710764849f8fc081149daa38f0d72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 12:21:02 +0200 Subject: [PATCH 1416/2365] add patch for HHBlits and JackHmmer scripts to avoid hardcoded number of cores to use --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index cab8b7153a..c3325e0a46 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -75,11 +75,13 @@ exts_list = [ 'patches': [ 'AlphaFold-%(version)s_fix-packages.patch', 'AlphaFold-%(version)s_data-dep-paths.patch', + 'AlphaFold-%(version)s_n-cpu.patch', ], 'checksums': [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch + '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a', # AlphaFold-2.0.0_n-cpu.patch ], }), ] From 56b829a99644fd3b51ccc8b9decc327383b245ad Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 16 Aug 2021 11:25:50 +0000 Subject: [PATCH 1417/2365] Missing Python-3.8.6 added --- .../h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index 1c6f7bec0d..231c60d49b 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -36,6 +36,7 @@ builddependencies = [ dependencies = [ ('Perl', '5.32.0'), + ('Python', '3.8.6'), ] _binaries = [ @@ -45,21 +46,18 @@ _binaries = [ 'hhmake', 'hhfilter', 'hhconsensus', ] -fix_perl_shebang_for = ['scripts/*.pl'] -fix_python_shebang_for = ['scripts/*.py'] +_scriptfiles = [ + 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +] + +fix_perl_shebang_for = ['scripts/*pl'] sanity_check_paths = { 'files': ['bin/%s' % x for x in _binaries] + - ['scripts/ffindex.py', 'scripts/hh_reader.py', 'scripts/hhmakemodel.pl', 'scripts/splitfasta.pl'], + ['scripts/%s' % y for y in _scriptfiles], 'dirs': ['data', 'scripts'] } -sanity_check_commands = [ - "hhsearch -h", - "ffindex.py --help", - "hhmakemodel.pl 2>&1 | grep 'hhmakemodel.pl from HHsuite'", -] - modextrapaths = { 'PATH': 'scripts', 'PERL5LIB': 'scripts', From 58d0d75e66bb3c927559bec2e93e452ec09beca4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 15:12:33 +0200 Subject: [PATCH 1418/2365] include stereo_chemical_props.txt in AlphaFold installaiton directory, switch to installing AlphaFold via 'components' because it now requires multiple source files --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 63 +++++++++++++------ 1 file changed, 45 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index c3325e0a46..dafa3b1612 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -27,6 +27,44 @@ dependencies = [ ('jax', '0.2.19'), # also provides absl-py ] +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + 'v%(version)s.tar.gz', + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp -a %s .", + }, + ], + 'patches': [ + 'AlphaFold-%(version)s_fix-packages.patch', + 'AlphaFold-%(version)s_data-dep-paths.patch', + 'AlphaFold-%(version)s_n-cpu.patch', + 'AlphaFold-2.0.0_fix-scp-path.patch', + ], + 'checksums': [ + '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch + '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a', # AlphaFold-2.0.0_n-cpu.patch + '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + use_pip = True exts_list = [ @@ -69,31 +107,17 @@ exts_list = [ # see https://github.com/google/ml_collections/issues/7 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", }), - (name, version, { - 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], - 'sources': ['v%(version)s.tar.gz'], - 'patches': [ - 'AlphaFold-%(version)s_fix-packages.patch', - 'AlphaFold-%(version)s_data-dep-paths.patch', - 'AlphaFold-%(version)s_n-cpu.patch', - ], - 'checksums': [ - '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz - '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch - '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a', # AlphaFold-2.0.0_n-cpu.patch - ], - }), ] postinstallcmds = [ "mkdir -p %(installdir)s/bin", # run_alphafold.py script is missing a shebang... "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", - "cat %(builddir)s/AlphaFold/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", "chmod a+x %(installdir)s/bin/run_alphafold.py", "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", - "cp -a %(builddir)s/AlphaFold/alphafold-%(version)s/scripts %(installdir)s/", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, ] sanity_check_paths = { @@ -101,7 +125,10 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } -sanity_check_commands = ["alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'"] +sanity_check_commands = [ + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] sanity_pip_check = True From 4c08b361cafc0f9f020695fa9b49bcfe81ae0793 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 17:19:39 +0200 Subject: [PATCH 1419/2365] include patched OpenMM as component in AlphaFold installation --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 37 +++++++++++++++++-- 1 file changed, 34 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index dafa3b1612..f91253267d 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -9,8 +9,12 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ + # CMake/oxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), # required for installing dm-tree ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), ] dependencies = [ @@ -19,7 +23,6 @@ dependencies = [ ('PyYAML', '5.3.1'), ('TensorFlow', '2.4.1'), ('Biopython', '1.78'), - ('OpenMM', '7.5.1'), # for simtk ('HH-suite', '3.3.0'), ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), @@ -27,11 +30,29 @@ dependencies = [ ('jax', '0.2.19'), # also provides absl-py ] +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + # required to install OpenMM Python API + 'installopts': " && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s", + }), (name, version, { 'easyblock': 'PythonPackage', 'source_urls': [ @@ -39,7 +60,10 @@ components = [ 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, ], 'sources': [ - 'v%(version)s.tar.gz', + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, { 'download_filename': 'stereo_chemical_props.txt', 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, @@ -121,15 +145,22 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/run_alphafold.py'], + 'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } sanity_check_commands = [ + "python -m simtk.testInstallation", "python -c 'import alphafold'", "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + sanity_pip_check = True moduleclass = 'bio' From 0c563c5dc0b12eb182a3a98d22e620a638a78768 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 17:21:38 +0200 Subject: [PATCH 1420/2365] don't pick up on \SLURM_CPUS_ON_NODE, only add environment variable to avoid hardcoding core count for jackhmmer and hhblits --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index f91253267d..ecfaeb43f0 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -81,7 +81,7 @@ components = [ '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch - '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a', # AlphaFold-2.0.0_n-cpu.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch ], 'start_dir': 'alphafold-%(version)s', From a22e8864b84067164d3c070c4796ae294b3cb405 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 17:37:07 +0200 Subject: [PATCH 1421/2365] fix default paths to downloaded AlphaFold data --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index ecfaeb43f0..b0ff243dc7 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -80,7 +80,7 @@ components = [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch + '1d426748bec4f0f3cc49448ebeb14c4350717f88287afd2aabf6738dea387d81', # AlphaFold-2.0.0_data-dep-paths.patch 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch ], From caea7a8ceaa35e70bf23bf90aa1531f8a6e0b785 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 16 Aug 2021 18:14:03 +0100 Subject: [PATCH 1422/2365] adding easyconfigs: HMMER-3.3.2-gompic-2020b.eb, HH-suite-3.3.0-gompic-2020b.eb --- .../h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb | 66 ++++++++++++++++++ .../h/HMMER/HMMER-3.3.2-gompic-2020b.eb | 68 +++++++++++++++++++ 2 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb new file mode 100644 index 0000000000..e3d70a3e26 --- /dev/null +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb @@ -0,0 +1,66 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Updated to use gompi-2020b toolchain: +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'HH-suite' +version = '3.3.0' + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """The HH-suite is an open-source software package +for sensitive protein sequence searching based on the pairwise +alignment of hidden Markov models (HMMs).""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Perl', '5.32.0'), + ('Python', '3.8.6'), +] + +_binaries = [ + 'hhalign', 'hhalign_mpi', 'hhalign_omp', + 'hhblits', 'hhblits_mpi', 'hhblits_omp', + 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp', + 'hhmake', 'hhfilter', 'hhconsensus', +] + +_scriptfiles = [ + 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +] + +fix_perl_shebang_for = ['scripts/*pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + ['scripts/%s' % y for y in _scriptfiles], + 'dirs': ['data', 'scripts'] +} + +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb new file mode 100644 index 0000000000..bb136efe34 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb @@ -0,0 +1,68 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] + +builddependencies = [('Python', '3.8.6')] + +configopts = '--enable-mpi' + +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From 77d40962bbfaf0f862e9816a5b76519ae8943650 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 16 Aug 2021 20:47:51 +0100 Subject: [PATCH 1423/2365] switch to SOURCELOWER_TAR_GZ --- easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb index bb136efe34..f26e9cbaaf 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb @@ -34,7 +34,7 @@ source_urls = [ 'http://eddylab.org/software/hmmer/', 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] -sources = ['hmmer-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] builddependencies = [('Python', '3.8.6')] From 92166e7ea895b65727117bd8f64133f2d3eae1a7 Mon Sep 17 00:00:00 2001 From: jedokaplan Date: Tue, 17 Aug 2021 17:29:44 +0800 Subject: [PATCH 1424/2365] adding easyconfigs: Qwt-6.1.5-GCCcore-10.2.0.eb --- .../q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9ffe3f5f9d --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.1.5' + +homepage = 'https://qwt.sourceforge.io/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Qwt-6.1.4_Fix_prefix_and_pkgconfig.patch'] +checksums = [ + '4076de63ec2b5e84379ddfebf27c7b29b8dc9074f3db7e2ca61d11a1d8adc041', # qwt-6.1.5.tar.bz2 + '82788aaa23e4bc764ab1f2769e9260d154976c7d7f043ba4e288330d6984b6a9', # Qwt-6.1.4_Fix_prefix_and_pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Qt5', '5.14.2'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' From e97cc492f8373a32fa2452eb7b3c76b1b0e0e0c3 Mon Sep 17 00:00:00 2001 From: jedokaplan Date: Tue, 17 Aug 2021 17:30:34 +0800 Subject: [PATCH 1425/2365] adding easyconfigs: QwtPolar-1.1.1-GCCcore-10.2.0.eb, QJson-0.9.0-GCCcore-10.2.0.eb --- .../q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++ .../QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb | 36 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fdf7452a36 --- /dev/null +++ b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'QJson' +version = '0.9.0' + +homepage = 'http://qjson.sourceforge.net/' +description = "QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/flavio/qjson/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e812617477f3c2bb990561767a4cd8b1d3803a52018d4878da302529552610d4'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] +dependencies = [ + ('Qt5', '5.14.2'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libqjson-qt5.%s' % SHLIB_EXT], + 'dirs': ['include/qjson-qt5', 'lib/cmake', 'lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0d2549e811 --- /dev/null +++ b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'QwtPolar' +version = '1.1.1' + +homepage = 'http://qwtpolar.sourceforge.net/' +description = "The QwtPolar library contains classes for displaying values on a polar coordinate system." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6168baa9dbc8d527ae1ebf2631313291a1d545da268a05f4caa52ceadbe8b295'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('Qwt', '6.1.5'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@INSTALL_PREFIX[ ]*=.*@INSTALL_PREFIX = %(installdir)s@g' qwtpolarconfig.pri && " +prebuildopts += "sed -i 's/QwtPolarExamples//g' qwtpolarconfig.pri && " +prebuildopts += "qmake qwtpolar.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwtpolar.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' From 7756ea500afce145dccbcc6f72369bb8d0570df9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Aug 2021 11:38:17 +0200 Subject: [PATCH 1426/2365] make run_alphafold.py print a warning when $ALPHAFOLD_DATA_DIR is not defined --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index b0ff243dc7..91d5b657e7 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -80,7 +80,7 @@ components = [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '1d426748bec4f0f3cc49448ebeb14c4350717f88287afd2aabf6738dea387d81', # AlphaFold-2.0.0_data-dep-paths.patch + '7223e297b23f90816219095696bc6453910c617add60b907a0d3e869da8733bb', # AlphaFold-2.0.0_data-dep-paths.patch 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch ], From 8962885123f356ef8d0e35dabf4eb1155116fa88 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 17 Aug 2021 13:22:24 +0200 Subject: [PATCH 1427/2365] setting crisprdav easyblock explicitely --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index d6b5db719a..10b6699305 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -1,3 +1,5 @@ +easyblock = 'EB_CRISPR_minus_DAV' + name = 'CRISPR-DAV' version = '2.3.4' From 3a641951d1192f20ea5e1268cdc787e9d1eaa52d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 17 Aug 2021 13:31:17 +0200 Subject: [PATCH 1428/2365] removing explicit crispr-dav easyblock --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index 10b6699305..d6b5db719a 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_CRISPR_minus_DAV' - name = 'CRISPR-DAV' version = '2.3.4' From 2545a7a1da56eabff8ba8e09e9a6edc6b6bc9f89 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 17 Aug 2021 15:45:33 +0200 Subject: [PATCH 1429/2365] Update CRISPR-DAV-2.3.4-foss-2020b.eb adding archive-zip perl module --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index d6b5db719a..176d5949c3 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -29,6 +29,7 @@ dependencies = [ ('SAMtools', '1.12'), ('BEDTools', '2.30.0'), ('FLASH', '2.2.00'), + ('Archive-Zip', '1.68'), ] moduleclass = 'bio' From 189e0cb94e6fca91baa023c4ba363b690796292c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Aug 2021 19:35:08 +0200 Subject: [PATCH 1430/2365] Add jax/fosscuda and use EasyBlock for jaxlib --- .../j/jax/jax-0.2.19-foss-2020b.eb | 64 +++++------ .../j/jax/jax-0.2.19-fosscuda-2020b.eb | 104 ++++++++++++++++++ 2 files changed, 129 insertions(+), 39 deletions(-) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index 1efc76bfb9..98dfee38c8 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -4,61 +4,53 @@ easyblock = 'PythonBundle' name = 'jax' version = '0.2.19' -local_jaxlib_ver = '0.1.70' homepage = 'https://pypi.python.org/pypi/jax' -description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and -more""" +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ ('Bazel', '3.7.2'), + ('Cython', '0.29.22'), ('pytest-xdist', '2.3.0'), - ('pytest-benchmark', '3.4.1'), ] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Cython', '0.29.22'), ('flatbuffers-python', '1.12'), ] # downloading TensorFlow tarball to avoid that Bazel downloads it during the build # note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE local_tf_commit = '4039feeb743bc42cd0a3d8146ce63fc05d23eb8d' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir -local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_commit - -local_jax_prebuildopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir - -local_jax_build_cmd = 'python build/build.py ' -local_jax_build_cmd += '--target_cpu_features=native ' -local_jax_build_cmd += '--bazel_startup_options="--output_user_root=%(builddir)s" ' -local_jax_build_cmd += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' -local_jax_build_cmd += '--bazel_options=--subcommands ' -local_jax_build_cmd += '--bazel_options=--jobs=%(parallel)s --bazel_options=--action_env=PYTHONPATH ' -local_jax_build_cmd += '--bazel_options=--action_env=EBPYTHONPREFIXES' +local_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir use_pip = True +default_easyblock = 'PythonPackage' default_component_specs = { 'sources': [SOURCE_TAR_GZ], 'source_urls': [PYPI_SOURCE], 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, } components = [ ('absl-py', '0.13.0', { 'options': {'modulename': 'absl'}, - 'easyblock': 'PythonPackage', 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], - 'use_pip': True, }), - ('jaxlib', local_jaxlib_ver, { - 'easyblock': 'PythonPackage', + ('jaxlib', '0.1.70', { + 'easyblock': 'EB_jaxlib', 'sources': [ - 'jaxlib-v%s.zip' % local_jaxlib_ver, + '%(name)s-v%(version)s.tar.gz', { 'download_filename': '%s.tar.gz' % local_tf_commit, 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, @@ -69,26 +61,24 @@ components = [ 'https://github.com/tensorflow/tensorflow/archive/' ], 'patches': [ - ('jaxlib-%s_no-tensorflow-download.patch' % local_jaxlib_ver, 1), - ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../tensorflow-%s' % local_tf_commit), + '%(name)s-%(version)s_add-bazel-args-to-shutdown.patch', + '%(name)s-%(version)s_no-tensorflow-download.patch', + ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../' + local_tf_dir), ], 'checksums': [ - # jaxlib-v0.1.70.zip - '1205b180de70c98899d842f75bb589599c10a3c7a1c6099475c3a7d39b2e44ac', + # jaxlib-v0.1.70.tar.gz + '5d136c4b72bb254a3700cbac276ebe77108841936ff6d728050775f24a8e36fe', # tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d.tar.gz '0f13410284b9186e436350e9617b3bed2d65f1dc1a220fd37ad9ef43c2035663', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', # jaxlib-0.1.70_no-tensorflow-download.patch '1496c6be9336fb563b997f8da83d690a9b3a0a6e29fdd87fac60409300a2fd95', # TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d-build-env.patch 'd067836b1d18d66a8c69fb3db311855c8a56c0106d42a11299a1733c385e9c22', ], - 'start_dir': 'jax-jaxlib-v%s' % local_jaxlib_ver, + 'start_dir': 'jax-jaxlib-v%(version)s', 'prebuildopts': local_jax_prebuildopts, - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, - 'buildcmd': local_jax_build_cmd, - 'install_src': 'dist/*.whl', }), ] @@ -97,17 +87,13 @@ exts_list = [ 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), (name, version, { - 'checksums': ['e55534680a05b6ced92dadde307bd3b2207efd1aaaec304e96197b00ad7560d3'], + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': ['fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c'], + 'runtest': 'pytest -n %(parallel)s tests', }), ] -# can't run tests in sanity check step, because build dependencies must be available -postinstallcmds = [ - "cd %%(builddir)s/jax-jaxlib-v%s && " - "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH " - "pytest -n auto tests" % local_jaxlib_ver, -] - sanity_pip_check = True moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb new file mode 100644 index 0000000000..0ef481960f --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -0,0 +1,104 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.2.19' +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('Cython', '0.29.22'), + ('pytest-xdist', '2.3.0'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('flatbuffers-python', '1.12'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = '4039feeb743bc42cd0a3d8146ce63fc05d23eb8d' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +local_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '0.13.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + }), + ('jaxlib', '0.1.70', { + 'easyblock': 'EB_jaxlib', + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + '%(name)s-%(version)s_add-bazel-args-to-shutdown.patch', + '%(name)s-%(version)s_no-tensorflow-download.patch', + ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../' + local_tf_dir), + ('TensorFlow-2.1.0_fix-cuda-build.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.1.70.tar.gz + '5d136c4b72bb254a3700cbac276ebe77108841936ff6d728050775f24a8e36fe', + # tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d.tar.gz + '0f13410284b9186e436350e9617b3bed2d65f1dc1a220fd37ad9ef43c2035663', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', + # jaxlib-0.1.70_no-tensorflow-download.patch + '1496c6be9336fb563b997f8da83d690a9b3a0a6e29fdd87fac60409300a2fd95', + # TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d-build-env.patch + 'd067836b1d18d66a8c69fb3db311855c8a56c0106d42a11299a1733c385e9c22', + # TensorFlow-2.1.0_fix-cuda-build.patch + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': ['fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c'], + 'runtest': 'pytest -n %(parallel)s tests', + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 39983df8a866c44b12f4f2378799ad264a14e280 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Aug 2021 09:47:43 +0200 Subject: [PATCH 1431/2365] Remove easyblock line --- easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 1 - easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index 98dfee38c8..f47e5feef2 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -48,7 +48,6 @@ components = [ 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], }), ('jaxlib', '0.1.70', { - 'easyblock': 'EB_jaxlib', 'sources': [ '%(name)s-v%(version)s.tar.gz', { diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index 0ef481960f..ab1419f22c 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -50,7 +50,6 @@ components = [ 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], }), ('jaxlib', '0.1.70', { - 'easyblock': 'EB_jaxlib', 'sources': [ '%(name)s-v%(version)s.tar.gz', { From 53ea3d04971a4f6f9a7443b6033f9cf868090423 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 18 Aug 2021 10:01:38 +0100 Subject: [PATCH 1432/2365] Use Archive URL for spatstat.geom extension in Seurat --- .../easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb index 331b937181..4e6edc0ad5 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb @@ -31,6 +31,7 @@ exts_list = [ 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], }), ('spatstat.geom', '2.2-0', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'], 'checksums': ['70b063a7f317f531b2afb3afaedb047fce81b39ee481a4067962529d6069634c'], }), ('spatstat.sparse', '2.0-0', { From 10f6d2783b944ad33ff874fa9bb38a12fae2c6c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Aug 2021 12:05:06 +0200 Subject: [PATCH 1433/2365] add naturalsort extension to recent R 4.x easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 +++ 6 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 3f73cf6e80..94ed0c5800 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2900,6 +2900,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 25bfe94116..f0423aca3a 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2910,6 +2910,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 600336ef2a..52d2afb33e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2936,6 +2936,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 6410c41672..1bb5fc2a92 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2941,6 +2941,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 9d7859add8..172d381e03 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2945,6 +2945,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 044bfdd295..22c4fba720 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2956,6 +2956,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From 4395f0b34562c75bf686270a4a3d6d63ce4686b8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 18 Aug 2021 12:53:42 +0100 Subject: [PATCH 1434/2365] Use Archive URL for spatstat.core extension --- .../easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb index 4e6edc0ad5..d71472a2d5 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb @@ -38,6 +38,7 @@ exts_list = [ 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], }), ('spatstat.core', '2.2-0', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'], 'checksums': ['0ecbc1ae688c8d4f41db3efa6253ac8db5c432ef714240d01a2b195950d65253'], }), ('Matrix', '1.3-4', { From 811cce081d608781e2710db3794faf6f6e9db20d Mon Sep 17 00:00:00 2001 From: software Date: Wed, 18 Aug 2021 16:09:25 +0000 Subject: [PATCH 1435/2365] Add finalfit and gtsummary to R-4.0.4 --- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 52d2afb33e..1116a5461a 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2939,6 +2939,21 @@ exts_list = [ ('naturalsort', '0.1.3', { 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], }), + ('finalfit', '1.0.3', { + 'checksums': ['bbfa841a2b1a7b1f8c153d773ff076a2e465e451815f8166ff0ce8c4018ff61e'], + }), + ('broom.helpers', '1.3.0', { + 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], + }), + ('sass', '0.4.0', { + 'checksums': ['7d06ca15239142a49e88bb3be494515abdd8c75f00f3f1b0ee7bccb55019bc2b'], + }), + ('gt', '0.3.1', { + 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], + }), + ('gtsummary', '1.4.2', { + 'checksums': ['3fe958077df9e604bf536eeda73eb825ee6ae7fcac716b7a42d5a9d867bd4122'], + }), ] moduleclass = 'lang' From 3f198e375b80601cff8c181c754855a1d1969b2c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 18 Aug 2021 18:00:45 +0100 Subject: [PATCH 1436/2365] Remove sass duplicate --- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 1116a5461a..af85bdbea5 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2945,9 +2945,6 @@ exts_list = [ ('broom.helpers', '1.3.0', { 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], }), - ('sass', '0.4.0', { - 'checksums': ['7d06ca15239142a49e88bb3be494515abdd8c75f00f3f1b0ee7bccb55019bc2b'], - }), ('gt', '0.3.1', { 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], }), From d9997db1dd9c3f7dc8a9f843e0d19482d595f50b Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:14:57 +0200 Subject: [PATCH 1437/2365] Update CRISPR-DAV-2.3.4-foss-2020b.eb renaming patchfile --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index 176d5949c3..e7460b08d0 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/pinetree1/crispr-dav/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch'] +patches = ['crispr-dav-2.3.4_remove_hardcoding.patch'] checksums = [ '49975cd48bdbf31fe5a9e2aaa3f5ed85d3cc6f65a422ee3aa8daed890159d2ae', # v2.3.4.tar.gz # crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch From 954eb67167284cd91da9632f680ddeb251a670c4 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:15:05 +0200 Subject: [PATCH 1438/2365] Create CRISPR-DAV-2.3.4-foss-2020b.eb renaming patchfile From 28e6c02b58ecb39f59445d6eadc39c51d3ebf580 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:17:30 +0200 Subject: [PATCH 1439/2365] Update Excel-Writer-XLSX-1.09-foss-2020b.eb better sanity check --- .../e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb index c5eb8676cc..103890e6bd 100644 --- a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb +++ b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -23,7 +23,7 @@ options = {'modulename': 'Excel::Writer::XLSX'} sanity_check_paths = { 'files': ['bin/extract_vba'], - 'dirs': ['lib', 'bin'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Excel/Writer/XLSX'], } sanity_check_commands = ['extract_vba --help 2>&1 | grep "This utility is used to extract the VBA project binary from an Excel"'] From bbc1cb2b70f4b7bfddde22c5cbe0bddd097c4f3a Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:18:20 +0200 Subject: [PATCH 1440/2365] Update FLASH-2.2.00-foss-2020b.eb better postinstallcmds --- easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb index 858caac9c7..30f9a87052 100644 --- a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb @@ -20,7 +20,7 @@ checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] files_to_copy = [(['flash2'], 'bin')] -postinstallcmds = ['ln -s %(installdir)s/bin/flash2 %(installdir)s/bin/flash'] +postinstallcmds = ["cd %(installdir)s/bin && ln -s flash2 flash"] sanity_check_paths = { 'files': ['bin/flash2', 'bin/flash'], 'dirs': [], From b15c189b5024917481dc621964ebdebaa2b1bb31 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:20:19 +0200 Subject: [PATCH 1441/2365] Update FLASH-2.2.00-foss-2020b.eb adding sanity_check_commands --- easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb index 30f9a87052..68775a2c86 100644 --- a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb @@ -21,9 +21,14 @@ checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] files_to_copy = [(['flash2'], 'bin')] postinstallcmds = ["cd %(installdir)s/bin && ln -s flash2 flash"] + sanity_check_paths = { 'files': ['bin/flash2', 'bin/flash'], 'dirs': [], } +sanity_check_commands = [ + "flash --help", +] + moduleclass = 'bio' From 1dadbf46264e8fa46a21cccf3bfc90a898fb7990 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:40:59 +0200 Subject: [PATCH 1442/2365] Update pysamstats-1.1.2-foss-2020b.eb adding sanity_check_commands --- .../easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb index b0cebf283a..ee98447bea 100644 --- a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb @@ -25,6 +25,10 @@ dependencies = [ ('PyTables', '3.6.1'), ] +sanity_check_commands = [ + "pysamstats --help", +] + sanity_pip_check = True moduleclass = 'bio' From 8ab14e7536104a88a8904b2f4c2233b6d52b97ed Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 19 Aug 2021 11:46:58 +0200 Subject: [PATCH 1443/2365] Update CRISPR-DAV-2.3.4-foss-2020b.eb removed naturalsort, added comment about it --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index e7460b08d0..fdf461c95d 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -16,13 +16,14 @@ checksums = [ '41475a09754d65cc2c88d4161be6eacdfc98242bccbe49778c4f1f74210a6cb2', ] +# also needs `naturalsort`, which is now an R extension - see https://github.com/easybuilders/easybuild-easyconfigs/pull/13762 +# if missing, try reinstalling R (https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip) dependencies = [ ('R', '4.0.3'), ('Perl', '5.32.0'), ('NGS', '2.10.9'), ('Pysam', '0.16.0.1'), ('Excel-Writer-XLSX', '1.09'), - ('naturalsort', '0.1.3'), ('pysamstats', '1.1.2'), ('ABRA2', '2.23'), ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), From 0bb6b9e23027f7abeced634c4042da4f3dce5cee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Aug 2021 16:48:34 +0200 Subject: [PATCH 1444/2365] fix suggestions for ABRA2, CRISPR-DAV, PRINSEQ easyconfigs --- .../a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb | 5 ++--- .../CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 6 ++---- .../PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb | 18 ++++++++---------- 3 files changed, 12 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb index 734e544fc9..f62a0b1e28 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb @@ -41,8 +41,7 @@ sanity_check_paths = { 'dirs': [], } -modextravars = { - "LC_ALL": "en_US.UTF-8", -} +# required to work around localization bug, see https://github.com/mozack/abra2/issues/25 +modextravars = {'LC_ALL': 'en_US.UTF-8'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index fdf461c95d..e4693c5f0e 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -9,17 +9,15 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/pinetree1/crispr-dav/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['crispr-dav-2.3.4_remove_hardcoding.patch'] +patches = ['CRISPR-DAV-%(version)s_remove_hardcoding.patch'] checksums = [ '49975cd48bdbf31fe5a9e2aaa3f5ed85d3cc6f65a422ee3aa8daed890159d2ae', # v2.3.4.tar.gz # crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch '41475a09754d65cc2c88d4161be6eacdfc98242bccbe49778c4f1f74210a6cb2', ] -# also needs `naturalsort`, which is now an R extension - see https://github.com/easybuilders/easybuild-easyconfigs/pull/13762 -# if missing, try reinstalling R (https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip) dependencies = [ - ('R', '4.0.3'), + ('R', '4.0.3'), # provides naturalsort R package ('Perl', '5.32.0'), ('NGS', '2.10.9'), ('Pysam', '0.16.0.1'), diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb index c7576441ae..c2fccb2c6a 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb @@ -77,23 +77,21 @@ exts_list = [ }), ] -# this is the script which relies in many extra Perl libraries so we verify it's working fine -sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] +fix_perl_shebang_for = ["*.pl"] -modextrapaths = { - 'PATH': '', - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', -} +postinstallcmds = ["chmod +x %(installdir)s/*.pl"] -postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", - "chmod +x %(installdir)s/*.pl", -] +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] sanity_check_paths = { 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], 'dirs': [] } +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} moduleclass = 'bio' From 83637da6d430291ec5df28c8f949ef42f44b2ee1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Aug 2021 17:27:08 +0200 Subject: [PATCH 1445/2365] fix long line in Excel-Writer-XLSX easyconfig --- .../e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb index 103890e6bd..cffa913c11 100644 --- a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb +++ b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -26,7 +26,8 @@ sanity_check_paths = { 'dirs': ['lib/perl5/site_perl/%(perlver)s/Excel/Writer/XLSX'], } -sanity_check_commands = ['extract_vba --help 2>&1 | grep "This utility is used to extract the VBA project binary from an Excel"'] - +sanity_check_commands = [ + 'extract_vba --help 2>&1 | grep "This utility is used to extract the VBA project binary from an Excel"', +] moduleclass = 'tools' From 1daefb2510f18d617d97ad7cb6a13875a63b0b16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Aug 2021 19:03:52 +0200 Subject: [PATCH 1446/2365] stick to SAMtools 1.11 as dependency for CRISPR-DAV --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index e4693c5f0e..52537f135f 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -25,7 +25,7 @@ dependencies = [ ('pysamstats', '1.1.2'), ('ABRA2', '2.23'), ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), - ('SAMtools', '1.12'), + ('SAMtools', '1.11'), ('BEDTools', '2.30.0'), ('FLASH', '2.2.00'), ('Archive-Zip', '1.68'), From 52c0533f7df6c0aa56d3e9cb2cc830620c7dca23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 11:21:48 +0200 Subject: [PATCH 1447/2365] fix import check for CRISPResso2 --- .../CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb index 571c2db3c0..9cf48eb4e3 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -34,10 +34,9 @@ dependencies = [ ('Bowtie2', '2.4.2'), ('Seaborn', '0.9.1', '-Python-%(pyver)s'), ] + download_dep_fail = True use_pip = True -options = {'modulename': False} -sanity_pip_check = True # strip out too strict version requirements for dependencies preinstallopts = "sed -i 's/,<=[0-9]*//g' setup.py && sed -i 's/==/>=/g' setup.py && " @@ -56,6 +55,10 @@ sanity_check_commands = [ local_test_cmd, ] +sanity_pip_check = True + +options = {'modulename': name} + modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} moduleclass = 'bio' From 7672224760438e7391889a0f69054f08575e0d0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 11:22:44 +0200 Subject: [PATCH 1448/2365] stick to SAMtools 1.11 for CRISPResso2 with foss/2020b --- .../c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb index 9cf48eb4e3..4024c882cd 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -30,7 +30,7 @@ dependencies = [ ('matplotlib', '2.2.5', '-Python-%(pyver)s'), ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), ('FLASH', '2.2.00'), - ('SAMtools', '1.12'), + ('SAMtools', '1.11'), ('Bowtie2', '2.4.2'), ('Seaborn', '0.9.1', '-Python-%(pyver)s'), ] From c28851a1df38877849343547e30db2decdb577d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 13:32:18 +0200 Subject: [PATCH 1449/2365] adding easyconfigs: CRISPResso2-2.2.1-foss-2020b.eb --- .../CRISPResso2-2.2.1-foss-2020b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb new file mode 100644 index 0000000000..10d20ead47 --- /dev/null +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb @@ -0,0 +1,63 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'CRISPResso2' +version = '2.2.1' + +homepage = 'https://github.com/pinellolab/CRISPResso2/' +description = """CRISPResso2 is a software pipeline designed to enable rapid and +intuitive interpretation of genome editing experiments.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [ + {'source_urls': ['https://github.com/pinellolab/CRISPResso2/archive/'], + 'filename': 'v%(version)s.tar.gz'}, + {'source_urls': ['https://crispresso.pinellolab.partners.org/static/demo/'], + 'filename': 'base_editor_v%(version)s.fastq.gz', 'download_filename': 'base_editor.fastq.gz', + 'extract_cmd': 'cp %s %(builddir)s'}] +checksums = [ + '8bc46661759dbe300e927f353d5859ec0abd1ee4ddcaf4e18dacc6859be2fcb7', # v2.2.1.tar.gz + '371aad07a164721188deaa80ca7589f5cd4b871119d90d55a984c6d9c8d31c7a', # base_editor_v2.2.1.fastq.gz +] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('FLASH', '2.2.00'), + ('SAMtools', '1.11'), + ('Bowtie2', '2.4.2'), + ('Seaborn', '0.11.1'), +] + +download_dep_fail = True +use_pip = True + +# strip out too strict version requirements for dependencies +preinstallopts = "sed -i 's/,<=[0-9]*//g' setup.py && sed -i 's/==/>=/g' setup.py && " + +# this is an example command from: +# https://github.com/pinellolab/CRISPResso2#example-run-base-editing-experiment +local_seq_str = 'GGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTAC' +local_seq_str += 'AAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATG' +local_seq_str += 'GGGAGGACATCGATGTCACCTCCAATGACTAGGGTGG' +local_test_cmd = "CRISPResso --fastq_r1 %(builddir)s/base_editor_v%(version)s.fastq.gz " +local_test_cmd += "--amplicon_seq %s " % local_seq_str +local_test_cmd += "--guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 10 " +local_test_cmd += "--quantification_window_center -10 --base_editor_output" +sanity_check_commands = [ + "CRISPResso -h", + local_test_cmd, +] + +sanity_pip_check = True + +options = {'modulename': name} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} + +moduleclass = 'bio' From 7db3b2c215cc8ebd477c9d0d7a5eb1a5e3a07926 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 20 Aug 2021 17:35:34 +0200 Subject: [PATCH 1450/2365] adding easyconfigs: Cartopy-0.19.0.post1-foss-2020b.eb, Fiona-1.8.20-foss-2020b.eb, Cartopy-0.19.0.post1-intel-2020b.eb, Fiona-1.8.20-intel-2020b.eb, Shapely-1.8a1-iccifort-2020.4.304.eb --- .../Cartopy-0.19.0.post1-foss-2020b.eb | 51 +++++++++++++++++++ .../Cartopy-0.19.0.post1-intel-2020b.eb | 51 +++++++++++++++++++ .../f/Fiona/Fiona-1.8.20-foss-2020b.eb | 49 ++++++++++++++++++ .../f/Fiona/Fiona-1.8.20-intel-2020b.eb | 49 ++++++++++++++++++ .../Shapely-1.8a1-iccifort-2020.4.304.eb | 26 ++++++++++ 5 files changed, 226 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb new file mode 100644 index 0000000000..804988f11b --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.19.0.post1' + +homepage = 'https://scitools.org.uk/cartopy/docs/latest/' +description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Fiona', '1.8.20'), + ('GDAL', '3.2.1'), + ('GEOS', '3.9.1'), + ('matplotlib', '3.3.3'), + ('pyproj', '3.0.1'), + ('SciPy-bundle', '2020.11'), + ('Shapely', '1.8a1'), + ('lxml', '4.6.2'), + ('Pillow', '8.0.1'), + ('PROJ', '7.2.1'), + ('PyYAML', '5.3.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_list = [ + ('OWSLib', '0.24.1', { + 'checksums': ['4973c2ba65ec850a3fcc1fb94cefe5ed2fed83aaf2a5e2135c78810ad2a8f0e1'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.4', { + 'checksums': ['bebe5c608129f2997e88510c00010b9a78581b394924c0e3ecd131d52415165d'], + }), + ('pyshp', '2.1.3', { + 'modulename': 'shapefile', + 'checksums': ['e32b4a6832a3b97986df442df63b4c4a7dcc846b326c903189530a5cc6df0260'], + }), + (name, version, { + 'checksums': ['4b8b4773a98ed7009fe17d9b6ec87ac3ac62b7d14634d7768c190eadc647d576'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb new file mode 100644 index 0000000000..8928cbebb2 --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.19.0.post1' + +homepage = 'https://scitools.org.uk/cartopy/docs/latest/' +description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Fiona', '1.8.20'), + ('GDAL', '3.2.1'), + ('GEOS', '3.9.1'), + ('matplotlib', '3.3.3'), + ('pyproj', '3.0.1'), + ('SciPy-bundle', '2020.11'), + ('Shapely', '1.8a1'), + ('lxml', '4.6.2'), + ('Pillow', '8.0.1'), + ('PROJ', '7.2.1'), + ('PyYAML', '5.3.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_list = [ + ('OWSLib', '0.24.1', { + 'checksums': ['4973c2ba65ec850a3fcc1fb94cefe5ed2fed83aaf2a5e2135c78810ad2a8f0e1'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.4', { + 'checksums': ['bebe5c608129f2997e88510c00010b9a78581b394924c0e3ecd131d52415165d'], + }), + ('pyshp', '2.1.3', { + 'modulename': 'shapefile', + 'checksums': ['e32b4a6832a3b97986df442df63b4c4a7dcc846b326c903189530a5cc6df0260'], + }), + (name, version, { + 'checksums': ['4b8b4773a98ed7009fe17d9b6ec87ac3ac62b7d14634d7768c190eadc647d576'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb new file mode 100644 index 0000000000..370e0e41f5 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.8.20' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('GDAL', '3.2.1'), + ('Shapely', '1.8a1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'checksums': ['a70502d2857b82f749c09cb0dea3726787747933a2a1599b5ab787d74e3c143b'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb new file mode 100644 index 0000000000..7457c0fdab --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.8.20' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('GDAL', '3.2.1'), + ('Shapely', '1.8a1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'checksums': ['a70502d2857b82f749c09cb0dea3726787747933a2a1599b5ab787d74e3c143b'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..a87575e17a --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '1.8a1' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a748ab74c187060264e7ce838aaac30eead2a791bbea8cc3ab1dfc3cc0b4d067'] + +dependencies = [ + ('Python', '3.8.6'), + ('GEOS', '3.9.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 25d2e5d68d7c74285bceb319d52ca8989390ab02 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 20 Aug 2021 17:48:08 +0200 Subject: [PATCH 1451/2365] removing download_dep_fail, since its a bundle --- .../easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb | 1 - .../easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb | 1 - easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb | 1 - easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb index 804988f11b..4ce73ac7ec 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb @@ -27,7 +27,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('OWSLib', '0.24.1', { diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb index 8928cbebb2..2301189a3a 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb @@ -27,7 +27,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('OWSLib', '0.24.1', { diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb index 370e0e41f5..70c9cf78c3 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb @@ -21,7 +21,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb index 7457c0fdab..47f6971d11 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb @@ -21,7 +21,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From 122ff66b6a7adf0f79b01a606ff7e397f149f894 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 20 Aug 2021 17:53:12 +0200 Subject: [PATCH 1452/2365] Update Fiona-1.8.20-foss-2020b.eb removing extra line --- easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb index 70c9cf78c3..d218269306 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb @@ -38,8 +38,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/fio'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 38ab072e7999f424a19ab27ba1466ec66d9a27ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 18:29:33 +0200 Subject: [PATCH 1453/2365] remove duplicate sanity_pip_check in Fiona easyconfig + add custom sanity check command --- easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb | 5 ++++- easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb | 7 ++++--- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb index d218269306..fd9e2798fc 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb @@ -21,7 +21,6 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True exts_list = [ ('cligj', '0.7.2', { @@ -43,4 +42,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["fio --help"] + +sanity_pip_check = True + moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb index 47f6971d11..4deaf15039 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb @@ -21,7 +21,6 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True exts_list = [ ('cligj', '0.7.2', { @@ -38,11 +37,13 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/fio'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["fio --help"] + +sanity_pip_check = True + moduleclass = 'data' From 8cdc98095879f253f0e1846628ab3aec95abe1f4 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sat, 21 Aug 2021 14:50:25 +1000 Subject: [PATCH 1454/2365] Create TetGen-1.6.0-GCCcore-10.2.0.eb New version, new compiler --- .../t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..34b80d080b --- /dev/null +++ b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'TetGen' +version = '1.6.0' + +homepage = 'http://wias-berlin.de/software/index.jsp?id=TetGen' +description = """ A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# Fill in a form and download from above URL +sources = ['tetgen1.6.0.tar.gz'] +checksums = ['87b5e61ebd3a471fc4f2cdd7124c2b11dd6639f4feb1f941a5d2f5110d05ce39'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +separate_build_dir = True + +skipsteps = ['install'] + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin/ && cp tetgen %(installdir)s/bin/', + 'mkdir -p %(installdir)s/lib/ && cp libtet.a %(installdir)s/lib/', +] + +sanity_check_paths = { + 'files': ['bin/tetgen', 'lib/libtet.a'], + 'dirs': [], +} + +moduleclass = 'numlib' From f05893db9313f331578578a897e3670d500502bc Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 21 Aug 2021 09:38:14 +0100 Subject: [PATCH 1455/2365] sort out bug introduced by --new-pr --- ...a-20210309-fosscuda-2020b-PyTorch-1.9.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb diff --git a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 0000000000..f6675c6e95 --- /dev/null +++ b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Mish-Cuda' +version = '20210309' +local_commit = '6f38976' +local_ptver = '1.9.0' +versionsuffix = '-PyTorch-%(local_ptver)s' + +homepage = 'https://github.com/JunnYu/mish-cuda' +description = """Mish-Cuda: Self Regularized Non-Monotonic Activation Function""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/JunnYu/mish-cuda/archive/'] +sources = [{'download_filename': local_commit + '.zip', 'filename': SOURCELOWER_ZIP}] +checksums = ['529a3afd00fa4b1bf73f65249a82d38659779d7d8bdb230fa32d37eb95f5622c'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', local_ptver), +] + +preinstallopts = 'export TORCH_CUDA_ARCH_LIST="%(cuda_cc_semicolon_sep)s" && ' + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From 52f88caca5377755a08fcae5bd069af014ff0f7e Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 21 Aug 2021 09:50:24 +0100 Subject: [PATCH 1456/2365] correct syntax --- .../Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb index f6675c6e95..fa7173c514 100644 --- a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb @@ -4,7 +4,7 @@ name = 'Mish-Cuda' version = '20210309' local_commit = '6f38976' local_ptver = '1.9.0' -versionsuffix = '-PyTorch-%(local_ptver)s' +versionsuffix = '-PyTorch-%s' % local_ptver homepage = 'https://github.com/JunnYu/mish-cuda' description = """Mish-Cuda: Self Regularized Non-Monotonic Activation Function""" From 9464b7155d9d8fbfd87985e7a2cd6e7b3e437751 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sat, 21 Aug 2021 20:35:06 +1000 Subject: [PATCH 1457/2365] Update easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb index 34b80d080b..9b22fcf1e0 100644 --- a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["%(namelower)s -h"] + moduleclass = 'numlib' From f727b770a003e059868976576bd910b9fd73498d Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sat, 21 Aug 2021 20:35:16 +1000 Subject: [PATCH 1458/2365] Update easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb index 9b22fcf1e0..08661910bc 100644 --- a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb @@ -17,8 +17,6 @@ builddependencies = [ ('binutils', '2.35'), ] -separate_build_dir = True - skipsteps = ['install'] postinstallcmds = [ From 8afb531a978d8e25628d29398bf570880b0e6b56 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sat, 21 Aug 2021 20:50:22 +1000 Subject: [PATCH 1459/2365] Create unrar-6.0.2-GCCcore-10.2.0.eb New version, new compiler --- .../u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9081313486 --- /dev/null +++ b/easybuild/easyconfigs/u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'unrar' +version = '6.0.2' + +homepage = 'https://www.rarlab.com/' +description = "RAR is a powerful archive manager." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://www.rarlab.com/rar/'] +sources = ['unrarsrc-%(version)s.tar.gz'] +checksums = ['81bf188333f89c976780a477af27f651f54aa7da9312303d8d1a804696d3edd3'] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' +installopts = 'DESTDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/unrar'], + 'dirs': [], +} + +moduleclass = 'tools' From d275570eddb41f41cb4b5ba7b35888ad7f99ae4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Aug 2021 19:55:50 +0200 Subject: [PATCH 1460/2365] add patches for jaxlib and jax to fix/skip failing tests + use 'CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true' for running jax tests --- .../j/jax/jax-0.2.19-fosscuda-2020b.eb | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index ab1419f22c..b0b732b729 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -64,6 +64,7 @@ components = [ 'patches': [ '%(name)s-%(version)s_add-bazel-args-to-shutdown.patch', '%(name)s-%(version)s_no-tensorflow-download.patch', + '%(name)s-%(version)s_fix-gpu-translation-rule.patch', ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../' + local_tf_dir), ('TensorFlow-2.1.0_fix-cuda-build.patch', '../' + local_tf_dir), ], @@ -76,6 +77,8 @@ components = [ 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', # jaxlib-0.1.70_no-tensorflow-download.patch '1496c6be9336fb563b997f8da83d690a9b3a0a6e29fdd87fac60409300a2fd95', + # jaxlib-0.1.70_fix-gpu-translation-rule.patch + 'ce3cf8ee3b393f6580fb88bc39cc2660be46f2a48a315a3779403725ad49f946', # TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d-build-env.patch 'd067836b1d18d66a8c69fb3db311855c8a56c0106d42a11299a1733c385e9c22', # TensorFlow-2.1.0_fix-cuda-build.patch @@ -93,8 +96,19 @@ exts_list = [ (name, version, { 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], - 'checksums': ['fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c'], - 'runtest': 'pytest -n %(parallel)s tests', + 'patches': ['jax-%(version)s_skip-heap-profiler-test.patch'], + 'checksums': [ + 'fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c', # jax-v0.2.19.tar.gz + # jax-0.2.19_skip-heap-profiler-test.patch + 'a431ce1b6588b5098872f36575dc2c5023b1010760bf6aaa889125c9a09227b0', + ], + # deliberately not testing in parallel, as that results in (additional) failing tests; + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform when running GPU tests in parallel, + # to avoid each test fully allocating the GPU memory..., + # see https://github.com/google/jax/issues/7323 and + # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; + # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; + 'runtest': 'CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests', }), ] From a25af68dadfed8855d712972075c6f9d784c3e30 Mon Sep 17 00:00:00 2001 From: software Date: Mon, 23 Aug 2021 10:07:53 +0000 Subject: [PATCH 1461/2365] Port update to other recent R easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 12 ++++++++++++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 12 ++++++++++++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 12 ++++++++++++ 3 files changed, 36 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 1bb5fc2a92..2fa4574e87 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2944,6 +2944,18 @@ exts_list = [ ('naturalsort', '0.1.3', { 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], }), + ('finalfit', '1.0.3', { + 'checksums': ['bbfa841a2b1a7b1f8c153d773ff076a2e465e451815f8166ff0ce8c4018ff61e'], + }), + ('broom.helpers', '1.3.0', { + 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], + }), + ('gt', '0.3.1', { + 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], + }), + ('gtsummary', '1.4.2', { + 'checksums': ['3fe958077df9e604bf536eeda73eb825ee6ae7fcac716b7a42d5a9d867bd4122'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 172d381e03..10ac6803fa 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2948,6 +2948,18 @@ exts_list = [ ('naturalsort', '0.1.3', { 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], }), + ('finalfit', '1.0.3', { + 'checksums': ['bbfa841a2b1a7b1f8c153d773ff076a2e465e451815f8166ff0ce8c4018ff61e'], + }), + ('broom.helpers', '1.3.0', { + 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], + }), + ('gt', '0.3.1', { + 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], + }), + ('gtsummary', '1.4.2', { + 'checksums': ['3fe958077df9e604bf536eeda73eb825ee6ae7fcac716b7a42d5a9d867bd4122'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 22c4fba720..a4b7463583 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2959,6 +2959,18 @@ exts_list = [ ('naturalsort', '0.1.3', { 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], }), + ('finalfit', '1.0.3', { + 'checksums': ['bbfa841a2b1a7b1f8c153d773ff076a2e465e451815f8166ff0ce8c4018ff61e'], + }), + ('broom.helpers', '1.3.0', { + 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], + }), + ('gt', '0.3.1', { + 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], + }), + ('gtsummary', '1.4.2', { + 'checksums': ['3fe958077df9e604bf536eeda73eb825ee6ae7fcac716b7a42d5a9d867bd4122'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], From f4e4fbadad8a453cb08ffd0df0bab228062cc564 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Aug 2021 12:30:35 +0200 Subject: [PATCH 1462/2365] adding easyconfigs: neptune-client-0.10.5-foss-2020b.eb --- .../neptune-client-0.10.5-foss-2020b.eb | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb new file mode 100644 index 0000000000..f0f48378f5 --- /dev/null +++ b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb @@ -0,0 +1,80 @@ +easyblock = 'PythonBundle' + +name = 'neptune-client' +version = '0.10.5' + +homepage = 'https://docs.neptune.ai' +description = """ +Neptune is an experiment tracking hub that brings organization and collaboration to your data science team. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('GitPython', '3.1.14'), + ('Pillow-SIMD', '7.1.2'), + ('PyYAML', '5.3.1'), +] + +use_pip = True + +exts_list = [ + ('monotonic', '1.6', { + 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('pyrsistent', '0.18.0', { + 'checksums': ['773c781216f8c2900b42a7b638d5b517bb134ae1acbebe4d1e8f1f41ea60eb4b'], + }), + ('swagger-spec-validator', '2.7.3', { + 'checksums': ['f4f23ee4dbd52bfcde90b1144dde22304add6260e9f29252e9fd7814c9b8fd16'], + }), + ('jsonref', '0.2', { + 'checksums': ['f3c45b121cf6257eafabdc3a8008763aed1cd7da06dbabc59a9e4d2a5e4e6697'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('simplejson', '3.17.4', { + 'checksums': ['2af85e028714c4b6cb2eb6fc03aa91f39ffd654f2eb2f6f8f860e14aeefa6be1'], + }), + ('typing-extensions', '3.10.0.0', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342'], + }), + ('bravado-core', '5.17.0', { + 'checksums': ['b3b06ae86d3c80de5694340e55df7c9097857ff965b76642979e2a961f332abf'], + }), + ('bravado', '11.0.3', { + 'checksums': ['1bb6ef75d84140c851fffe6420baaee5037d840070cfe11d60913be6ab8e0530'], + }), + ('PyJWT', '2.1.0', { + 'modulename': 'jwt', + 'checksums': ['fba44e7898bbca160a2b2b501f492824fc8382485d3a6f11ba5d0c1937ce6130'], + }), + ('blinker', '1.4', { + 'checksums': ['471aee25f3992bd325afa3772f1063dbdbbca947a041b8b89466dc00d606f8b6'], + }), + ('oauthlib', '3.1.1', { + 'checksums': ['8f0215fcc533dd8dd1bee6f4c412d4f0cd7297307d43ac61666389e3bc3198a3'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('websocket-client', '0.59.0', { + 'modulename': 'websocket', + 'checksums': ['d376bd60eace9d437ab6d7ee16f4ab4e821c9dae591e1b783c58ebd8aaf80c5c'], + }), + (name, version, { + 'modulename': 'neptune', + 'checksums': ['cb534c0db8e9fc6c6f1f578943ce76fd46d16fb42c6fbc2e2fa2e92b5125ef5e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From f46608219836db973e5e7e4b27cbd7df7ae9ffe2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Aug 2021 14:34:22 +0200 Subject: [PATCH 1463/2365] remove extensions in base Python from neptune-client-0.10.5-foss-2020b.eb --- .../neptune-client-0.10.5-foss-2020b.eb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb index f0f48378f5..e48419cb64 100644 --- a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb +++ b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb @@ -24,24 +24,12 @@ exts_list = [ ('monotonic', '1.6', { 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], }), - ('msgpack', '1.0.2', { - 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], - }), - ('pyrsistent', '0.18.0', { - 'checksums': ['773c781216f8c2900b42a7b638d5b517bb134ae1acbebe4d1e8f1f41ea60eb4b'], - }), ('swagger-spec-validator', '2.7.3', { 'checksums': ['f4f23ee4dbd52bfcde90b1144dde22304add6260e9f29252e9fd7814c9b8fd16'], }), ('jsonref', '0.2', { 'checksums': ['f3c45b121cf6257eafabdc3a8008763aed1cd7da06dbabc59a9e4d2a5e4e6697'], }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('simplejson', '3.17.4', { - 'checksums': ['2af85e028714c4b6cb2eb6fc03aa91f39ffd654f2eb2f6f8f860e14aeefa6be1'], - }), ('typing-extensions', '3.10.0.0', { 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', 'checksums': ['50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342'], From d4c89155761695960ec36fbd8c64c2ac3fa00a1d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 23 Aug 2021 18:36:35 +0200 Subject: [PATCH 1464/2365] Clean-up FORD v6.1.1 EB file for GCCcore/10.2.0 --- easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb index f51c81c928..25617e478e 100644 --- a/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb @@ -8,15 +8,12 @@ description = 'FORD is an automatic documentation generator for modern Fortran p toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -dependencies = [ - ('Python', '3.8.6'), -] - builddependencies = [ ('binutils', '2.35'), ] dependencies = [ + ('Python', '3.8.6'), ('Graphviz', '2.47.0', '-Java-11'), ('BeautifulSoup', '4.9.3'), ] From aa15ba119ce0968d464592594f06180a40bdd370 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 24 Aug 2021 10:56:46 +0200 Subject: [PATCH 1465/2365] adding easyconfigs: sympy-1.7.1-intel-2020b.eb, gmpy2-2.1.0b5-iccifort-2020.4.304.eb --- .../gmpy2-2.1.0b5-iccifort-2020.4.304.eb | 25 +++++++++++++ .../s/sympy/sympy-1.7.1-intel-2020b.eb | 35 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..3d95fae8ad --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.0b5' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8951bcfc61c0f40102b92a4777daf9eb85445b537c4d09086deb0e097190bef0'] + +dependencies = [ + ('Python', '3.8.6'), + ('GMP', '6.2.0'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb new file mode 100644 index 0000000000..8e61d9b6f4 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.7.1' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a3de9261e97535b83bb8607b0da2c7d03126650fafea2b2789657b229c246b2e'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('gmpy2', '2.1.0b5'), +] + +download_dep_fail = True +use_pip = True + +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +moduleclass = 'math' From 4a3b6c8a99d886d87f918c7ac9db85628d307ff1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 24 Aug 2021 14:07:40 +0100 Subject: [PATCH 1466/2365] Add pkg-config to builddependencies --- .../easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb index 26842544fe..7b91aa07cb 100644 --- a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb @@ -24,6 +24,7 @@ checksums = [ # Bundled libraries can be globally disabled with the option useshared=yes # However, it is preferable to use the bundled libraries due to the very old versions of some of them +builddependencies = [('pkg-config', '0.29.2')] dependencies = [('Pango', '1.47.0')] skipsteps = ['configure'] From da2c8df55a5b4cf01d901f922f0f0f404e824936 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Aug 2021 16:24:31 +0200 Subject: [PATCH 1467/2365] consistently add pkg-config as build dependency for GDAL 3.2.1 --- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb | 4 ++++ easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb index efb8bd1d9a..bcba374a61 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb @@ -20,6 +20,10 @@ checksums = [ '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch ] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + dependencies = [ ('Python', '3.8.6'), ('netCDF', '4.7.4'), diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb index f41af638de..7416633742 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb @@ -24,6 +24,10 @@ checksums = [ 'fdf6a84d16141ccc9bc4ce98a762357ba374dea87d1f2a41a1a23be80b7ca69d', # GDAL-3.2.1_cpp-conformance.patch ] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + dependencies = [ ('Python', '3.8.6'), ('netCDF', '4.7.4'), From accea07ca2993318489d0238cca54785fb5bde20 Mon Sep 17 00:00:00 2001 From: spottho1 Date: Tue, 24 Aug 2021 16:39:49 +0200 Subject: [PATCH 1468/2365] add '--release' flag when calling setup.py --- .../tensorflow-probability-0.12.1-foss-2020b.eb | 1 + .../tensorflow-probability-0.12.1-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb index a33fbf38cd..8996e23128 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb @@ -31,6 +31,7 @@ exts_list = [ 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), (name, version, { + 'installopts': '--install-option="--release"', 'modulename': 'tensorflow_probability', 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/probability/archive/'], diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb index 28b222eb33..c31071c495 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb @@ -31,6 +31,7 @@ exts_list = [ 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), (name, version, { + 'installopts': '--install-option="--release"', 'modulename': 'tensorflow_probability', 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/probability/archive/'], From 6b037c9c378781890bbd2a047e334cec6e331108 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 24 Aug 2021 19:04:33 +0200 Subject: [PATCH 1469/2365] adding easyconfigs: PyGEOS-0.10.2-intel-2020b.eb --- .../p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb diff --git a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb new file mode 100644 index 0000000000..34cef2e071 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'PyGEOS' +version = '0.10.2' + +homepage = "https://pygeos.readthedocs.io" +description = """PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in + the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance + improvement when operating on arrays of geometries.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['08cd7fe047a7d7f9f94eaa9a65e0b4fd4057ffebc15e6179a0290a9576a0bbbc'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('GEOS', '3.9.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'geo' From fff383ca90844cde396a4a417703b4e5c82f015b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Aug 2021 00:35:03 +0200 Subject: [PATCH 1470/2365] Update easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb --- easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb index 73df2b8f6b..f157cad034 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb @@ -41,4 +41,6 @@ sanity_check_commands = [ "pyretisrun --help", ] +sanity_pip_check = True + moduleclass = 'chem' From b8af4469b709d7d167bbecd3f2d179b4c3d7ba7a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Aug 2021 00:35:09 +0200 Subject: [PATCH 1471/2365] Update easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb --- easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb index 223cac2960..bd934ce0e1 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb @@ -41,4 +41,6 @@ sanity_check_commands = [ "pyretisrun --help", ] +sanity_pip_check = True + moduleclass = 'chem' From f220aa98ade280a9de28f3be1e1e11a4d576c76f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Wed, 25 Aug 2021 08:58:14 +0200 Subject: [PATCH 1472/2365] adding easyconfigs: hipSYCL-0.9.1-gcccuda-2020b.eb --- .../h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb diff --git a/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb new file mode 100644 index 0000000000..91fe900751 --- /dev/null +++ b/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'hipSYCL' +version = '0.9.1' + +homepage = 'https://github.com/illuhad/hipSYCL' +description = """hipSYCL is a modern SYCL implementation targeting CPUs and +GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP""" + +toolchain = {'name': 'gcccuda', 'version': '2020b'} + +source_urls = ["https://github.com/illuhad/hipSYCL/archive/refs/tags/"] +sources = ["v%(version)s.tar.gz"] +checksums = ['0a1ae3a79c743fd826dd9d666e0b9cec8b66940756d4ab6e4961e93604dff559'] + +dependencies = [ + ('Boost', '1.74.0'), + ('Clang', '11.0.1'), + ('Python', '3.8.6'), +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +configopts = '-DCMAKE_C_COMPILER="$EBROOTCLANG/bin/clang" ' +configopts += '-DCMAKE_CXX_COMPILER="$EBROOTCLANG/bin/clang++" ' +configopts += '-DLLVM_DIR=$EBROOTCLANG ' +configopts += '-DCLANG_EXECUTABLE_PATH=$EBROOTCLANG/bin/clang++ ' +configopts += '-DWITH_CPU_BACKEND=ON ' +configopts += '-DWITH_CUDA_BACKEND=ON ' + +sanity_check_paths = { + 'files': ['bin/syclcc-clang', 'include/sycl/sycl.hpp', + 'lib/hipSYCL/librt-backend-cuda.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'include/hipSYCL', 'include/SYCL', 'lib'], +} +sanity_check_commands = ['syclcc --help'] + +moduleclass = 'compiler' From e78b12ffc526a903bb7b494c37ca710683b79366 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 25 Aug 2021 09:21:49 +0100 Subject: [PATCH 1473/2365] adding easyconfigs: JAGS-4.3.0-foss-2021a.eb, rjags-4-10-foss-2020b-R-4.0.3.eb, rjags-4-10-foss-2020b-R-4.0.4.eb, rjags-4-10-foss-2020b-R-4.0.5.eb, rjags-4-10-fosscuda-2020b-R-4.0.3.eb, rjags-4-10-fosscuda-2020b-R-4.0.4.eb, rjags-4-10-fosscuda-2020b-R-4.0.5.eb, rjags-4-10-foss-2021a-R-4.1.0.eb --- .../r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb | 29 +++++++++++++++++++ .../r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb | 29 +++++++++++++++++++ .../r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb | 29 +++++++++++++++++++ .../rjags-4-10-fosscuda-2020b-R-4.0.3.eb | 29 +++++++++++++++++++ .../rjags-4-10-fosscuda-2020b-R-4.0.4.eb | 29 +++++++++++++++++++ .../rjags-4-10-fosscuda-2020b-R-4.0.5.eb | 29 +++++++++++++++++++ 6 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.3.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.4.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.5.eb diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..415dee78ed --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.3'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..7694a11ea4 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.4'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb new file mode 100644 index 0000000000..9de5eae895 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.5'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..42d5cdf10f --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.3'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..eafcc9b44f --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.4.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.4'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.5.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.5.eb new file mode 100644 index 0000000000..bb7c0dda50 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.5.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.5'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' From f7a93d0b1a6c24db6d8308e2c09e53e6118e8f5e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 25 Aug 2021 09:39:08 +0100 Subject: [PATCH 1474/2365] Add missing JAGS for fosscuda/2020b --- .../j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..78f0374a76 --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.0' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download') +] +sources = [SOURCE_TAR_GZ] +checksums = ['8ac5dd57982bfd7d5f0ee384499d62f3e0bb35b5f1660feb368545f1186371fc'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' From f00491bba6d1d8552b45a72745470e19e1dcada6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 25 Aug 2021 12:07:31 +0200 Subject: [PATCH 1475/2365] Add git to build deps Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 2 ++ easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index f47e5feef2..ddce20e23f 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -14,6 +14,8 @@ builddependencies = [ ('Bazel', '3.7.2'), ('Cython', '0.29.22'), ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.28.0', '-nodocs'), ] dependencies = [ diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index b0b732b729..41f5cbd5db 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -14,6 +14,8 @@ builddependencies = [ ('Bazel', '3.7.2'), ('Cython', '0.29.22'), ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.28.0', '-nodocs'), ] dependencies = [ From 95f9f4acbd39d62ebcc6de05367e083d54987a03 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Aug 2021 10:28:30 +0200 Subject: [PATCH 1476/2365] x264 needs pkg-config as builddep --- easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb index ab66b16bf1..002c636220 100644 --- a/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb @@ -20,6 +20,7 @@ checksums = ['4dba5ab9e744f85d8a37ccdcc9467d27c5409c7e4f7e397580b5921be09b4d1e'] builddependencies = [ ('binutils', '2.35'), + ('pkg-config', '0.29.2'), ('NASM', '2.15.05'), ] From 49311b6d714b673dc16b9d7209d323f8646a0a61 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Aug 2021 11:04:44 +0200 Subject: [PATCH 1477/2365] x264: Explicitly turn off bashcompletion. --- easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb index 002c636220..c7bbcc82b2 100644 --- a/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('NASM', '2.15.05'), ] -configopts = " --enable-shared --enable-static" +configopts = " --enable-shared --enable-static --disable-bashcompletion" sanity_check_paths = { 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', From a60e5bfbfd297079b46ee8743bed22dfe76f4d02 Mon Sep 17 00:00:00 2001 From: Stig Rune Jensen Date: Thu, 26 Aug 2021 12:49:19 +0200 Subject: [PATCH 1478/2365] adding easyconfigs: hipSYCL-0.9.1-GCC-10.2.0.eb --- .../h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb b/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..98698a165f --- /dev/null +++ b/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'hipSYCL' +version = '0.9.1' + +homepage = 'https://github.com/illuhad/hipSYCL' +description = """hipSYCL is a modern SYCL implementation targeting CPUs and +GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ["https://github.com/illuhad/hipSYCL/archive/refs/tags/"] +sources = ["v%(version)s.tar.gz"] +checksums = ['0a1ae3a79c743fd826dd9d666e0b9cec8b66940756d4ab6e4961e93604dff559'] + +dependencies = [ + ('Boost', '1.74.0'), + ('Clang', '11.0.1'), + ('Python', '3.8.6'), +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +configopts = '-DCMAKE_C_COMPILER="$EBROOTCLANG/bin/clang" ' +configopts += '-DCMAKE_CXX_COMPILER="$EBROOTCLANG/bin/clang++" ' +configopts += '-DLLVM_DIR=$EBROOTCLANG ' +configopts += '-DCLANG_EXECUTABLE_PATH=$EBROOTCLANG/bin/clang++ ' +configopts += '-DWITH_CPU_BACKEND=ON ' +configopts += '-DWITH_CUDA_BACKEND=OFF ' +configopts += '-DWITH_ROCM_BACKEND=OFF ' + +sanity_check_paths = { + 'files': ['bin/syclcc-clang', 'include/sycl/sycl.hpp', + 'lib/hipSYCL/librt-backend-omp.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'include/hipSYCL', 'include/SYCL', 'lib'], +} +sanity_check_commands = ['syclcc --help'] + +moduleclass = 'compiler' From aef495a39e88e5c67d1d1f08199889b1a9758b27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 26 Aug 2021 15:46:51 +0200 Subject: [PATCH 1479/2365] add archive source URL to Spark 3.x easyconfigs to fix broken download --- easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index 71ff15224d..b4585778e5 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -11,6 +11,7 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = [ + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' ] sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] From b856c1d46bd9f8f6f1fc73163fa03fbb49f990c2 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Thu, 26 Aug 2021 17:05:10 +0200 Subject: [PATCH 1480/2365] skip test_collect_shards on single gpu systems --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index 95baaba3bc..a32c54ea29 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -37,6 +37,7 @@ patches = [ 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', 'PyTorch-1.8.1_skip-nccl-error-tests.patch', + 'PyTorch-1.8.1_fix_test_collect_shards.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -72,6 +73,7 @@ checksums = [ # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', '33704164ad2da7426a6c21482389826345b92690d37cbf938896eef421a62575', # PyTorch-1.8.1_skip-nccl-error-tests.patch + '8d0f60bb4025ca90bbf21d945867a934738560323d232e3b69ae478c364156d3', # PyTorch-1.8.1_fix_test_collect_shards.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] From 9564a0f5602cb40927048b5dce38a81261bfed05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Aug 2021 10:51:14 +0200 Subject: [PATCH 1481/2365] limit parallelism to 10 for jax with foss/2020b, to avoid failing tests because not enough threads can be started --- easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index ddce20e23f..d7edc77e8a 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -34,6 +34,10 @@ local_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_bu use_pip = True +# running the tests with lots of cores results in test failures because not enough threads can be started, +# so limit to a reasonable number of cores to use at maximum +maxparallel = 10 + default_easyblock = 'PythonPackage' default_component_specs = { 'sources': [SOURCE_TAR_GZ], From 7dc832e67847bc2eb07a7e29053d3a3f093d24ec Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 27 Aug 2021 12:49:33 +0100 Subject: [PATCH 1482/2365] Remove versionsuffix for newer toolchains --- .../i/inferCNV/inferCNV-1.3.3-foss-2020b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b.eb new file mode 100644 index 0000000000..7236c47e7f --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'RPackage' + +name = 'inferCNV' +version = '1.3.3' +local_biocver = '3.12' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +source_urls = [GITHUB_SOURCE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['693f7399a232a6cdd7f84bb4038420bdc5ca681545f9b124edb256c390fba541'] + +github_account = 'broadinstitute' +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('R', '4.0.3'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-10', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +options = {'modulename': 'infercnv'} + +moduleclass = 'bio' From a7528851928ab329c176bab4d06c820193e15eb5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 28 Aug 2021 10:39:23 +0100 Subject: [PATCH 1483/2365] adding easyconfigs: pangolin-3.1.11-foss-2020b.eb --- .../p/pangolin/pangolin-3.1.11-foss-2020b.eb | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb new file mode 100644 index 0000000000..a782c5e9a6 --- /dev/null +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb @@ -0,0 +1,81 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on a EC provided by Paul Jähne +# uploaded by J. Sassmannshausen + +easyblock = 'PythonBundle' + +name = 'pangolin' +version = '3.1.11' + +homepage = 'https://cov-lineages.org/pangolin.html' +description = """Software package for assigning SARS-CoV-2 genome sequences to global lineages. +This module also contains the faToVcf tool""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Biopython', '1.78'), + ('gofasta', '0.0.5', '', True), + ('minimap2', '2.18'), + ('Pysam', '0.16.0.1'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('snakemake', '6.1.0'), + ('UShER', '0.4.1'), + ('scikit-learn', '0.23.2'), + ('Kent_tools', '411'), +] + +use_pip = True +sanity_pip_check = True + +github_account = 'cov-lineages' +exts_default_options = { + 'source_urls': [GITHUB_SOURCE], + 'sources': [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], +} + +exts_list = [ + (name, version, { + 'checksums': ['ce64a3ef84de5b11d5c9f21f76341cae23c0fabbf46cc3c1b7b244701b36efbc'], + }), + ('pangoLEARN', '2021-08-09', { + 'modulename': 'pangoLEARN', + 'sources': [{ + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], + 'checksums': ['ece55bc37b3e35dbdff2432fb8b9ea76fa53fe993394a425d1df67147484a81e'], + }), + ('scorpio', '0.3.12', { + 'checksums': ['48390ed1c1a79bb5f801083042cdeddee060e2277f40c293fd30384882aced81'], + }), + ('constellations', '0.0.13', { + 'checksums': ['4aa3edae9491a59621ef6a3b5bbd21a13c68355986f6c097e46a1397d5b1d24b'], + }), + ('pango-designation', '1.2.59', { + 'checksums': ['bd6c11b376c2f6955afa9e96938464184e5f6db22334589cbbbfefe1cbe35e86'], + }), +] + +local_binaries = [ + 'constellations', 'extract_definitions.py', 'pango_designation', 'pangoLEARN', + 'pangolearn.smk', 'pangolin', 'scorpio', 'type_constellations.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'pangolin -v', + 'pangolin -pv', + 'scorpio -v', +] + +moduleclass = 'bio' From 5090511b19e4fd9b63cd23b476bd0d1267488a3f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 28 Aug 2021 15:04:32 +0100 Subject: [PATCH 1484/2365] remove unneeded source_urls --- easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb index a67dbeea4c..6297f03ff6 100644 --- a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb @@ -9,7 +9,6 @@ description = """Imageio is a Python library that provides an easy interface to toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] From 4f7fb07bf81476654ee656c00651d11d8063cf4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Aug 2021 12:12:06 +0200 Subject: [PATCH 1485/2365] avoid that existing OpenMM Python bindings get wiped + run tests for run_alphafold.py script --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 91d5b657e7..084f05c335 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -33,6 +33,11 @@ dependencies = [ local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' @@ -50,8 +55,7 @@ components = [ ], 'start_dir': 'openmm-%(version)s', 'preinstallopts': local_openmm_preinstallopts, - # required to install OpenMM Python API - 'installopts': " && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s", + 'installopts': local_openmm_installopts, }), (name, version, { 'easyblock': 'PythonPackage', @@ -142,12 +146,16 @@ postinstallcmds = [ "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", ] sanity_check_paths = { 'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts', 'stereo_chemical_props.txt'], } sanity_check_commands = [ @@ -156,11 +164,11 @@ sanity_check_commands = [ "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] +sanity_pip_check = True + modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', } -sanity_pip_check = True - moduleclass = 'bio' From 336102a67231bf0f4d04d75aa26fa7204e9b1875 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Aug 2021 13:47:17 +0200 Subject: [PATCH 1486/2365] fix AlphaFold sanity check (stereo_chemical_props.txt is a file, not a directory) --- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 084f05c335..68e9ef8b85 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -154,8 +154,8 @@ postinstallcmds = [ sanity_check_paths = { 'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts', 'stereo_chemical_props.txt'], + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } sanity_check_commands = [ From 40696130275caca4fc1b6f6d8f1e3333c1b40622 Mon Sep 17 00:00:00 2001 From: Guillaume Moutier Date: Mon, 30 Aug 2021 08:28:31 -0400 Subject: [PATCH 1487/2365] fix sanity check error --- .../o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb | 17 ++++++++++++++++- .../OpenCV-4.5.1-fosscuda-2020b-contrib.eb | 17 ++++++++++++++++- 2 files changed, 32 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb index 82699bcc1e..cf24b5ca03 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb @@ -37,6 +37,8 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # for numpy ('zlib', '1.2.11'), ('FFmpeg', '4.3.1'), + ('freetype', '2.10.3'), + ('HarfBuzz', '2.6.7'), ('libjpeg-turbo', '2.0.5'), ('libpng', '1.6.37'), ('LibTIFF', '4.1.0'), @@ -50,7 +52,20 @@ dependencies = [ ('HDF5', '1.10.7'), # needed by hdf from contrib ] -configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules' +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules ' +configopts += '-DFREETYPE_FOUND=ON ' +configopts += '-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/ ' +configopts += '-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DHARFBUZZ_FOUND=ON ' +configopts += '-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz ' +configopts += '-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DBUILD_opencv_python2=OFF ' enhance_sanity_check = True diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb index dd102dc3ae..5fe200231f 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb @@ -37,6 +37,8 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # for numpy ('zlib', '1.2.11'), ('FFmpeg', '4.3.1'), + ('freetype', '2.10.3'), + ('HarfBuzz', '2.6.7'), ('libjpeg-turbo', '2.0.5'), ('libpng', '1.6.37'), ('LibTIFF', '4.1.0'), @@ -50,7 +52,20 @@ dependencies = [ ('HDF5', '1.10.7'), # needed by hdf from contrib ] -configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules' +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules ' +configopts += '-DFREETYPE_FOUND=ON ' +configopts += '-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/ ' +configopts += '-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DHARFBUZZ_FOUND=ON ' +configopts += '-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz ' +configopts += '-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DBUILD_opencv_python2=OFF ' enhance_sanity_check = True From 3e198cb3f7bad6ba15a03978de3c17d13cd43fdb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Aug 2021 15:13:06 +0200 Subject: [PATCH 1488/2365] collapse PDBFixer easyconfig as extension into AlphaFold easyconfig, to avoid depending on two variants of OpenMM --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 68e9ef8b85..624edcc5ab 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -26,7 +26,6 @@ dependencies = [ ('HH-suite', '3.3.0'), ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), - ('PDBFixer', '1.7'), ('jax', '0.2.19'), # also provides absl-py ] @@ -96,6 +95,11 @@ components = [ use_pip = True exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), ('toolz', '0.11.1', { 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], }), @@ -153,12 +157,13 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } sanity_check_commands = [ + "pdbfixer --help", "python -m simtk.testInstallation", "python -c 'import alphafold'", "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", From 8b69d1d49268a7fb5a788de32345caad6deacc0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Aug 2021 15:19:29 +0200 Subject: [PATCH 1489/2365] consistently use %(version)s template in list of patches for AlphaFold --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 624edcc5ab..bcfc97f3b6 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -77,7 +77,7 @@ components = [ 'AlphaFold-%(version)s_fix-packages.patch', 'AlphaFold-%(version)s_data-dep-paths.patch', 'AlphaFold-%(version)s_n-cpu.patch', - 'AlphaFold-2.0.0_fix-scp-path.patch', + 'AlphaFold-%(version)s_fix-scp-path.patch', ], 'checksums': [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz From 1870a38d413304b64b612af118ba94ec35da8c8c Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 30 Aug 2021 13:44:22 +0000 Subject: [PATCH 1490/2365] medaka updated to latest version and foss-2020b, required by artic (PR# 13852), WIP --- .../m/medaka/medaka-1.4.3-foss-2020b.eb | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb new file mode 100644 index 0000000000..b82b55027f --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -0,0 +1,83 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.4.3' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('Python', '3.8.6'), # includes cffi + # TensorFlow 2.2.2 required by medaka 1.4.3, see requirements.txt + ('TensorFlow', '2.2.2'), + ('Biopython', '1.78'), + ('h5py', '3.1.0'), + # Pysam 0.16.0.1 is strictly required, see requirements.txt + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.12'), + # minimap2 is version 2.18 in pangolin, so we need the same version here + ('minimap2', '2.18'), + ('HTSlib', '1.11'), # for tabix, bgzip + ('Racon', '1.4.21'), + ('spoa', '4.0.7'), + ('networkx', '2.6.2'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.8'), + ('ont-fast5-api', '3.3.0'), + ('pyfaidx', '0.5.9.5'), +] + +use_pip = True + +exts_list = [ + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], + }), + ('parasail', '1.2.4', { + 'checksums': ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'], + }), + ('isal', '0.10.0', { + 'checksums': ['3f89471065c2837d1235877dbdcdbd8b7649068723026b0582010fa106a71ff3'], + }), + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + ('whatshap', '1.1', { + 'checksums': ['4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + (name, version, { + 'patches': ['medaka-1.4.3_use-SAMtools-dep.patch'], + 'checksums': [ + '59997b5fdaff6f2040f2df2d3d3eb2d6d1805916a720e8275309caf4d2d4b8a5', # medaka-1.4.3.tar.gz + '06b1d8344035ebcfaf1893e62f37db9b4cab0053ad7a073113630872d44be33e', # medaka-1.4.3_use-SAMtools-dep.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["medaka --help"] + +moduleclass = 'bio' From 603b1c28080dca84c5b1d6a83e9f8157e2149e4f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 30 Aug 2021 17:27:38 +0200 Subject: [PATCH 1491/2365] adding easyconfigs: Bazel-2.0.0-GCCcore-10.2.0.eb --- .../b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bac3fa512e --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +name = 'Bazel' +version = '2.0.0' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = ['Bazel-0.29.1_fix-gold-flag.patch'] +checksums = [ + '724da3c656f68e787a86ebb9844773aa1c2e3a873cc39462a8f1b336153d6cbb', # bazel-2.0.0-dist.zip + '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), + ('Zip', '3.0'), +] +dependencies = [('Java', '1.8', '', True)] + +runtest = True +testopts = ' '.join([ + '--', + '//examples/cpp:hello-success_test', + '//examples/py/...', + '//examples/py_native:test', + '//examples/shell/...', +]) + +moduleclass = 'devel' From 33681b50c5b75445b2ca49b7eda4cadb414692e2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 30 Aug 2021 18:09:15 +0200 Subject: [PATCH 1492/2365] Use Java 11 --- easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb index bac3fa512e..64cebdfa53 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Python', '3.8.6'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '11', '', True)] runtest = True testopts = ' '.join([ From e3a27d9b051b10924700985b415eceaab091cb5e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Aug 2021 20:45:30 +0100 Subject: [PATCH 1493/2365] switch to PCRE in GDAL 3.2.1 and 3.3.0 --- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb | 4 ++-- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb | 4 ++-- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb index a164b3b035..71748cbee2 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -37,7 +37,7 @@ dependencies = [ ('LibTIFF', '4.1.0'), ('zlib', '1.2.11'), ('cURL', '7.72.0'), - ('PCRE2', '10.35'), + ('PCRE', '8.44'), ('PROJ', '7.2.1'), ('libgeotiff', '1.6.0'), ('SciPy-bundle', '2020.11'), @@ -50,7 +50,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' -configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb index bcba374a61..606bd64d0d 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb @@ -37,7 +37,7 @@ dependencies = [ ('LibTIFF', '4.1.0'), ('zlib', '1.2.11'), ('cURL', '7.72.0'), - ('PCRE2', '10.35'), + ('PCRE', '8.44'), ('PROJ', '7.2.1'), ('libgeotiff', '1.6.0'), ('SciPy-bundle', '2020.11'), @@ -50,7 +50,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' -configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb index 7416633742..09c2c1bb82 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb @@ -41,7 +41,7 @@ dependencies = [ ('LibTIFF', '4.1.0'), ('zlib', '1.2.11'), ('cURL', '7.72.0'), - ('PCRE2', '10.35'), + ('PCRE', '8.44'), ('PROJ', '7.2.1'), ('libgeotiff', '1.6.0'), ('SciPy-bundle', '2020.11'), @@ -54,7 +54,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' -configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' prebuildopts = "env LDSHARED='icc -shared' " From 3e6ba65ad3bddb0c87b8c10ebb46b94ba68274c1 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 31 Aug 2021 13:47:37 +0200 Subject: [PATCH 1494/2365] adding easyconfigs: GMT-6.2.0-foss-2019b.eb, GMT-6.2.0-foss-2020b.eb --- .../easyconfigs/g/GMT/GMT-6.2.0-foss-2020b.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2020b.eb new file mode 100644 index 0000000000..51623405d1 --- /dev/null +++ b/easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2020b.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'GMT' +version = '6.2.0' +local_gshhg_ver = '2.3.7' +local_dcw_ver = '2.0.0' + +homepage = 'https://www.generic-mapping-tools.org/' +description = """GMT is an open source collection of about 80 command-line tools for manipulating + geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, + etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps + to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another + 40 more specialized and discipline-specific tools. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +# 'https://gmt.soest.hawaii.edu/files/download?name=' needs browser with javascript magic +source_urls = [ + 'ftp://ftp.soest.hawaii.edu/gmt', + 'ftp://ftp.soest.hawaii.edu/gshhg', + 'ftp://ftp.soest.hawaii.edu/dcw', +] +sources = [ + '%(namelower)s-%(version)s-src.tar.gz', + # coastlines, rivers, and political boundaries + 'gshhg-gmt-%s.tar.gz' % local_gshhg_ver, + # country polygons + 'dcw-gmt-%s.tar.gz' % local_dcw_ver, +] +patches = ['GMT-5.1.2_netCDF.patch'] +checksums = [ + 'ab7062912aeead1021770fad4756e0a99860fde8ea9b428fb00c22fa15a3bbfc', # gmt-6.2.0-src.tar.gz + '9bb1a956fca0718c083bef842e625797535a00ce81f175df08b042c2a92cfe7f', # gshhg-gmt-2.3.7.tar.gz + 'd71d209c837a805fed0773c03fadbb26e8c90eb6b68e496ac4a1298c3246cc7a', # dcw-gmt-2.0.0.tar.gz + '2ebe26d55521fba8d0eae48f662611491f7cc0e489833bded11628e9a71f252f', # GMT-5.1.2_netCDF.patch +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('PCRE', '8.44'), + ('GDAL', '3.2.1'), + ('netCDF', '4.7.4'), + ('Ghostscript', '9.53.3'), + ('cURL', '7.72.0'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +configopts = '-DCOPY_GSHHG=TRUE -DGSHHG_ROOT=%%(builddir)s/gshhg-gmt-%s ' % local_gshhg_ver +configopts += '-DCOPY_DCW=TRUE -DDCW_ROOT=%%(builddir)s/dcw-gmt-%s ' % local_dcw_ver + +sanity_check_paths = { + 'files': ['bin/%s' % b for b in ['gmt', 'isogmt', 'gmtswitch', 'gmt_shell_functions.sh']] + + ['lib64/libgmt.%s.%s' % (SHLIB_EXT, version)], + 'dirs': ['include/%(namelower)s', 'share'] +} + +modextrapaths = {'GMTHOME': ''} + +moduleclass = 'geo' From 47f41b39d8f7a1ca5a4651bf44d786061f2d1144 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Tue, 31 Aug 2021 14:24:50 +0200 Subject: [PATCH 1495/2365] adding easyconfigs: Centrifuge-1.0.4-gompi-2020b.eb --- .../Centrifuge-1.0.4-gompi-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2020b.eb diff --git a/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2020b.eb b/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2020b.eb new file mode 100644 index 0000000000..10d20754e0 --- /dev/null +++ b/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Centrifuge' +version = '1.0.4' + +homepage = 'https://ccb.jhu.edu/software/centrifuge' +description = 'Classifier for metagenomic sequences' + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/DaehwanKimLab/centrifuge/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '929daed0f84739f7636cc1ea2757527e83373f107107ffeb5937a403ba5201bc', # v1.0.4.tar.gz +] + +dependencies = [ + ('NGS', '2.10.9'), + ('ncbi-vdb', '2.10.9'), +] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CXXFLAGS" ' +buildopts += 'USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB' + +installopts = "prefix=%(installdir)s" + +fix_perl_shebang_for = ['bin/centrifuge*.pl'] + +sanity_check_paths = { + 'files': ['bin/centrifuge%s' % x for x in ['', '-build', '-build-bin', '-class', '-download', + '-inspect', '-inspect-bin']], + 'dirs': [], +} + +sanity_check_commands = ["centrifuge --help"] + +moduleclass = 'bio' From 81cc86546e1713bf2c5f18c578d3c83ce387171e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 31 Aug 2021 16:45:17 +0200 Subject: [PATCH 1496/2365] Update and rename TensorFlow-2.2.2-foss-2020b.eb to TensorFlow-2.2.3-foss-2020b.eb Add tests and fix deps --- .../TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 194 ++++++++++++++++++ 1 file changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb new file mode 100644 index 0000000000..d1d6fc11dc --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -0,0 +1,194 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.2.3' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '2.0.0'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), # For h5py + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('SWIG', '4.0.2'), + ('zlib', '1.2.11'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + # TF <= 2.4 needs h5py 2.10, later versions allow 3.x + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + # h5py-2.10.0_avoid-mpi-init.patch + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', + ], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + }), + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('google-auth', '1.35.0', { + 'modulename': 'google.auth', + 'checksums': ['b7033be9028c188ee30200b204ea00ed82ea1162e8ac1df4aa6ded19a191d88e'], + }), + ('oauthlib', '3.1.1', { + 'checksums': ['8f0215fcc533dd8dd1bee6f4c412d4f0cd7297307d43ac61666389e3bc3198a3'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.5', { + 'checksums': ['4ab58e6c3dc6ccf112f921fcced40e5426fba266768986ea502228488276eaba'], + }), + ('Werkzeug', '2.0.1', { + 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], + }), + ('absl-py', '0.12.0', { + 'modulename': 'absl', + 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.39.0', { + 'modulename': 'grpc', + 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard', '2.2.2', { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['a3feb73e1221c0a512398ad2cd08570fb082d8a2ba364aa0562543ecbd3659ef'], + }), + ('tensorboard-plugin-wit', '1.8.0', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard-plugin-profile', '2.2.0', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['fcd2f4a17c53fb080390044459ee03fb8d9e8d109ae5838516fdcbda69ce99f9'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', '2.2.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['d09dacdd127f2579cea8d5af21f4a918036b8ae246adc82f26b61f91cc247dc2'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + # For tests + ('portpicker', '1.4.0', { + 'checksums': ['c2831ff4328a21e928ffc9e52124bcafacaf5816d38a1a72dc329680dc1bb7ba'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.1.0_fix-system-jsoncpp.patch', + 'TensorFlow-2.1.0_fix-system-nasm.patch', + 'TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch', + 'TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch', + 'TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch', + 'TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + ], + 'checksums': [ + '5e6c779ca8392864d436d88893461dcce783c3a8d46dcb2b2f2ee8ece3cc4538', # v2.2.3.tar.gz + # TensorFlow-2.1.0_fix-system-jsoncpp.patch + 'd0c8ca54a9e2c232908016e08b982dbb63765de3472253cba5ae38d823d5f156', + # TensorFlow-2.1.0_fix-system-nasm.patch + '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', + # TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch + '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', + # TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch + '85c3023892e21692e14750e43a7d1db3c83c6e86a75ac1559c9dba39e0a160ae', + # TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch + 'd80e0103aeefb5244b57dd0e01bb7a0c1e6a750fba41833706547be87d3829e4', + # TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch + '9588f324b4ac5b90e77f8c1d64bd65f3ef64677f82603c0742e4f3a9e99ac171', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'with_xla': True, + }), +] + +moduleclass = 'lib' From 95c73551eb8f844c9f3cb255fa4d83f9b9b11550 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Aug 2021 16:59:43 +0200 Subject: [PATCH 1497/2365] adding easyconfigs: AlphaFold-2.0.0-fosscuda-2020b.eb --- .../AlphaFold-2.0.0-fosscuda-2020b.eb | 186 ++++++++++++++++++ 1 file changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..fe2744c806 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb @@ -0,0 +1,186 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.0.0' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + # CMake/oxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.4.1'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.19'), # also provides absl-py +] + +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp -a %s .", + }, + ], + 'patches': [ + 'AlphaFold-%(version)s_fix-packages.patch', + 'AlphaFold-%(version)s_data-dep-paths.patch', + 'AlphaFold-%(version)s_n-cpu.patch', + 'AlphaFold-%(version)s_fix-scp-path.patch', + ], + 'checksums': [ + '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '7223e297b23f90816219095696bc6453910c617add60b907a0d3e869da8733bb', # AlphaFold-2.0.0_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + # source tarball on PyPI is missing requirements.txt, + # see https://github.com/deepmind/dm-haiku/issues/44 + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + 'modulename': 'haiku', + }), + ('dm-tree', '0.1.6', { + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + 'modulename': 'tree', + }), + ('websocket-client', '1.2.1', { + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + 'modulename': 'websocket', + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + # see https://github.com/google/ml_collections/issues/7 + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', +} + +moduleclass = 'bio' From 4de99af174183b8e13b08f2a8936fea609a4f9fe Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 31 Aug 2021 18:16:22 +0200 Subject: [PATCH 1498/2365] Fix usage of /usr/bin/perl in HMMER. --- .../easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb | 14 ++++++++++++-- .../h/HMMER/HMMER-3.3.2-gompic-2020b.eb | 14 ++++++++++++-- .../easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb | 14 ++++++++++++-- 3 files changed, 36 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb index a39fc442b6..6d95f779fa 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb @@ -35,12 +35,22 @@ source_urls = [ 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] sources = ['hmmer-%(version)s.tar.gz'] -checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] -builddependencies = [('Python', '3.8.6')] +builddependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0', '-minimal'), +] configopts = '--enable-mpi' +buildopts = ' V=1 ' + +testopts = buildopts runtest = 'check' installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb index f26e9cbaaf..bb4ec04a67 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb @@ -35,12 +35,22 @@ source_urls = [ 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] sources = [SOURCELOWER_TAR_GZ] -checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] -builddependencies = [('Python', '3.8.6')] +builddependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0', '-minimal'), +] configopts = '--enable-mpi' +buildopts = ' V=1 ' + +testopts = buildopts runtest = 'check' installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb index ea00c7b7ec..0f903bc063 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb @@ -35,12 +35,22 @@ source_urls = [ 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] sources = ['hmmer-%(version)s.tar.gz'] -checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] -builddependencies = [('Python', '3.8.6')] +builddependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0', '-minimal'), +] configopts = '--enable-mpi' +buildopts = ' V=1 ' + +testopts = buildopts runtest = 'check' installopts = ' && cd easel && make install' From 625ba6177e44264c8c38030f294d24e463011eb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Sep 2021 08:50:52 +0200 Subject: [PATCH 1499/2365] fix typo in comment in AlphaFold easyconfigs (oxygen -> Doxygen) --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index bcfc97f3b6..c36bafa819 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -9,7 +9,7 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ - # CMake/oxygen/SWIG are required for building OpenMM + # CMake/Doxygen/SWIG are required for building OpenMM ('CMake', '3.18.4'), ('Doxygen', '1.8.20'), # required for installing dm-tree diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb index fe2744c806..08ad07e950 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb @@ -9,7 +9,7 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ - # CMake/oxygen/SWIG are required for building OpenMM + # CMake/Doxygen/SWIG are required for building OpenMM ('CMake', '3.18.4'), ('Doxygen', '1.8.20'), # required for installing dm-tree From 500c61df6782a2c637a27ec359118b98125b30b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Sep 2021 09:36:03 +0200 Subject: [PATCH 1500/2365] consistently use patch for HMMER 3.3.2 to use Perl provided through EasyBuild --- easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb | 2 +- easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb index 6d95f779fa..55a9044d7f 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb @@ -34,7 +34,7 @@ source_urls = [ 'http://eddylab.org/software/hmmer/', 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] -sources = ['hmmer-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_fix_perl.patch'] checksums = [ '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb index 0f903bc063..3c33d7fa1e 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb @@ -34,7 +34,7 @@ source_urls = [ 'http://eddylab.org/software/hmmer/', 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] -sources = ['hmmer-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_fix_perl.patch'] checksums = [ '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz From bc3e4f87483a747d59f3b2e2f277233b5c000c14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Sep 2021 19:39:42 +0200 Subject: [PATCH 1501/2365] add missing flex build dependency for leidenalg --- easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb | 1 + .../easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb index b5307684eb..6df451ff57 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('PyYAML', '5.3.1'), ('Bison', '3.7.1'), ('libtool', '2.4.6'), + ('flex', '2.6.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb index 66efa3a2fc..8aad4bf9f1 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('PyYAML', '5.3.1'), ('Bison', '3.7.1'), ('libtool', '2.4.6'), + ('flex', '2.6.4'), ] dependencies = [ From 4cdc16cac25538452e771793fd6d11a5a490671c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 11:00:23 +0200 Subject: [PATCH 1502/2365] adding easyconfigs: scanpy-1.8.1-foss-2020b.eb --- .../s/scanpy/scanpy-1.8.1-foss-2020b.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb new file mode 100644 index 0000000000..76668a416a --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.8.1' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('networkx', '2.5'), + ('numba', '0.52.0'), + ('PyTables', '3.6.1'), + ('statsmodels', '0.12.1'), + ('scikit-learn', '0.23.2'), + ('Seaborn', '0.11.1'), + ('tqdm', '4.56.2'), + ('leidenalg', '0.8.3'), +] + +use_pip = True + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('anndata', '0.7.6', { + 'checksums': ['a3cc67bba9a4cd4b5984aec64c4f577c2d5a4695f4064027f8e6a9dac1f508b2'], + }), + ('pynndescent', '0.5.4', { + 'checksums': ['221124cbad8e3cf3ed421a4089d80ac5a29d3215e76cb49effc1df887533d2a8'], + }), + ('umap-learn', '0.5.1', { + 'modulename': 'umap', + 'checksums': ['3e3e5e526109866012a9da79f423c922edc379c6cac9bf65ea08fbb9dd93ff3a'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.4', { + 'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'], + }), + (name, version, { + 'checksums': ['1b8603a868d783bd6c18c8db763a450153feefc8daed862c440749790d47c654'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", + "scanpy --help", +] + +moduleclass = 'bio' From 7b8c1cfff8b2a51ec2cc951ce80d7666a7e8b8e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 11:44:32 +0200 Subject: [PATCH 1503/2365] use numba 0.53.1 as dependency for scanpy 1.8.1 --- easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb index 76668a416a..bc44c5abc4 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb @@ -18,7 +18,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('h5py', '3.1.0'), ('networkx', '2.5'), - ('numba', '0.52.0'), + ('numba', '0.53.1'), ('PyTables', '3.6.1'), ('statsmodels', '0.12.1'), ('scikit-learn', '0.23.2'), From 05b6b2427afa19e8320f55c8b695e6ebba4a5715 Mon Sep 17 00:00:00 2001 From: Loris Bennett Date: Fri, 3 Sep 2021 14:11:16 +0200 Subject: [PATCH 1504/2365] {vis}[GCCcore-10.2.0] GtkSourceView v3.24.11 --- .../GtkSourceView-3.24.11-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0319076daf --- /dev/null +++ b/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GtkSourceView' +version = '3.24.11' + +homepage = 'https://wiki.gnome.org/Projects/GtkSourceView' +description = """ + GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ + widget for multiline text editing. GtkSourceView adds support for syntax + highlighting, undo/redo, file loading and saving, search and replace, a + completion system, printing, displaying line numbers, and other features + typical of a source code editor. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['691b074a37b2a307f7f48edc5b8c7afa7301709be56378ccf9cc9735909077fd'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.66.1'), +] + +dependencies = [ + ('GLib', '2.66.1'), + ('GTK+', '3.24.23'), + ('libxml2', '2.9.10'), +] + +configopts = "--disable-silent-rules --enable-introspection=yes " + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['include/%(namelower)s-%(version_major)s.0', 'share'], +} + +moduleclass = 'vis' From a48d8c006d8f4e081779717dad3c9014346b1dd9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 14:38:42 +0200 Subject: [PATCH 1505/2365] remove SHA256 checksum for IMOD 4.11.5 source tarball + fix installation on top of Python 3 --- .../i/IMOD/IMOD-4.11.5-foss-2020b.eb | 19 +++++++++++++------ .../i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 18 +++++++++++++----- 2 files changed, 26 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index 1758cf4d8a..0a9e8fa035 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -16,17 +16,20 @@ Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'openmp': True} -sources = [SOURCE_TAR_GZ] -checksums = ['5c50f1457134fe5113b95e0939d3181b948d211f25d9a05ad2b4ec0f23251c79'] - -# mercurial repository +# download manually from mercurial repository and create source tarball: # hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD # get lunch # cd IMOD # hg update -r IMOD_4-11-5 # cd .. # tar czf IMOD-4.11.5.tar.gz IMOD - +sources = [SOURCE_TAR_GZ] +patches = ['IMOD-%(version)s_fix-csvtohtml-py3.patch'] +checksums = [ + # can't include a valid checksum for source tarball, since it has to be created manually + None, # IMOD-4.11.5.tar.gz + '8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971', # IMOD-4.11.5_fix-csvtohtml-py3.patch +] dependencies = [ ('LibTIFF', '4.1.0'), @@ -61,7 +64,11 @@ configure_cmd += ' #' # avoid passing unknown arg --prefix prebuildopts = local_exports # create some missing directories required for installation process: -preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&' +preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p && ' + +# patch hardcoded /usr/bin/python to use Python included as dependency +preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && " +preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && " modextravars = { 'IMOD_DIR': "%(installdir)s", diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index 803e0308fe..733bdf9aa9 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -18,17 +18,21 @@ toolchainopts = {'pic': True, 'openmp': True} # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] -sources = [SOURCE_TAR_GZ] -checksums = ['5c50f1457134fe5113b95e0939d3181b948d211f25d9a05ad2b4ec0f23251c79'] - -# mercurial repository +# download manually from mercurial repository and create source tarball: # hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD # get lunch # cd IMOD # hg update -r IMOD_4-11-5 # cd .. # tar czf IMOD-4.11.5.tar.gz IMOD - +sources = [SOURCE_TAR_GZ] +# can't include a valid checksum, since tarball has to be created manually +patches = ['IMOD-%(version)s_fix-csvtohtml-py3.patch'] +checksums = [ + # can't include a valid checksum for source tarball, since it has to be created manually + None, # IMOD-4.11.5.tar.gz + '8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971', # IMOD-4.11.5_fix-csvtohtml-py3.patch +] dependencies = [ ('LibTIFF', '4.1.0'), @@ -75,6 +79,10 @@ prebuildopts = local_exports # create some missing directories required for installation process: preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&' +# patch hardcoded /usr/bin/python to use Python included as dependency +preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && " +preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && " + modextravars = { 'IMOD_DIR': "%(installdir)s", 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', From c0a5a3790b21328d818a751e6305299687d52873 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 15:27:20 +0200 Subject: [PATCH 1506/2365] set parallel = 1 for IMOD 4.11.5 to avoid failing parallel build --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index 0a9e8fa035..650693addb 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -39,6 +39,9 @@ dependencies = [ ('Python', '3.8.6'), ] +# parallel build sometimes fails +parallel = 1 + # modify all qmake pro files in order to pass CFLAGS local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&" diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index 733bdf9aa9..33a8617ba3 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -42,6 +42,9 @@ dependencies = [ ('Python', '3.8.6'), ] +# parallel build sometimes fails +parallel = 1 + # replace hardcoded CUDA compute capabilitites in machines/rhlinux. local_cuda_replace = 'echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|' local_cuda_replace += ' awk \'{' From 12a6084fc897cca3b5c3ea3c6833bf4948f5a037 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 15:58:36 +0200 Subject: [PATCH 1507/2365] also patch IMOD's makeqhp script to not use /usr/bin/python --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb | 1 + easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index 650693addb..fa2d35b964 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -72,6 +72,7 @@ preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/ # patch hardcoded /usr/bin/python to use Python included as dependency preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && " preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && " +preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && " modextravars = { 'IMOD_DIR': "%(installdir)s", diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index 33a8617ba3..d2bc021cbb 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -85,6 +85,7 @@ preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/ # patch hardcoded /usr/bin/python to use Python included as dependency preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && " preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && " +preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && " modextravars = { 'IMOD_DIR': "%(installdir)s", From 9fda75b4a81b55d3f0fb676d3ac54396a022b922 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 16:57:33 +0200 Subject: [PATCH 1508/2365] fix source URL for Yasm 1.3.0 (+ add missing checksum) --- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb index 30cc501dda..4614e5786e 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb @@ -21,7 +21,7 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = ['https://www.tortall.net/projects/yasm/releases/'] +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] From a0b354d893e5a419f8297a52ffa05bba9d0c51b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 19:57:36 +0200 Subject: [PATCH 1509/2365] adding easyconfigs: AutoGeneS-1.0.4-foss-2020b.eb --- .../a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb new file mode 100644 index 0000000000..d37a02530c --- /dev/null +++ b/easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'AutoGeneS' +version = '1.0.4' + +homepage = 'https://github.com/theislab/AutoGeneS' +description = """AutoGeneS automatically extracts informative genes and reveals the cellular heterogeneity +of bulk RNA samples.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('dill', '0.3.3'), + ('scikit-learn', '0.23.2'), + ('h5py', '3.1.0'), +] + +use_pip = True + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('anndata', '0.7.6', { + 'checksums': ['a3cc67bba9a4cd4b5984aec64c4f577c2d5a4695f4064027f8e6a9dac1f508b2'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('autogenes', version, { + 'checksums': ['8daa6e9aa97c7ddf45ab0906307a4875a25bd99301be0838bb17e313d837446a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From a686d75f954eb4791b45c84c3fcf050d3ca61e1c Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Fri, 3 Sep 2021 22:55:07 +0200 Subject: [PATCH 1510/2365] adding easyconfigs: SLEPc-3.14.2-foss-2020b.eb --- .../s/SLEPc/SLEPc-3.14.2-foss-2020b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.14.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.14.2-foss-2020b.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.14.2-foss-2020b.eb new file mode 100644 index 0000000000..87ff7d8c44 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.14.2-foss-2020b.eb @@ -0,0 +1,21 @@ +name = 'SLEPc' +version = '3.14.2' + +homepage = 'https://slepc.upv.es/' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://slepc.upv.es/download/distrib'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3e54578dda1f4c54d35ac27d02f70a43f6837906cb7604dbcec0e033cfb264c8'] + +dependencies = [('PETSc', '3.14.4')] + +petsc_arch = 'installed-arch-linux2-c-opt' + +moduleclass = 'numlib' From 5bc2540faa62240727a85ecf91b1bf145b4aadb7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Sep 2021 14:36:08 +0100 Subject: [PATCH 1511/2365] adding easyconfigs: Yices-2.6.2-GCCcore-10.2.0.eb --- .../y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d6c493931c --- /dev/null +++ b/easybuild/easyconfigs/y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Yices' +version = '2.6.2' + +homepage = "https://yices.csl.sri.com/index.html" +description = """Yices 2 is an SMT solver that decides the satisfiability of formulas containing uninterpreted + function symbols with equality, real and integer arithmetic, bitvectors, scalar types, and tuples. Yices 2 supports + both linear and nonlinear arithmetic.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://yices.csl.sri.com/releases/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +checksums = ['1f205c056dd430f830c688fba6c87d8bd07bd8fa05f65936e12c27e71fa3576a'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('GMP', '6.2.0'), + ('gperf', '3.1'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libyices.a', 'lib/libyices.%s' % SHLIB_EXT, 'include/yices.h'], + 'dirs': [], +} + +sanity_check_commands = ['%s --help' % x for x in ['yices', 'yices-sat', 'yices-smt', 'yices-smt2']] + +moduleclass = 'tools' From 29df952187cfceaeeadf1af3c7dba8e60c0c12d5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Sep 2021 14:36:43 +0100 Subject: [PATCH 1512/2365] adding easyconfigs: BuDDy-2.4-GCCcore-10.2.0.eb --- .../b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..719cac72c8 --- /dev/null +++ b/easybuild/easyconfigs/b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'BuDDy' +version = '2.4' + +homepage = "http://buddy.sourceforge.net/" +description = """A Binary Decision Diagram library, with many highly efficient vectorized BDD operations, dynamic + variable reordering, automated garbage collection, a C++ interface with automatic reference counting, and much + more.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d3df80a6a669d9ae408cb46012ff17bd33d855529d20f3a7e563d0d913358836'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libbdd.a', 'lib/libbdd.%s' % SHLIB_EXT, 'include/bdd.h'], + 'dirs': [], +} + +moduleclass = 'tools' From 9bb8ea32b5fdc5a6439352fb2fb7f4e548f99912 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Sep 2021 14:37:24 +0100 Subject: [PATCH 1513/2365] adding easyconfigs: libtecla-1.6.3-GCCcore-10.2.0.eb --- .../libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..383ab0e181 --- /dev/null +++ b/easybuild/easyconfigs/l/libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libtecla' +version = '1.6.3' + +homepage = "https://sites.astro.caltech.edu/~mcs/tecla/" +description = """The tecla library provides UNIX and LINUX programs with interactive command line editing facilities, + similar to those of the UNIX tcsh shell. In addition to simple command-line editing, it supports recall of previously + entered command lines, TAB completion of file names or other tokens, and in-line wild-card expansion of filenames. + The internal functions which perform file-name completion and wild-card expansion are also available externally for + optional use by programs. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://sites.astro.caltech.edu/~mcs/tecla/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2757cc55040859fcf8f59a0b7b26e0184a22bece44ed9568a4534a478c1ee1a'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('ncurses', '6.2'), +] + +configopts = '--with-man-pages=no' + +sanity_check_paths = { + 'files': ['bin/enhance', 'lib/libtecla.a', 'lib/libtecla.%s' % SHLIB_EXT, 'include/libtecla.h'], + 'dirs': [], +} + +moduleclass = 'tools' From 6eeea20816df084a86720be2ec365aa364c14648 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Sep 2021 14:45:40 +0100 Subject: [PATCH 1514/2365] adding easyconfigs: Maude-3.1-GCCcore-10.2.0.eb --- .../m/Maude/Maude-3.1-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..038cb68a58 --- /dev/null +++ b/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Maude' +version = '3.1' + +homepage = "https://maude.cs.illinois.edu/w/index.php/The_Maude_System" +description = """Maude is a high-performance reflective language and system supporting both equational and rewriting + logic specification and programming for a wide range of applications. Maude has been influenced in important ways by + the OBJ3 language, which can be regarded as an equational logic sublanguage. Besides supporting equational + specification and programming, Maude also supports rewriting logic computation. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://maude.cs.illinois.edu/w/images/d/d3/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b112d7843f65217e3b5a9d40461698ef8dab7cbbe830af21216dfb924dc88a2f'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('BuDDy', '2.4'), + ('GMP', '6.2.0'), + ('libsigsegv', '2.13'), + ('libtecla', '1.6.3'), + ('Yices', '2.6.2'), +] + +# Building in parallel sometimes errors +maxparallel = 1 + +runtest = 'check' + +modextravars = {'MAUDE_LIB': '%(installdir)s/share'} + +sanity_check_paths = { + 'files': ['share/%s.maude' % x for x in ['file', 'linear', 'prelude', 'smt']], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'tools' From 5ea349de35e9487c4f4cb7463c174cbd1a4f636e Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 4 Sep 2021 15:53:11 +0100 Subject: [PATCH 1515/2365] Update easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb index 038cb68a58..f9de690f36 100644 --- a/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb @@ -37,7 +37,7 @@ runtest = 'check' modextravars = {'MAUDE_LIB': '%(installdir)s/share'} sanity_check_paths = { - 'files': ['share/%s.maude' % x for x in ['file', 'linear', 'prelude', 'smt']], + 'files': ['bin/maude'] + ['share/%s.maude' % x for x in ['file', 'linear', 'prelude', 'smt']], 'dirs': [], } From 5f5aaa42cf6293d8b4f5eb86fd5c8bbdb569d08f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Sep 2021 10:08:36 +0200 Subject: [PATCH 1516/2365] fix shebang for RepeatMasker 4.1.2-p1 Perl script --- .../r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb index 726cafbe03..9d3c0d8724 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb @@ -39,7 +39,8 @@ local_default_search_engine = 'RMBlast' preinstall_cmd = './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' preinstall_cmd += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' preinstall_cmd += '-default_search_engine %s' % local_default_search_engine.lower() -# preinstall_cmd += '-libdir="RepeatMasker/Libraries" + +fix_perl_shebang_for = ['RepeatMasker'] sanity_check_paths = { 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], From f36ea91cca7de8ceb34e46f9494134eba92349e8 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 6 Sep 2021 17:28:14 +0200 Subject: [PATCH 1517/2365] add missing brotli dependency to freetype --- .../b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb | 36 +++++++++++++++++++ .../freetype-2.10.3-GCCcore-10.2.0.eb | 1 + 2 files changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..72c9f12ad6 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' +name = 'Brotli' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +separate_build_dir = True + +dependencies = [('binutils', '2.35')] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb index c9318c29a8..841fd64593 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb @@ -27,6 +27,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('libpng', '1.6.37'), ('zlib', '1.2.11'), + ('Brotli', '1.0.9'), ] configopts = '--enable-freetype-config --with-harfbuzz=no' From 08b21bec28222d54c655a2a613125faaed3306c0 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 7 Sep 2021 18:42:34 +0200 Subject: [PATCH 1518/2365] adding easyconfigs: TOML-Fortran-0.2.2-GCC-10.2.0.eb, TOML-Fortran-0.2.2-iccifort-2020.4.304.eb --- .../TOML-Fortran-0.2.2-GCC-10.2.0.eb | 26 +++++++++++++++++++ .../TOML-Fortran-0.2.2-iccifort-2020.4.304.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..f10a440e00 --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.2.2' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c3e5e1f57de00977b5e41d3a857ddb7e6b41f0b9116ed608cf89f295d9ef24c6'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['include/toml-f/GNU-10.2.0/tomlf.mod', 'lib/libtoml-f.a'], + 'dirs': ['include/toml-f/GNU-10.2.0', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..5b63c17184 --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.2.2' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c3e5e1f57de00977b5e41d3a857ddb7e6b41f0b9116ed608cf89f295d9ef24c6'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['include/toml-f/Intel-19.1.3.20200925/tomlf.mod', 'lib/libtoml-f.a'], + 'dirs': ['include/toml-f/Intel-19.1.3.20200925', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From d35338e5873fab9faa3ab1845f62a9b3602d87fb Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 7 Sep 2021 19:11:30 +0200 Subject: [PATCH 1519/2365] adding easyconfigs: python-docx-0.8.11-GCCcore-10.2.0.eb --- .../python-docx-0.8.11-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f5f38e7600 --- /dev/null +++ b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'python-docx' +version = '0.8.11' + +homepage = 'https://python-docx.readthedocs.io/en/latest/' +description = 'python-docx is a Python library for creating and updating Microsoft Word (.docx) files' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1105d233a0956dd8dd1e710d20b159e2d72ac3c301041b95f4d4ceb3e0ebebc4'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('lxml', '4.6.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'docx'} + +moduleclass = 'tools' From 707907d08e356e38740bfd971f6b749b13570576 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 8 Sep 2021 14:55:44 +0200 Subject: [PATCH 1520/2365] Do not use cp -a when not needed. --- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 4 ++-- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index c36bafa819..fa55dd0f5a 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -70,7 +70,7 @@ components = [ { 'download_filename': 'stereo_chemical_props.txt', 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, - 'extract_cmd': "cp -a %s .", + 'extract_cmd': "cp %s .", }, ], 'patches': [ @@ -149,7 +149,7 @@ postinstallcmds = [ "chmod a+x %(installdir)s/bin/run_alphafold.py", "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", - "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, # run tests for run_alphafold.py script; # shouldn't do this in sanity check to avoid breaking use of --module-only "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb index 08ad07e950..4d23d09d29 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb @@ -70,7 +70,7 @@ components = [ { 'download_filename': 'stereo_chemical_props.txt', 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, - 'extract_cmd': "cp -a %s .", + 'extract_cmd': "cp %s .", }, ], 'patches': [ @@ -149,7 +149,7 @@ postinstallcmds = [ "chmod a+x %(installdir)s/bin/run_alphafold.py", "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", - "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, # run tests for run_alphafold.py script; # shouldn't do this in sanity check to avoid breaking use of --module-only "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " From 78fd0399b81528d1dca928e24a2e9e6c0a08a781 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Sep 2021 18:20:19 +0200 Subject: [PATCH 1521/2365] drop enabling of separate_build_dir, already done by default by CMakeMake --- .../easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb | 2 -- .../t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb index f10a440e00..53a8eb3a50 100644 --- a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb @@ -16,8 +16,6 @@ builddependencies = [ ('CMake', '3.18.4'), ] -separate_build_dir = True - sanity_check_paths = { 'files': ['include/toml-f/GNU-10.2.0/tomlf.mod', 'lib/libtoml-f.a'], 'dirs': ['include/toml-f/GNU-10.2.0', 'lib/pkgconfig', 'share'], diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb index 5b63c17184..2a70b5b676 100644 --- a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb @@ -16,8 +16,6 @@ builddependencies = [ ('CMake', '3.18.4'), ] -separate_build_dir = True - sanity_check_paths = { 'files': ['include/toml-f/Intel-19.1.3.20200925/tomlf.mod', 'lib/libtoml-f.a'], 'dirs': ['include/toml-f/Intel-19.1.3.20200925', 'lib/pkgconfig', 'share'], From 0481637e6d100b69092ef69659a29eeced287d4e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 10 Sep 2021 10:35:34 +0200 Subject: [PATCH 1522/2365] switch AdapterRemoval from GCCcore 10.2.0 to GCC 10.2.0 --- .../AdapterRemoval-2.3.2-GCC-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..310e4f767d --- /dev/null +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.2.0.eb @@ -0,0 +1,38 @@ + +easyblock = 'ConfigureMake' + +name = 'AdapterRemoval' +version = '2.3.2' + +homepage = 'https://github.com/MikkelSchubert/adapterremoval' +description = """AdapterRemoval searches for and removes remnant adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases + from the 3' end of reads following adapter removal.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'MikkelSchubert' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ded7e08fb64e1b19f5c3de623de276d9cbb657a52b23a844ff74576d1b4f8d4'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] +} + +sanity_check_commands = [('%(name)s', '--version')] + +moduleclass = 'bio' From e27f42c8b425e35f2cd52a8f2f0633a756611160 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Sep 2021 13:14:05 +0200 Subject: [PATCH 1523/2365] TensorFlow 2.4.1: add UnZip builddependency --- .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index b3b7e48529..ed118dbbdd 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py + ('UnZip', '6.0.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 7693cdd06a..a9a6494a69 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py + ('UnZip', '6.0.0'), ] dependencies = [ ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), From b8546abddecba01220a8b896838bd1950ef9e950 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Sep 2021 13:14:30 +0200 Subject: [PATCH 1524/2365] TensorFlow 2.5.0: add UnZip builddependency --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 015fdb2f97..edb84d52b2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py + ('UnZip', '6.0.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index bafbef6444..230444abd3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py + ('UnZip', '6.0.0'), ] dependencies = [ ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), From 9e3bce3ce31f33e8899dfa5674c8fc2692b48df6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Sep 2021 13:21:23 +0200 Subject: [PATCH 1525/2365] TensorFlow 2.5.0: add UnZip builddependency --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 2 +- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index edb84d52b2..b8e0b20e47 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 230444abd3..7c571141ea 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), From 13a52311b014ec61b10a1c06878eeb3f30687900 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Sep 2021 13:21:50 +0200 Subject: [PATCH 1526/2365] TensorFlow 2.4.1: add UnZip builddependency --- .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 2 +- .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index ed118dbbdd..2c463ccdf3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index a9a6494a69..34a3a4c37f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), From 6cb8e3c75a23351d15591bb2bc0dff051b47a5c7 Mon Sep 17 00:00:00 2001 From: Guillaume Moutier Date: Fri, 10 Sep 2021 11:31:43 -0400 Subject: [PATCH 1527/2365] fix checksum for lhs R extension --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 94ed0c5800..911665c64d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -1493,7 +1493,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.1', { 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index f0423aca3a..2f3e45e81f 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -1502,7 +1502,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.1', { 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index af85bdbea5..2629887653 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -1521,7 +1521,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 2fa4574e87..2bd26acea1 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -1525,7 +1525,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 10ac6803fa..aa82021528 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -1533,7 +1533,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index a4b7463583..caaf872995 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -1543,7 +1543,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], From 63bfb9b4a51b0d53720454c06cf071c53d41baa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Sep 2021 21:57:25 +0200 Subject: [PATCH 1528/2365] accept both valid SHA256 checksums for lhs 1.1.1 extension in recent R easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 ++- 6 files changed, 12 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 911665c64d..d8bbd8572a 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -1493,7 +1493,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.1', { 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 2f3e45e81f..9e5053e29b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -1502,7 +1502,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.1', { 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 2629887653..e3dbbcb551 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -1521,7 +1521,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 2bd26acea1..9d9ad1166d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -1525,7 +1525,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index aa82021528..d1f3feab30 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -1533,7 +1533,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index caaf872995..2f1b150a61 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -1543,7 +1543,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], From fd9d61b1cf8492499e08ecbf172a4144d52a803c Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 11 Sep 2021 16:59:57 +0200 Subject: [PATCH 1529/2365] adding easyconfigs: abtem-1.0.0b24-fosscuda-2020b.eb, ASE-3.22.0-fosscuda-2020b.eb, imageio-2.9.0-fosscuda-2020b.eb --- .../a/ASE/ASE-3.22.0-fosscuda-2020b.eb | 47 +++++++++++++++++++ .../i/imageio/imageio-2.9.0-fosscuda-2020b.eb | 25 ++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..1754c068f5 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Flask', '1.1.2'), + ('matplotlib', '3.3.3'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['e60259c7b50867b1cb817caf938fcc1ed383702413df6d2e1afe7ea07f65acee'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..2213be1626 --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.9.0' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow', '8.0.1'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 58571999c577b069410275ed653805143ae2f68b Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 11 Sep 2021 17:28:10 +0200 Subject: [PATCH 1530/2365] Removing check_ldshared as suggested by @boegel --- easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb | 4 ---- .../easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb | 3 --- 2 files changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb index a31426b7e1..e1212c2381 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb @@ -24,10 +24,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -# required because we're building Python packages (MarkupSafe, -# ase-ext) using Intel compilers on top of Python built with GCC. -check_ldshared = True - exts_list = [ ('pytest-mock', '3.6.1', { 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb index 362e25c782..bedc11e904 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -40,9 +40,6 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -# required because we're building a Python package using Intel compilers on top of Python built with GCC. -check_ldshared = True - sanity_check_paths = { 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', '-runscript', '-setup', '-upfplot']], From 0ce788cc3468f4f6902a23e3ff6fafb8803603d7 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 13 Sep 2021 11:03:17 +0200 Subject: [PATCH 1531/2365] adding easyconfigs: OrthoFinder-2.5.4-foss-2020b.eb --- .../OrthoFinder-2.5.4-foss-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb new file mode 100644 index 0000000000..3c6475ccad --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'OrthoFinder' +version = '2.5.4' + +homepage = 'https://github.com/davidemms/OrthoFinder' +description = "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'davidemms' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9d8bd52426ebab4a5f377f8699cc9ee16559152830c9a67229c2ba81326d3f51'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('BLAST+', '2.11.0'), + ('DIAMOND', '2.0.7'), + ('FastME', '2.1.6.1'), + ('MCL', '14.137'), + ('MMseqs2', '13-45111'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'scripts_of'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['convert_orthofinder_tree_ids', 'make_ultrametric', 'orthofinder', + 'primary_transcript']], + 'dirs': ['ExampleData', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["orthofinder --help"] + +moduleclass = 'bio' From 237c5ea19ae90502fa7092513a8903fbe800cb3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Sep 2021 11:29:16 +0200 Subject: [PATCH 1532/2365] remove binutils build dependency, since GCC toolchain is used MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb index 7b8029d378..d835df6e32 100644 --- a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb @@ -13,7 +13,6 @@ sources = ['FastME-v%(version)s.tar.gz'] checksums = ['fae0609576873cb137ad4f63529b3ccba8f747b857c23c7870236aba440076ca'] builddependencies = [ - ('binutils', '2.35'), ('Autotools', '20200321'), ] From 4f8287c3e8c733b9ef0ee29df0d2b57c85cdf937 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Sep 2021 11:42:39 +0200 Subject: [PATCH 1533/2365] reuse existing easyconfigs for DIAMOND 2.0.7 and MMseqs2 13-45111 as dependencies for OrthoFinder 2.5.2 --- .../easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb index ff9a4ad647..abe97dde5d 100644 --- a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb @@ -17,10 +17,10 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('BLAST+', '2.11.0'), - ('DIAMOND', '2.0.6'), + ('DIAMOND', '2.0.7'), ('FastME', '2.1.6.1'), ('MCL', '14.137'), - ('MMseqs2', '12-113e3'), + ('MMseqs2', '13-45111'), ] download_dep_fail = True From 10b67a636fe427243284b9e896e2f534beee57a3 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 13 Sep 2021 16:38:25 +0200 Subject: [PATCH 1534/2365] adding easyconfigs: isoCirc-1.0.4-foss-2020b.eb --- .../i/isoCirc/isoCirc-1.0.4-foss-2020b.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb new file mode 100644 index 0000000000..7f0bf29567 --- /dev/null +++ b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'isoCirc' +version = '1.0.4' + +homepage = 'https://github.com/Xinglab/isoCirc' +description = """isoCirc: computational pipeline to identify high-confidence +BSJs and full-length circRNA isoforms from isoCirc long-read data +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Pysam', '0.16.0.1'), + ('pybedtools', '0.8.2'), + ('minimap2', '2.18'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('argcomplete', '1.12.3', { + 'checksums': ['2c7dbffd8c045ea534921e63b0be6fe65e88599990d8dc408ac8c542b72a5445'], + }), + ('argh', '0.26.2', { + 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], + }), + ('crlibm', '1.0.3', { + 'checksums': ['48e17981f90d69c6bb0013f68bacbe7a157de864a533d15dd196ca7e98348a35'], + }), + ('gffutils', '0.10.1', { + 'checksums': ['a8fc39006d7aa353147238160640e2210b168f7849cb99896be3fc9441e351cb'], + }), + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], + }), + ('pyfaidx', '0.6.2', { + 'checksums': ['d1258f8d053cba0c90fe329254e8ec59eb28b535b48d9d06e8c7f1d74b8e4531'], + }), + ('pyinterval', '1.2.0', { + 'modulename': 'interval', + 'checksums': ['8c46224a05815affa803ed5620432236bba620a246701b860d98ae7358a41d21'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/Xinglab/isoCirc/archive'], + 'start_dir': 'isoCirc_pipeline', + 'checksums': ['c5879820d7e61b4fc25a4357df8967d65f6d6c05aff705d5338a16707ffa849d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['isocirc', 'isocircPlot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "isocirc --help", + ( + "cd %(builddir)s/%(name)s/%(name)s-%(version)s/test_data && " + "isocirc -t 1 read_toy.fa chr16_toy.fa chr16_toy.gtf chr16_circRNA_toy.bed output" + ), +] + +moduleclass = 'bio' From bcce7022b4bff366bdb562d34649c103e3caffc6 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 14 Sep 2021 09:44:40 +0200 Subject: [PATCH 1535/2365] adding easyconfigs: CIRI-long-1.0.2-foss-2020b.eb --- .../c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb new file mode 100644 index 0000000000..1a6d54aa7e --- /dev/null +++ b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'CIRI-long' +version = '1.0.2' + +homepage = 'https://github.com/bioinfo-biols/CIRI-long/' +description = "Circular RNA Identification for Long-Reads Nanopore Sequencing Data" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('Pysam', '0.16.0.1'), + ('minimap2', '2.18'), + ('Cython', '0.29.22'), + ('SAMtools', '1.12'), + ('Biopython', '1.78'), + ('pyspoa', '0.0.8'), +] + +use_pip = True + +exts_list = [ + ('mappy', '2.17', { + 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], + }), + ('python-Levenshtein', '0.12.1', { + 'modulename': 'Levenshtein', + 'checksums': ['554e273a88060d177e7b3c1e6ea9158dde11563bfae8f7f661f73f47e5ff0911'], + }), + ('bwapy', '0.1.4', { + 'checksums': ['fcdad0c7311753d550b3a3aefbc2619380e7e35e7aeaa386fd491cba47e71824'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + (name, version, { + 'modulename': 'CIRI_long', + 'preinstallopts': "make lib && sed -i '/install_requires/,+4d' setup.py && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/bioinfo-biols/CIRI-long/archive'], + 'checksums': ['4c83d18fb147cc37be99b79f94acbbc24caa9954286afc8ff24058a9db7e9e48'], + }), +] + +sanity_check_paths = { + 'files': ['bin/CIRI-long'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'cd %(builddir)s/CIRIlong/%(name)s-%(version)s && make test', + 'CIRI-long --help', +] +sanity_pip_check = True + +moduleclass = 'bio' From 91ea3c2c326b76713ecfdba6f5784a23c02838b8 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 14 Sep 2021 09:52:43 +0200 Subject: [PATCH 1536/2365] isoCirc: don't use download_dep_fail --- easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb index 7f0bf29567..be32d45ae9 100644 --- a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb @@ -21,8 +21,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True -sanity_pip_check = True exts_list = [ ('argcomplete', '1.12.3', { @@ -59,7 +57,6 @@ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['isocirc', 'isocircPlot']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } - sanity_check_commands = [ "isocirc --help", ( @@ -67,5 +64,6 @@ sanity_check_commands = [ "isocirc -t 1 read_toy.fa chr16_toy.fa chr16_toy.gtf chr16_circRNA_toy.bed output" ), ] +sanity_pip_check = True moduleclass = 'bio' From c19d8ac31c03f9384671984d2b05d0e178b3797c Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 14 Sep 2021 10:09:04 +0200 Subject: [PATCH 1537/2365] CIRI-long: avoid multivariant deps --- easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb index 1a6d54aa7e..136959b5a0 100644 --- a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb @@ -15,7 +15,7 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('minimap2', '2.18'), ('Cython', '0.29.22'), - ('SAMtools', '1.12'), + ('SAMtools', '1.11'), ('Biopython', '1.78'), ('pyspoa', '0.0.8'), ] From 6fc6bd3eb5b6bf26c5e631369a783548b40aec4c Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 14 Sep 2021 11:33:59 +0200 Subject: [PATCH 1538/2365] Fix name, homepage, description. Patch issue 53. Patch multithreading --- ...bTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..bbc631dca5 --- /dev/null +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'abTEM' +version = '1.0.0b24' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/abTEM' +description = """abTEM provides a Python API for running simulations +of Transmission Electron Microscopy images.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch', + 'abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch', +] +checksums = [ + '503e7775f9764cf8298cbd2d06c4a36a9c83efbd84d58721eee638adfd1e626e', # abtem-1.0.0b24.tar.gz + # abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch + '49eee97f444ff16b45745adcd70dbbf63d5ddb842d7d6539ec303f388b4293da', + '0d4a0500e4947e4967858e6644969796d5bd76bc556a9c09fdc80461dcbcaed6', # abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('h5py', '3.1.0'), + ('numba', '0.53.1'), + ('pyFFTW', '0.12.0'), + ('tqdm', '4.56.2'), + ('imageio', '2.9.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 97df40102cf4055ba2d7879b11058b8683c87110 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Sep 2021 12:04:22 +0200 Subject: [PATCH 1539/2365] use proper dependency for python-Levenshtein in CIRI-long easyconfig --- .../c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb | 8 +----- .../python-Levenshtein-0.12.1-foss-2020b.eb | 25 +++++++++++++++++++ 2 files changed, 26 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb index 136959b5a0..a52d587933 100644 --- a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb @@ -18,6 +18,7 @@ dependencies = [ ('SAMtools', '1.11'), ('Biopython', '1.78'), ('pyspoa', '0.0.8'), + ('python-Levenshtein', '0.12.1'), ] use_pip = True @@ -26,16 +27,9 @@ exts_list = [ ('mappy', '2.17', { 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], }), - ('python-Levenshtein', '0.12.1', { - 'modulename': 'Levenshtein', - 'checksums': ['554e273a88060d177e7b3c1e6ea9158dde11563bfae8f7f661f73f47e5ff0911'], - }), ('bwapy', '0.1.4', { 'checksums': ['fcdad0c7311753d550b3a3aefbc2619380e7e35e7aeaa386fd491cba47e71824'], }), - ('nose', '1.3.7', { - 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], - }), (name, version, { 'modulename': 'CIRI_long', 'preinstallopts': "make lib && sed -i '/install_requires/,+4d' setup.py && ", diff --git a/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb new file mode 100644 index 0000000000..9934a63e08 --- /dev/null +++ b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'python-Levenshtein' +version = '0.12.1' + +homepage = 'https://pypi.org/project/python-Levenshtein/' +description = 'Python extension for computing string edit distances and similarities.' + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['554e273a88060d177e7b3c1e6ea9158dde11563bfae8f7f661f73f47e5ff0911'] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'Levenshtein'} + +sanity_pip_check = True + +moduleclass = 'data' From b57893787fb9c19da50a319ec979d8bae797bad8 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 14 Sep 2021 12:59:21 +0200 Subject: [PATCH 1540/2365] isoCirc: use packaged pyfaidx --- easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb index be32d45ae9..1e5a19bc40 100644 --- a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb @@ -18,6 +18,7 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('pybedtools', '0.8.2'), ('minimap2', '2.18'), + ('pyfaidx', '0.5.9.5'), ] use_pip = True @@ -38,9 +39,6 @@ exts_list = [ ('mappy', '2.20', { 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], }), - ('pyfaidx', '0.6.2', { - 'checksums': ['d1258f8d053cba0c90fe329254e8ec59eb28b535b48d9d06e8c7f1d74b8e4531'], - }), ('pyinterval', '1.2.0', { 'modulename': 'interval', 'checksums': ['8c46224a05815affa803ed5620432236bba620a246701b860d98ae7358a41d21'], From 2b985280c7581c978b3e2d53da5b242c00972d2e Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Wed, 15 Sep 2021 10:56:06 +0200 Subject: [PATCH 1541/2365] adding easyconfigs: longread_umi-0.3.2-foss-2020b.eb, VSEARCH-2.18.0-GCC-10.2.0.eb, Racon-1.4.13-GCCcore-10.2.0.eb, medaka-1.4.3-foss-2020b.eb, cutadapt-3.4-GCCcore-10.2.0.eb, edlib-1.3.9-GCC-10.2.0.eb, python-isal-0.11.0-GCCcore-10.2.0.eb, ISA-L-2.30.0-GCCcore-10.2.0.eb and patches: Racon-1.4.13-std_invalid_argument.patch --- .../c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb | 52 ++++++++++++ .../e/edlib/edlib-1.3.9-GCC-10.2.0.eb | 22 ++++++ .../i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb | 46 +++++++++++ .../longread_umi-0.3.2-foss-2020b.eb | 79 +++++++++++++++++++ .../m/medaka/medaka-1.4.3-foss-2020b.eb | 77 ++++++++++++++++++ .../v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb | 40 ++++++++++ 6 files changed, 316 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..64cfa8b253 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb @@ -0,0 +1,52 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '3.4' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('python-isal', '0.11.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + ('dnaio', '0.5.1', { + 'checksums': ['c68ecffbf653dfe122f1c10fb8d7c5957ad68acc5c9035c66f81eba1a591d31c'], + }), + (name, version, { + 'checksums': ['eb8d52d45a7d38bd3ddc901eb397599bca8716a20d39e2b1feeb20242352dab2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cutadapt --help", "cutadapt --version"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb new file mode 100644 index 0000000000..e79e34bf1e --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'edlib' +version = '1.3.9' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766'] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..df76b6b84f --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.30.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['bcf592c04fdfa19e723d2adf53d3e0f4efd5b956bb618fed54a1108d76a6eb56'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [('NASM', '2.15.05')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +_bins = ['bin/igzip'] +_includes = ['include/%(namelower)s.h'] +_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test', 'types']] +_libs = ['lib/libisal.%s' % l for l in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _bins + _includes + _libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb new file mode 100644 index 0000000000..dc667caa8c --- /dev/null +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -0,0 +1,79 @@ +easyblock = 'Bundle' + +name = 'longread_umi' +version = '0.3.2' + +homepage = 'https://github.com/SorenKarst/longread_umi' +description = "A collection of scripts for processing longread UMI data." +github_account = 'SorenKarst' + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('cutadapt', '3.4'), + ('BCFtools', '1.11'), + ('BWA', '0.7.17'), + ('Filtlong', '0.2.0'), + ('gawk', '5.1.0'), + ('medaka', '1.4.3'), + ('minimap2', '2.18'), + ('parallel', '20210322'), + ('Pysam', '0.16.0.1'), + ('Racon', '1.4.13'), + ('SAMtools', '1.11'), + ('seqtk', '1.3'), + ('VSEARCH', '2.18.0'), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'], + 'start_dir': '%(name)s-%(version)s', + }), + ('Porechop', '0.2.4', { + 'easyblock': 'PythonPackage', + 'source_urls': ['https://github.com/rrwick/Porechop/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +# Adapt the build-in tool check, but make it fail on error +local_deps_patch = ( + "sed -i" + "-e '2s;^;set -e ;' " + "-e 's/USEARCH=usearch/USEARCH=vsearch/'" + "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;'" + "%(installdir)s/scripts/dependencies.sh" +) + +postinstallcmds = [ + 'find %(installdir)s -name "*.sh" -exec chmod +x {} \;', + 'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi', + 'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/', + local_deps_patch, +] + +sanity_check_paths = { + 'files': ['bin/longread_umi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'longread_umi -h | grep qc_pipeline', + 'longread_umi nanopore_pipeline -h | grep rrna_operon', + 'source %(installdir)s/scripts/dependencies.sh && longread_umi_version_dump', +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb new file mode 100644 index 0000000000..e789ea6b68 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -0,0 +1,77 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.4.3' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('Python', '3.8.6'), + ('TensorFlow', '2.5.0'), + ('Biopython', '1.78'), + ('h5py', '3.1.0'), + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.11'), + ('minimap2', '2.18'), + ('HTSlib', '1.11'), + ('Racon', '1.4.13'), + ('spoa', '4.0.7'), + ('networkx', '2.5'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.8'), + ('ont-fast5-api', '3.3.0'), + ('pyfaidx', '0.5.9.5'), + ('python-isal', '0.11.0'), +] + +use_pip = True + +exts_list = [ + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], + }), + ('parasail', '1.2.4', { + 'checksums': ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'], + }), + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + ('whatshap', '1.1', { + 'checksums': ['4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + (name, version, { + 'patches': ['medaka-1.4.3_use-SAMtools-dep.patch'], + 'preinstallopts': 'sed -i -e "s/h5py<3.0.0/h5py/" -e "s/tensorflow==2.2.2/tensorflow/" requirements.txt &&', + 'checksums': [ + '59997b5fdaff6f2040f2df2d3d3eb2d6d1805916a720e8275309caf4d2d4b8a5', # medaka-1.4.3.tar.gz + '06b1d8344035ebcfaf1893e62f37db9b4cab0053ad7a073113630872d44be33e', # medaka-1.4.3_use-SAMtools-dep.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["medaka --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..0e0ca81463 --- /dev/null +++ b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'VSEARCH' +version = '2.18.0' + +homepage = 'https://github.com/torognes/vsearch' +description = """VSEARCH supports de novo and reference based chimera detection, + clustering, full-length and prefix dereplication, rereplication, + reverse complementation, masking, all-vs-all pairwise global alignment, + exact and global alignment searching, shuffling, subsampling and sorting. + It also supports FASTQ file analysis, filtering, + conversion and merging of paired-end reads.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/torognes/vsearch/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['faa585ec2767e15a8ad3c2b78921b789a3b174fe3b0eecb3397b1c795808e982'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-pdfman ' + +sanity_check_paths = { + 'files': ['bin/vsearch'], + 'dirs': [], +} + +sanity_check_commands = ['vsearch --help'] + +moduleclass = 'bio' From e3ea5d035455b8f265c20df96200097659c59b36 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 12:26:50 +0000 Subject: [PATCH 1542/2365] ETE bumped to 3.1.2, required for artic --- .../easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb new file mode 100644 index 0000000000..f4d0c02af9 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.2' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +checksums = ['4fc987b8c529889d6608fab1101f1455cb5cbd42722788de6aea9c7d0a8e59e9'] + +dependencies = [ + ('lxml', '4.6.2'), + ('Python', '3.8.6'), + ('PyQt5', '5.15.1'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From 4f9c812212656fa9c6525e37a6645da85449a9a6 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 12:36:31 +0000 Subject: [PATCH 1543/2365] {bio}[GCCcore/10.2.0] LSD2 bumped to 2.2, required for artic #13852 --- .../l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..82407cd707 --- /dev/null +++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'LSD2' +version = '2.2' + +homepage = 'https://github.com/tothuhien/lsd2' +description = "Least-squares methods to estimate rates and dates from phylogenies" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'tothuhien' + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v.%(version)s.tar.gz'] +patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch'] +checksums = [ + '6573398d0e77bc5fe76587d8676428b77fe15fe6e45fb8526f448d1c739d3cd9', # v.2.2.tar.gz + # LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch + '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6', +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 45811fd418231eb73e359d956d186cbb406e901b Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 13:36:43 +0000 Subject: [PATCH 1544/2365] {bio}[GCCcore/10.2.0] Longshot bumped to 0.4.3, required for artic #13852 --- .../Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..07d70a35c9 --- /dev/null +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +# Updated to 0.4.3 and GCCcore-10.2.0 +# J. Sassmannshausen (GSTT/NHS UK) +# +easyblock = 'Binary' + +name = 'Longshot' +version = '0.4.3' + +homepage = 'https://github.com/pjedge/longshot' +description = """Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific + Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs + a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can + be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/pjedge/longshot/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb2a27a165567ed10b43eb915b195d72193005008d6a91e0d9393282f22f3192'] + +builddependencies = [ + ('binutils', '2.35'), + ('Rust', '1.52.1'), + ('Clang', '11.0.1'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +extract_sources = True + +install_cmd = "cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From ddd6b974b8d48ea9774deb61c7434aff9308da19 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 13:40:18 +0000 Subject: [PATCH 1545/2365] {bio}[GCCcore/10.2.0] Muscle bumped to 3.8.31, required for artic #13852 --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6487d58f18 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' From fe1c53df108c2adb7557c3752659be0c1b753484 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 13:43:12 +0000 Subject: [PATCH 1546/2365] {bio}[GCCcore/10.2.0] Racon bumped to 1.4.21, required for artic #13852 --- .../r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dfa9bddcee --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.4.21' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/lbcb-sci/racon/releases/download/%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['df99208ebef6a12e1da11a31dade2eafe13a4cd80b4917cce44d44d879b5aee4'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' From 0ed2ec9a172f0f980e544d5680549f8e49a6ab9a Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 13:55:03 +0000 Subject: [PATCH 1547/2365] {lang}[GCCcore/10.2.0] Rust bumped to 1.52.1, required for artic #13852 --- .../r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c8843bcda9 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.52.1' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +checksums = ['3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' From 3d78b7a9109fb33cec66b658e00354c91c13aa17 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 13:57:14 +0000 Subject: [PATCH 1548/2365] {bio}[GCCcore/10.2.0] edlib bumped to 1.3.9, required for artic #13852 --- .../e/edlib/edlib-1.3.9-GCC-10.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb new file mode 100644 index 0000000000..e79e34bf1e --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'edlib' +version = '1.3.9' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766'] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' From af34022f86052e18229abf5ebc0bd166621ecef7 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 14:00:06 +0000 Subject: [PATCH 1549/2365] {tools}[foss/2020b] networkx bumped to 2.6.2, required for artic #13852 --- .../n/networkx/networkx-2.6.2-foss-2020b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb new file mode 100644 index 0000000000..8a5bed3a71 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.6.2' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2306f1950ce772c5a59a57f5486d59bb9cab98497c45fc49cbc45ac0dec119bb'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 4adcf47ed858b89226071c1a8b5ce94593b5a956 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Sep 2021 16:59:28 +0200 Subject: [PATCH 1550/2365] make binutils a build-only dependency for Brotli + add sanity check command --- .../easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb index 72c9f12ad6..8626bb2733 100644 --- a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb @@ -1,4 +1,5 @@ easyblock = 'CMakeMake' + name = 'Brotli' version = '1.0.9' @@ -19,11 +20,8 @@ checksums = [ '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch ] -separate_build_dir = True - -dependencies = [('binutils', '2.35')] - builddependencies = [ + ('binutils', '2.35'), ('CMake', '3.18.4'), ] @@ -33,4 +31,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["brotli --help"] + moduleclass = 'lib' From f4ea19c36f900ba0c7b64c80d970d5c1dc9b4eea Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 16:22:47 +0000 Subject: [PATCH 1551/2365] Included TF-2.2.3, patched to remove the hard-coded TF version --- .../m/medaka/medaka-1.4.3-foss-2020b.eb | 33 ++++++++++++++++--- 1 file changed, 28 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index b82b55027f..8c4f387a62 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -19,10 +19,10 @@ builddependencies = [('Autotools', '20200321')] dependencies = [ ('Python', '3.8.6'), # includes cffi - # TensorFlow 2.2.2 required by medaka 1.4.3, see requirements.txt - ('TensorFlow', '2.2.2'), + # TensorFlow 2.2.3 required by medaka 1.4.3, see requirements.txt + # We need to patch medaka to use that version, see below. + ('TensorFlow', '2.2.3'), ('Biopython', '1.78'), - ('h5py', '3.1.0'), # Pysam 0.16.0.1 is strictly required, see requirements.txt ('Pysam', '0.16.0.1'), ('SAMtools', '1.12'), @@ -34,13 +34,32 @@ dependencies = [ ('networkx', '2.6.2'), ('edlib', '1.3.9'), ('pyspoa', '0.0.8'), - ('ont-fast5-api', '3.3.0'), ('pyfaidx', '0.5.9.5'), ] use_pip = True +sanity_pip_check = True exts_list = [ + # TF <= 2.4 needs h5py 2.10, later versions allow 3.x + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + # h5py-2.10.0_avoid-mpi-init.patch + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', + ], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + }), + # This is a requirement for ont-fast5-api below + ('progressbar33', '2.4', { + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + # ont-fast-5-api in EB uses h5py-3.x, but see above. So we put it here + ('ont-fast5-api', '3.3.0', { + 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], + }), ('mappy', '2.20', { 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], }), @@ -63,10 +82,14 @@ exts_list = [ 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], }), (name, version, { - 'patches': ['medaka-1.4.3_use-SAMtools-dep.patch'], + 'patches': [ + 'medaka-1.4.3_use-SAMtools-dep.patch', + 'medaka-1.4.3-TF-version-fix.patch', + ], 'checksums': [ '59997b5fdaff6f2040f2df2d3d3eb2d6d1805916a720e8275309caf4d2d4b8a5', # medaka-1.4.3.tar.gz '06b1d8344035ebcfaf1893e62f37db9b4cab0053ad7a073113630872d44be33e', # medaka-1.4.3_use-SAMtools-dep.patch + 'cdafcd05150a8193747d8d240d9b2d3499ae901483917e9252bb91b02fa56b03', # medaka-1.4.3-TF-version-fix.patch ], }), ] From eefa2966625f0cf388c0b109c2e7225e8b94b273 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 16:51:40 +0000 Subject: [PATCH 1552/2365] Added missing binutils --- .../easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb index 6487d58f18..2230dff6fc 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb @@ -20,6 +20,10 @@ checksums = [ '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch ] +builddependencies = [ + ('binutils', '2.35'), +] + files_to_copy = [ (["muscle"], 'bin')] From 0e1758365645d6cb6c66834902c62d5f03148c8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 11:05:42 +0200 Subject: [PATCH 1553/2365] don't install h5py 2.10.0 as extension in medaka easyconfig, already included with TensorFlow 2.2.3 --- .../m/medaka/medaka-1.4.3-foss-2020b.eb | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 8c4f387a62..17bab30f8a 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -41,22 +41,13 @@ use_pip = True sanity_pip_check = True exts_list = [ - # TF <= 2.4 needs h5py 2.10, later versions allow 3.x - ('h5py', '2.10.0', { - 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], - 'checksums': [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - # h5py-2.10.0_avoid-mpi-init.patch - '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', - ], - 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', - }), - # This is a requirement for ont-fast5-api below + # required for ont-fast5-api ('progressbar33', '2.4', { 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], 'modulename': 'progressbar', }), - # ont-fast-5-api in EB uses h5py-3.x, but see above. So we put it here + # ont-fast-5-api easyconfig depends on h5py but we need to stick to h5py 2.x for TensorFlow 2.2.3, + # so we install it as an extension here ('ont-fast5-api', '3.3.0', { 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], }), From d8f2a30139737a8296e4db343d8c77c5e72bd0df Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 09:15:12 +0000 Subject: [PATCH 1554/2365] adding easyconfigs: rampart-1.2.0-foss-2020b.eb --- .../r/rampart/rampart-1.2.0-foss-2020b.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb b/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb new file mode 100644 index 0000000000..e4b3d5e9c7 --- /dev/null +++ b/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb @@ -0,0 +1,67 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# updated to version 1.0.6 +# J. Sassmannshausen (GSTT(NHS) +# +easyblock = 'PythonBundle' + +name = 'rampart' +version = '1.2.0' + +homepage = "https://github.com/artic-network/rampart/" +description = "Read Assignment, Mapping, and Phylogenetic Analysis in Real Time." +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('nodejs', '12.19.0'), + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('snakemake', '6.1.0'), + ('minimap2', '2.20'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + # This is not upstream version, but artic tweaked one, which is exactly required. + ('Porechop', '0.3.2pre', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/Porechop/archive'], + 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], + }), + ('binlorry', '1.3.1', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/rambaut/binlorry/archive'], + 'checksums': ['001b74cad497b7253b821ceaac8c0b829b2787396a896fc2d3940a704a149b48'], + }), +] + +# Don't ever try to install unpacked source of nodejs globally! +# Always use 'npm install -g downloaded_file.tar.gz` or you will end up having broken links and installation will fail. +# -d (debug) and --timing can show errors while downloading dependencies +local_install_cmd = "npm install -d --timing --prefix %(installdir)s -g v%(version)s.tar.gz" + +components = [ + (name, version, { + 'easyblock': 'Binary', + 'source_urls': ['https://github.com/artic-network/rampart/archive/'], + 'sources': [{ + 'filename': 'v%(version)s.tar.gz', + # Don't extract downloaded .tar.gz, just copy that to builddir + 'extract_cmd': "cp %s .", + }], + 'checksums': ['96dc10a429e39c1ab241a76c4706a50754908f79f821b5d047be7f420aaf15be'], + 'install_cmd': local_install_cmd, + }), +] + +sanity_check_paths = { + 'files': ['bin/binlorry', 'bin/porechop', 'bin/rampart'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'rampart --help' +] + +moduleclass = 'bio' From 502f4c558b50c82bb20b11397143748d9ff0d39a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 11:19:24 +0200 Subject: [PATCH 1555/2365] replace patch by sed command in preinstallopts to loosen up TensorFlow version requirement for medaka --- .../easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 17bab30f8a..c6ebdb1694 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -38,7 +38,6 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True exts_list = [ # required for ont-fast5-api @@ -73,15 +72,13 @@ exts_list = [ 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], }), (name, version, { - 'patches': [ - 'medaka-1.4.3_use-SAMtools-dep.patch', - 'medaka-1.4.3-TF-version-fix.patch', - ], + 'patches': ['medaka-1.4.3_use-SAMtools-dep.patch'], 'checksums': [ '59997b5fdaff6f2040f2df2d3d3eb2d6d1805916a720e8275309caf4d2d4b8a5', # medaka-1.4.3.tar.gz '06b1d8344035ebcfaf1893e62f37db9b4cab0053ad7a073113630872d44be33e', # medaka-1.4.3_use-SAMtools-dep.patch - 'cdafcd05150a8193747d8d240d9b2d3499ae901483917e9252bb91b02fa56b03', # medaka-1.4.3-TF-version-fix.patch ], + # loosen up TensorFlow version requirements, see also https://github.com/nanoporetech/medaka/issues/323 + 'preinstallopts': "sed -i 's/tensorflow==/tensorflow~=/g' requirements.txt && ", }), ] From a4d91563f4872bf148f4c95b5958cd344c3ecced Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 11:29:11 +0200 Subject: [PATCH 1556/2365] add Python + pkg-config as build dependencies for Rust 1.52.1 with GCCcore/10.2.0 --- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index c8843bcda9..2e64f84446 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -16,6 +16,8 @@ checksums = ['3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98'] builddependencies = [ ('binutils', '2.35'), ('CMake', '3.18.4'), + ('Python', '3.8.6'), + ('pkg-config', '0.29.2'), ] dependencies = [ From 9ad83a3f90688f5d5fa2fba37968fb5b0ce9f40b Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 09:42:30 +0000 Subject: [PATCH 1557/2365] minimap downgraded to 2.18 for consistency --- easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb b/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb index e4b3d5e9c7..841aded314 100644 --- a/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.8.6'), ('Biopython', '1.78'), ('snakemake', '6.1.0'), - ('minimap2', '2.20'), + ('minimap2', '2.18'), ] use_pip = True From 51ee1044775d072d81aaf77a45c608571c40c4d6 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 09:48:05 +0000 Subject: [PATCH 1558/2365] adding easyconfigs: Eigen-3.3.9-GCCcore-10.2.0.eb --- .../e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..749a4d82e8 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.3.9' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['0fa5cafe78f66d2b501b43016858070d52ba47bd9b1016b0165a7b8e04675677'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.35'), # to make CMake compiler health check pass on old systems + ('CMake', '3.18.4'), +] + +moduleclass = 'math' From 0f66682ac7a80b6b17a30fd1362217a6327cf6ca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Thu, 16 Sep 2021 11:27:54 +0100 Subject: [PATCH 1559/2365] Update medaka-1.4.3-foss-2020b.eb networkx version changed to 2.5 for consistency --- easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index c6ebdb1694..4cdca5b141 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -31,7 +31,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix, bgzip ('Racon', '1.4.21'), ('spoa', '4.0.7'), - ('networkx', '2.6.2'), + ('networkx', '2.5'), ('edlib', '1.3.9'), ('pyspoa', '0.0.8'), ('pyfaidx', '0.5.9.5'), From a446f4545759f78c80b56a5f3856daeaa18c7ed0 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 14:06:43 +0000 Subject: [PATCH 1560/2365] adding easyconfigs: python-parasail-1.2.4-foss-2020b.eb --- .../python-parasail-1.2.4-foss-2020b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb new file mode 100644 index 0000000000..cd8f3bb5c6 --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.2.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'] + +builddependencies = [ + ('parasail', '2.4.3'), +] +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' From ede0af2f599e9cc4d92446db0b202cbde984d43d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 17:30:38 +0200 Subject: [PATCH 1561/2365] stick to SAMtools 1.11 as dependency for medaka with foss/2020b --- easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 4cdca5b141..38b5e7d0ff 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -25,7 +25,7 @@ dependencies = [ ('Biopython', '1.78'), # Pysam 0.16.0.1 is strictly required, see requirements.txt ('Pysam', '0.16.0.1'), - ('SAMtools', '1.12'), + ('SAMtools', '1.11'), # minimap2 is version 2.18 in pangolin, so we need the same version here ('minimap2', '2.18'), ('HTSlib', '1.11'), # for tabix, bgzip From 5052cde8c2e99d83c4fc2b255f24f26b3c3c6e45 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 15:43:26 +0000 Subject: [PATCH 1562/2365] adding easyconfigs: PhyML-3.3.20200621-foss-2020b.eb --- .../p/PhyML/PhyML-3.3.20200621-foss-2020b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb new file mode 100644 index 0000000000..bb74149322 --- /dev/null +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated to version 3.3.20200621 +# J. Sassmannshausen (GSTT/NHS) + +easyblock = 'ConfigureMake' + +name = 'PhyML' +version = '3.3.20200621' + +homepage = 'https://github.com/stephaneguindon/phyml' +description = "Phylogenetic estimation using (Maximum) Likelihood" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/stephaneguindon/phyml/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8243923ee08c74cab609a4b086ade66c6156fc2b24450e2a500108dc644c867'] + +builddependencies = [ + ('Autoconf', '2.69'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = 'sh autogen.sh && ' + +configopts = ['--enable-phyml', '--enable-phytime', '--enable-phyrex', '--enable-mpi --enable-phyml'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/phyml', 'bin/phyml-mpi', 'bin/phyrex', 'bin/phytime'], + 'dirs': [] +} + +moduleclass = 'bio' From 1611c3bd363652db1c29712cad5b2bc1a411c64f Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 16:30:42 +0000 Subject: [PATCH 1563/2365] Corrected the --enable-mpi build --- easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb index bb74149322..92820f73d6 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb @@ -26,7 +26,7 @@ builddependencies = [ preconfigopts = 'sh autogen.sh && ' -configopts = ['--enable-phyml', '--enable-phytime', '--enable-phyrex', '--enable-mpi --enable-phyml'] +configopts = ['--enable-phyml', '--enable-phytime', '--enable-phyrex', '--enable-mpi '] parallel = 1 From d40799c562272e8ab874256cc1f05df0b31b3b30 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 17:58:56 +0000 Subject: [PATCH 1564/2365] Updated file to final version, corrected version or artic to 24.6.2020 --- .../artic-ncov2019-2021.06.24-foss-2020b.eb | 128 ++++++++++++++++++ 1 file changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb new file mode 100644 index 0000000000..f9836bd918 --- /dev/null +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -0,0 +1,128 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to latest version 24. Jun 2021 and bumped to foss-2020b +# to use it with pangolin +# J. Sassmannshausen (GSTT/NHS UK) + +easyblock = 'PythonBundle' + +name = 'artic-ncov2019' +local_commit = 'b3f2dda5e6d95bc1c5d95a04d4ef37d304479477' +version = '2021.06.24' + +homepage = "https://github.com/artic-network/artic-ncov2019" +description = """Initial implementation of an ARTIC bioinformatics platform +for nanopore sequencing of nCoV2019 novel coronavirus.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('Pysam', '0.16.0.1'), + ('BWA', '0.7.17'), + ('Eigen', '3.3.9'), + ('minimap2', '2.20'), + ('SAMtools', '1.12'), + ('MUSCLE', '3.8.31'), + ('ETE', '3.1.2'), + ('MAFFT', '7.475', '-with-extensions'), + ('IQ-TREE', '2.1.2'), + ('snakemake', '6.1.0'), + ('Longshot', '0.4.3'), + ('medaka', '1.4.3'), + ('python-parasail', '1.2.4'), + ('PhyML', '3.3.20200621'), + ('nodejs', '12.19.0'), + ('goalign', '0.3.2', '', True), + ('gotree', '0.4.0', '', True), + ('rampart', '1.2.0'), + ('libdeflate', '1.7'), + ('nanopolish', '0.13.3'), + ('seqtk', '1.3'), + ('BCFtools', '1.12'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('zipp', '3.5.0', { + 'checksums': ['f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4'], + }), + ('pluggy', '1.0.0', { + 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], + }), + ('py', '1.10.0', { + 'checksums': ['21b81bda15b66ef5e1a777a21c4dcd9c20ad3efd0b3f817e7a809035269e1bd3'], + }), + ('wcwidth', '0.2.5', { + 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], + }), + ('attrs', '21.2.0', { + 'modulename': 'attr', + 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], + }), + ('importlib-metadata', '4.8.1', { + 'modulename': 'importlib_metadata', + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['f284b3e11256ad1e5d03ab86bb2ccd6f5339688ff17a4d797a0fe7df326f23b1'], + }), + ('more-itertools', '8.9.0', { + 'modulename': 'more_itertools', + 'checksums': ['8c746e0d09871661520da4f1241ba6b908dc903839733c8203b552cffaf173bd'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('pytest', '6.2.5', { + 'checksums': ['131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89'], + }), + ('tqdm', '4.62.2', { + 'checksums': ['a4d6d112e507ef98513ac119ead1159d286deab17dffedd96921412c2d236ff5'], + }), + ('fieldbioinformatics', '1.2.1', { + 'modulename': False, + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], + 'checksums': ['74b5fdb18dca57e73fbe872c5c4e25c110e7826fac7a062f0eb0a5453e4e7b20'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('PyVCF', '0.6.8', { + 'modulename': 'vcf', + 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], + }), + ('ont-fast5-api', '3.1.1', { + 'modulename': 'ont_fast5_api', + 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], + }), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/artic-network/artic-ncov2019/archive/'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, + }], + 'checksums': ['ac0dbf7d29038ace8e24dc172ae4dbba9a76d6803809c8f28a9fa228f98aecb6'], + }), +] +local_artic_bins = [ + 'artic', 'artic_fasta_header', 'artic_make_depth_mask', 'artic_mask', 'artic_vcf_filter', 'artic_vcf_merge' +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_artic_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'artic -v', +] + +moduleclass = 'bio' From 7e3186df09ddabdddc37b34231c4bac1821655aa Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 18:36:51 +0000 Subject: [PATCH 1565/2365] Added missing artic_get_stats script --- .../a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index f9836bd918..87e4bb0201 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -115,7 +115,8 @@ components = [ }), ] local_artic_bins = [ - 'artic', 'artic_fasta_header', 'artic_make_depth_mask', 'artic_mask', 'artic_vcf_filter', 'artic_vcf_merge' + 'artic', 'artic_fasta_header', 'artic_get_stats', 'artic_make_depth_mask', + 'artic_mask', 'artic_vcf_filter', 'artic_vcf_merge' ] sanity_check_paths = { 'files': ['bin/%s' % f for f in local_artic_bins], From b2bd39613a0535e97be95935331246875aa91077 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 20:57:22 +0200 Subject: [PATCH 1566/2365] update mappy + isal extensions in medaka 1.4.3 easyconfig using foss/2020b --- easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 38b5e7d0ff..2de5d46e27 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -50,14 +50,14 @@ exts_list = [ ('ont-fast5-api', '3.3.0', { 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], }), - ('mappy', '2.20', { - 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], + ('mappy', '2.22', { + 'checksums': ['219c93ab7f8d5d7c26face512a9e738a7306f3376ebfa3017eac70676ba97840'], }), ('parasail', '1.2.4', { 'checksums': ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'], }), - ('isal', '0.10.0', { - 'checksums': ['3f89471065c2837d1235877dbdcdbd8b7649068723026b0582010fa106a71ff3'], + ('isal', '0.11.1', { + 'checksums': ['8d07a07caacc3be4f478ceff8353941f360f922e8854ff1cbee4a44b443eb2af'], }), ('xopen', '1.1.0', { 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], From abff12392da3b8c514918f223b5411bc69112b85 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 17 Sep 2021 15:26:11 +0200 Subject: [PATCH 1567/2365] Fix TensorFlow 2.2.3 on PPC --- .../easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index d1d6fc11dc..c6b0c25ff6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -155,6 +155,7 @@ exts_list = [ 'TensorFlow-2.1.0_fix-system-nasm.patch', 'TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch', 'TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch', + 'TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch', 'TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch', 'TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', @@ -169,6 +170,8 @@ exts_list = [ '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', # TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch '85c3023892e21692e14750e43a7d1db3c83c6e86a75ac1559c9dba39e0a160ae', + # TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch + '23223e2f27677c9485ccb9ee8cae7818109ad600a83cc5514fbf7a9a4a0d719f', # TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch 'd80e0103aeefb5244b57dd0e01bb7a0c1e6a750fba41833706547be87d3829e4', # TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch From 1237c1162303c864e136cc94c053cd704c7ea0cd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 17 Sep 2021 15:33:09 +0200 Subject: [PATCH 1568/2365] Fix checksum --- .../easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index c6b0c25ff6..9678677ff3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -171,7 +171,7 @@ exts_list = [ # TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch '85c3023892e21692e14750e43a7d1db3c83c6e86a75ac1559c9dba39e0a160ae', # TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch - '23223e2f27677c9485ccb9ee8cae7818109ad600a83cc5514fbf7a9a4a0d719f', + '6e845c44c27477740d16e9c525cdd4c2a96ac3deb2709ac62e21c3de79c4583b', # TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch 'd80e0103aeefb5244b57dd0e01bb7a0c1e6a750fba41833706547be87d3829e4', # TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch From 8172c9506143eb245ec7317646cbd708e847eed6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 17:33:44 +0200 Subject: [PATCH 1569/2365] stick to gompi/2020b toolchain for IQ-TREE 2.1.2 --- .../i/IQ-TREE/IQ-TREE-2.1.2-gompi-2020b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-gompi-2020b.eb diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-gompi-2020b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-gompi-2020b.eb new file mode 100644 index 0000000000..9f3d8686a6 --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-gompi-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.1.2' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use_EB_LSD2.patch'] +checksums = [ + '3aaf5ac7f60d852ac8b733fb82832c049ca48b7203a6a865e99c5af359fcca5a', # v2.1.2.tar.gz + 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816', # IQ-TREE-2.1.2_use_EB_LSD2.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Eigen', '3.3.9'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.74.0'), + ('LSD2', '2.2'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = ["iqtree2 --help"] + +moduleclass = 'bio' From 2ad51b3076dc9c71a81b64fe500d7c9d68bc4613 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 17:48:29 +0200 Subject: [PATCH 1570/2365] bump python-isal to 0.11.1 (latest) and use in medaka 1.4.3 with foss/2020b --- .../m/medaka/medaka-1.4.3-foss-2020b.eb | 4 +-- .../python-isal-0.11.1-GCCcore-10.2.0.eb | 36 +++++++++++++++++++ 2 files changed, 37 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 2de5d46e27..6619e4a1e9 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -35,6 +35,7 @@ dependencies = [ ('edlib', '1.3.9'), ('pyspoa', '0.0.8'), ('pyfaidx', '0.5.9.5'), + ('python-isal', '0.11.1'), ] use_pip = True @@ -56,9 +57,6 @@ exts_list = [ ('parasail', '1.2.4', { 'checksums': ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'], }), - ('isal', '0.11.1', { - 'checksums': ['8d07a07caacc3be4f478ceff8353941f360f922e8854ff1cbee4a44b443eb2af'], - }), ('xopen', '1.1.0', { 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], }), diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8a7daf5569 --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '0.11.1' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'pycompression' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3959ce30f1043ae591bc9d6ee9edb5781c09cc15c69dd5361517d29b56327260'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('ISA-L', '2.30.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' +installopts = '--no-binary isal' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' From 0b8602a02a414096a892650702800b8efab39663 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 17:49:25 +0200 Subject: [PATCH 1571/2365] one sanity check command per line in cutadapt 3.4 easyconfigs --- .../easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb index 64cfa8b253..558e3819c5 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb @@ -47,6 +47,9 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["cutadapt --help", "cutadapt --version"] +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] moduleclass = 'bio' From cfb93727b9ea0eafbead21b58f7d5aae9dca64b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 20:23:31 +0200 Subject: [PATCH 1572/2365] bump dependency for python-isal to v0.11.1 + use dnaio 0.5.2 extension for cutadapt 3.4 --- .../easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb index 558e3819c5..f3ffcc20e0 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '3.8.6'), - ('python-isal', '0.11.0'), + ('python-isal', '0.11.1'), ] use_pip = True @@ -34,8 +34,8 @@ exts_list = [ ('xopen', '1.1.0', { 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], }), - ('dnaio', '0.5.1', { - 'checksums': ['c68ecffbf653dfe122f1c10fb8d7c5957ad68acc5c9035c66f81eba1a591d31c'], + ('dnaio', '0.5.2', { + 'checksums': ['549e1c6afa192a4bf79c112b57cc5e927b286ab9a3c2803d6577613a7e3ff180'], }), (name, version, { 'checksums': ['eb8d52d45a7d38bd3ddc901eb397599bca8716a20d39e2b1feeb20242352dab2'], From a27cb477787c00b028a598ec040b638539e0bd91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 20:24:20 +0200 Subject: [PATCH 1573/2365] bump Racon dependency to 1.4.21 in longread_umi 0.3.2 easyconfig --- .../easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index dc667caa8c..2ed9f132fb 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -20,7 +20,7 @@ dependencies = [ ('minimap2', '2.18'), ('parallel', '20210322'), ('Pysam', '0.16.0.1'), - ('Racon', '1.4.13'), + ('Racon', '1.4.21'), ('SAMtools', '1.11'), ('seqtk', '1.3'), ('VSEARCH', '2.18.0'), From 15944cd0746f95dc30347cbb3f1c5e27855bdbfd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 20:45:08 +0200 Subject: [PATCH 1574/2365] fix checksum in python-isal 0.11.1 easyconfig --- .../p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb index 8a7daf5569..a8d2cb81ce 100644 --- a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} github_account = 'pycompression' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['3959ce30f1043ae591bc9d6ee9edb5781c09cc15c69dd5361517d29b56327260'] +checksums = ['43d885814f1ee19f5c3a7e9ada3d696fe75f19c0853728fe0ade564bc021a78f'] builddependencies = [('binutils', '2.35')] From 7a5d662249d044fb6393a86ae1a364ed3977d95a Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 20 Sep 2021 12:16:31 +0000 Subject: [PATCH 1575/2365] Surplus ont-fast5-api module removed --- .../a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 87e4bb0201..706aca4a41 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -97,10 +97,6 @@ exts_list = [ 'modulename': 'vcf', 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], }), - ('ont-fast5-api', '3.1.1', { - 'modulename': 'ont_fast5_api', - 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], - }), ] components = [ From a4881f0f8d30d4858f8fe86176894f693f671877 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 20 Sep 2021 13:36:30 +0000 Subject: [PATCH 1576/2365] Downgraded SAMtools and BCFtools to 1.11, minimap2 to 2.18. Version for Eigen and TF need to stay as they are though (medaka)! --- .../artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 706aca4a41..085ca59dfe 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -22,8 +22,8 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('BWA', '0.7.17'), ('Eigen', '3.3.9'), - ('minimap2', '2.20'), - ('SAMtools', '1.12'), + ('minimap2', '2.18'), + ('SAMtools', '1.11'), ('MUSCLE', '3.8.31'), ('ETE', '3.1.2'), ('MAFFT', '7.475', '-with-extensions'), @@ -40,7 +40,7 @@ dependencies = [ ('libdeflate', '1.7'), ('nanopolish', '0.13.3'), ('seqtk', '1.3'), - ('BCFtools', '1.12'), + ('BCFtools', '1.11'), ] use_pip = True From 1c6ad7c42b77f9f10b80e64b635b6b2b7f994923 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 20 Sep 2021 14:42:21 +0000 Subject: [PATCH 1577/2365] Removed Eigen as dependency --- .../a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 085ca59dfe..6575f6de6e 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -21,7 +21,6 @@ dependencies = [ ('Biopython', '1.78'), ('Pysam', '0.16.0.1'), ('BWA', '0.7.17'), - ('Eigen', '3.3.9'), ('minimap2', '2.18'), ('SAMtools', '1.11'), ('MUSCLE', '3.8.31'), From 6e82ec2384868a6541c9ca4a5ab1bb881f98566c Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Mon, 20 Sep 2021 23:10:42 +0000 Subject: [PATCH 1578/2365] adding easyconfigs: vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb --- ...vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..3de8d93cef --- /dev/null +++ b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb @@ -0,0 +1,34 @@ + +easyblock = 'PackedBinary' + +name = 'vawk' +version = '0.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/cc2qe/vawk' +description = """An awk-like VCF parser +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '2.7.18'), +] + +source_urls = ['https://github.com/cc2qe/vawk/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['90cf5a57428ccaf3490ac98fc5c9f5f2c11ea2d1824188d9310bd34a8ef18d6f'] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env python' %(installdir)s/%(namelower)s", +] + +sanity_check_paths = { + 'files': ['vawk'], + 'dirs': [], +} + +sanity_check_commands = ["vawk -h"] + +moduleclass = 'bio' From df459ffa1d040e8fe806e41eb95c828f092fe72a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Tue, 21 Sep 2021 12:12:59 +0200 Subject: [PATCH 1579/2365] longread_umi: incorporate feedback --- .../l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index 2ed9f132fb..15db976ec6 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -46,9 +46,9 @@ components = [ }), ] -# Adapt the build-in tool check, but make it fail on error +# Adapt the built-in tool check but make it fail on error, replace usearch with vsearch and use our version local_deps_patch = ( - "sed -i" + "sed -i " "-e '2s;^;set -e ;' " "-e 's/USEARCH=usearch/USEARCH=vsearch/'" "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;'" @@ -58,6 +58,7 @@ local_deps_patch = ( postinstallcmds = [ 'find %(installdir)s -name "*.sh" -exec chmod +x {} \;', 'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi', + # Part of the installation process; longread uses porechop with custom adapters 'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/', local_deps_patch, ] From 81c06d25a2fcbc4821541447dc6e581044d15d46 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 21 Sep 2021 10:46:59 +0000 Subject: [PATCH 1580/2365] Removed apparently surplus Python modules as suggested, changed module name from False to artic --- .../artic-ncov2019-2021.06.24-foss-2020b.eb | 43 +++---------------- 1 file changed, 6 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 6575f6de6e..9aedc07f20 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -46,56 +46,25 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('zipp', '3.5.0', { - 'checksums': ['f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4'], - }), - ('pluggy', '1.0.0', { - 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], - }), - ('py', '1.10.0', { - 'checksums': ['21b81bda15b66ef5e1a777a21c4dcd9c20ad3efd0b3f817e7a809035269e1bd3'], - }), - ('wcwidth', '0.2.5', { - 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], - }), - ('attrs', '21.2.0', { - 'modulename': 'attr', - 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], - }), - ('importlib-metadata', '4.8.1', { - 'modulename': 'importlib_metadata', - 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', - 'checksums': ['f284b3e11256ad1e5d03ab86bb2ccd6f5339688ff17a4d797a0fe7df326f23b1'], - }), - ('more-itertools', '8.9.0', { - 'modulename': 'more_itertools', - 'checksums': ['8c746e0d09871661520da4f1241ba6b908dc903839733c8203b552cffaf173bd'], + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], }), ('args', '0.1.0', { 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], }), - ('pytest', '6.2.5', { - 'checksums': ['131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89'], + ('PyVCF', '0.6.8', { + 'modulename': 'vcf', + 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], }), ('tqdm', '4.62.2', { 'checksums': ['a4d6d112e507ef98513ac119ead1159d286deab17dffedd96921412c2d236ff5'], }), ('fieldbioinformatics', '1.2.1', { - 'modulename': False, + 'modulename': 'artic', 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], 'checksums': ['74b5fdb18dca57e73fbe872c5c4e25c110e7826fac7a062f0eb0a5453e4e7b20'], }), - ('clint', '0.5.1', { - 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], - }), - ('datrie', '0.8.2', { - 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], - }), - ('PyVCF', '0.6.8', { - 'modulename': 'vcf', - 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], - }), ] components = [ From 6b978b27a8e4858774042d99384deabd399ac99d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Tue, 21 Sep 2021 13:16:34 +0200 Subject: [PATCH 1581/2365] longread_umi: resolve conflicts --- .../easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index 3cbbee3f5c..9678677ff3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -170,11 +170,8 @@ exts_list = [ '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', # TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch '85c3023892e21692e14750e43a7d1db3c83c6e86a75ac1559c9dba39e0a160ae', -<<<<<<< HEAD -======= # TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch '6e845c44c27477740d16e9c525cdd4c2a96ac3deb2709ac62e21c3de79c4583b', ->>>>>>> upstream/develop # TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch 'd80e0103aeefb5244b57dd0e01bb7a0c1e6a750fba41833706547be87d3829e4', # TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch From fefe41992257cfef3f0d69bc02b6d354207d7ba0 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Tue, 21 Sep 2021 12:39:00 -0400 Subject: [PATCH 1582/2365] Update easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb Co-authored-by: SebastianAchilles --- .../v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb index 3de8d93cef..d526c59388 100644 --- a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb @@ -9,7 +9,7 @@ homepage = 'https://github.com/cc2qe/vawk' description = """An awk-like VCF parser """ -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [ ('Python', '2.7.18'), From 156c93bcd66229dbddf128b90a22a5081121bcc8 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Tue, 21 Sep 2021 20:12:30 +0200 Subject: [PATCH 1583/2365] Initial commit of ucx-py for foss 2020b --- .../u/ucx-py/ucx-py-0.21.0-foss-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb new file mode 100644 index 0000000000..afa7ab8a54 --- /dev/null +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'ucx-py' +version = '0.21.0' + +github_account = 'rapidsai' + +homepage = "https://ucx-py.readthedocs.io" +description = """UCX-Py is the Python interface for UCX, a low-level high-performance networking library. +UCX and UCX-Py supports several transport methods including InfiniBand and NVLink +while still using traditional networking protocols like TCP.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pynvml', '11.0.0', { + 'checksums': ['d5fc4a22d355b40c341d6ba0aa888a2d4d2253177d243900f8401b7e6cacb1bb'], + }), + (name, version, { + 'modulename': 'ucp', + 'patches': ['ucx-py-setup-get_ucx_incpath.patch'], + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': [ + '751da668ba43ad15b53cdb0bfd4084bd4b07200db57b604a9a09aa99d8a3bc1b', # v0.21.0.tar.gz + '123c9aee92ae6e8567e381bef0a4a590f1f7898708b3df1911e41d5ac498cdb3', # ucx-py-setup-get_ucx_incpath.patch + ], + }), +] + +moduleclass = 'lib' From 1bc0c795ba8855bc1cad99f480a8ce129d69062c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Wed, 22 Sep 2021 09:58:37 +0200 Subject: [PATCH 1584/2365] longread_umi: named sources --- .../l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index 15db976ec6..64b0518d0e 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -30,14 +30,14 @@ components = [ (name, version, { 'easyblock': 'Tarball', 'source_urls': [GITHUB_LOWER_SOURCE], - 'sources': ['v%(version)s.tar.gz'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], 'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'], 'start_dir': '%(name)s-%(version)s', }), ('Porechop', '0.2.4', { 'easyblock': 'PythonPackage', 'source_urls': ['https://github.com/rrwick/Porechop/archive'], - 'sources': ['v%(version)s.tar.gz'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], 'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'], 'start_dir': '%(name)s-%(version)s', 'use_pip': True, @@ -50,8 +50,8 @@ components = [ local_deps_patch = ( "sed -i " "-e '2s;^;set -e ;' " - "-e 's/USEARCH=usearch/USEARCH=vsearch/'" - "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;'" + "-e 's/USEARCH=usearch/USEARCH=vsearch/' " + "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;' " "%(installdir)s/scripts/dependencies.sh" ) From f16fd7fdae850e2ad9351742e0d9ea58a1e6cd43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Wed, 22 Sep 2021 13:49:13 +0200 Subject: [PATCH 1585/2365] longread_umi: add comment --- .../easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index 64b0518d0e..8b9541720e 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -34,6 +34,8 @@ components = [ 'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'], 'start_dir': '%(name)s-%(version)s', }), + # PythonPackage executes Bundle-level postinstallcmds for some reason, + # which rely on both components being installed, so Porechop is installed second ('Porechop', '0.2.4', { 'easyblock': 'PythonPackage', 'source_urls': ['https://github.com/rrwick/Porechop/archive'], From 5949ed1bb4561a45e09cf53ff42c90f5e8e4d5ed Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 22 Sep 2021 15:14:09 +0200 Subject: [PATCH 1586/2365] Dropping the h5py dep so Keras just uses h5py through the TensorFlow (req. h5py~=2.1.0) dep --- easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb index 48fc18c305..06a6be6a59 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb @@ -14,8 +14,7 @@ dependencies = [ ('Python', '3.8.6'), ('Theano', '1.1.2', '-PyMC'), ('PyYAML', '5.3.1'), - ('h5py', '3.1.0'), - ('TensorFlow', '2.4.1'), + ('TensorFlow', '2.4.1'), # provides h5py 2.1.0 ] use_pip = True From 38998fba1bafd6a2d16fd96098fdc6ea1ecfbd76 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 22 Sep 2021 15:20:28 +0200 Subject: [PATCH 1587/2365] Dropping the h5py dep so Keras just uses h5py through the TensorFlow (req. h5py~=2.1.0) dep --- easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb index 32ae992ae3..2f81c7cf31 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb @@ -14,8 +14,7 @@ dependencies = [ ('Python', '3.8.6'), ('Theano', '1.1.2', '-PyMC'), ('PyYAML', '5.3.1'), - ('h5py', '3.1.0'), - ('TensorFlow', '2.4.1'), + ('TensorFlow', '2.4.1'), # provides h5py 2.1.0 ] use_pip = True From b66dc21cb406e57db9c0d3e4ba078ed7b0ba2a07 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 23 Sep 2021 16:42:37 +0000 Subject: [PATCH 1588/2365] Upgraded Eigen to 3.3.9 as 3.3.7 version requires older GCC version --- .../easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb index d7aeb4c75d..9d020bb9a5 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -21,7 +21,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.7', '', True)] +builddependencies = [('Eigen', '3.3.9')] dependencies = [ ('zlib', '1.2.11'), From e160ef08070418132f0e20aaf3b12c6232265768 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 24 Sep 2021 17:15:48 +0200 Subject: [PATCH 1589/2365] Update version --- ...-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..9a44e9d742 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.22.1' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-{}'.format(local_tf_version) + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('flatbuffers', '1.12.0'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + 'checksums': ['c45bfcb9bd96852d79c62976eda12e9320b58b64f55bee3772877b3fc6243f2a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From f767bea8c44a0fce98cb3a22d5f4c3bc8501e11d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 24 Sep 2021 17:28:09 +0200 Subject: [PATCH 1590/2365] Update version --- .../h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb index 9a44e9d742..1382aa8245 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.8.6'), ('PyYAML', '5.3.1'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), - ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), + ('TensorFlow', local_tf_version), ] use_pip = True From e3cdab3e4bab6a5ce43cc910d99581190e12be9c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 24 Sep 2021 18:13:08 +0200 Subject: [PATCH 1591/2365] Fix jax test failures on recent kernels --- easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 9 ++++++++- easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 7 ++++++- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index d7edc77e8a..62e34b24ad 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -94,7 +94,14 @@ exts_list = [ (name, version, { 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], - 'checksums': ['fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c'], + 'patches': [ + 'jax-%(version)s_fix-update-of-cache-access-time.patch', + ], + 'checksums': [ + 'fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c', # jax-v0.2.19.tar.gz + # jax-0.2.19_fix-update-of-cache-access-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + ], 'runtest': 'pytest -n %(parallel)s tests', }), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index 41f5cbd5db..1da5dfa47a 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -98,9 +98,14 @@ exts_list = [ (name, version, { 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], - 'patches': ['jax-%(version)s_skip-heap-profiler-test.patch'], + 'patches': [ + 'jax-%(version)s_fix-update-of-cache-access-time.patch', + 'jax-%(version)s_skip-heap-profiler-test.patch' + ], 'checksums': [ 'fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c', # jax-v0.2.19.tar.gz + # jax-0.2.19_increase-cache-test-sleep-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', # jax-0.2.19_skip-heap-profiler-test.patch 'a431ce1b6588b5098872f36575dc2c5023b1010760bf6aaa889125c9a09227b0', ], From 56caf3b3b17128bf58217528a688c40e4bff9ec4 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Fri, 24 Sep 2021 20:19:15 -0400 Subject: [PATCH 1592/2365] Update easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb Co-authored-by: SebastianAchilles --- .../v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb index d526c59388..dca621dd7c 100644 --- a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb @@ -9,7 +9,7 @@ homepage = 'https://github.com/cc2qe/vawk' description = """An awk-like VCF parser """ -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchain = {'name': 'GCC', 'version': '10.2.0'} dependencies = [ ('Python', '2.7.18'), From 529deea13318e8fc8a7d294efba76bba16bcf381 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 25 Sep 2021 09:11:11 +0100 Subject: [PATCH 1593/2365] adding easyconfigs: HPDBSCAN-20210826-foss-2020b.eb --- .../HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb new file mode 100644 index 0000000000..f106d8a227 --- /dev/null +++ b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb @@ -0,0 +1,54 @@ +easyblock = 'CMakeMakeCp' + +name = 'HPDBSCAN' +version = '20210826' +local_commit = 'ae0c74c' + +homepage = 'https://github.com/Markus-Goetz/hpdbscan' +description = "Highly parallel density based spatial clustering for application with noise" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Markus-Goetz/hpdbscan/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['52ff343f77aeea5a425a911d88a57314c6bc877c18209eb53819d114421a868d'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('SciPy-bundle', '2020.11'), # for mpi4py + ('SWIG', '4.0.2'), +] + +# There is not an install method, so build in the source directory to simplify files_to_copy +separate_build_dir = False + +files_to_copy = [ + (['hpdbscan'], 'bin'), + (['libhpdbscan.%s' % SHLIB_EXT], 'lib'), + (['hpdbscan.py', '_hpdbscan.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'), + 'include', 'LICENSE.txt', +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/hpdbscan', 'lib/libhpdbscan.%s' % SHLIB_EXT, 'include/hpdbscan.h'], + 'dirs': [], +} + +# Check the Python bindings +_hpdbscan_python_check = 'python -c "import hpdbscan; import numpy; ' +_hpdbscan_python_check += 'clusterer = hpdbscan.HPDBSCAN(epsilon=0.3, min_points=4); ' +_hpdbscan_python_check += 'clusterer.cluster(numpy.random.rand(100, 3))"' + +sanity_check_commands = [ + "hpdbscan --help", + _hpdbscan_python_check, +] + +moduleclass = 'tools' From b6c1cfdd17f536dd8021890e2a8785763dbd3773 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Sat, 25 Sep 2021 11:26:57 +0200 Subject: [PATCH 1594/2365] Limit parallelism a bit more --- easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index 62e34b24ad..e583b752f4 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -36,7 +36,7 @@ use_pip = True # running the tests with lots of cores results in test failures because not enough threads can be started, # so limit to a reasonable number of cores to use at maximum -maxparallel = 10 +maxparallel = 5 default_easyblock = 'PythonPackage' default_component_specs = { From e52d092ee0e357ad116b2cef1e72f19a5f30b0db Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Sep 2021 09:45:19 +0200 Subject: [PATCH 1595/2365] use GCCcore toolchain and ad binutils as builddep --- .../v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb index dca621dd7c..aef3494ecb 100644 --- a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb @@ -9,8 +9,9 @@ homepage = 'https://github.com/cc2qe/vawk' description = """An awk-like VCF parser """ -toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '2.7.18'), ] From 1c38c06f1441f1b263e01ac65c942560f124c29d Mon Sep 17 00:00:00 2001 From: Zdenek Date: Tue, 28 Sep 2021 09:47:34 +0200 Subject: [PATCH 1596/2365] Adding author + short description to the top of the patch --- easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb index afa7ab8a54..3c5750df67 100644 --- a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb @@ -31,7 +31,7 @@ exts_list = [ 'sources': ['v%(version)s.tar.gz'], 'checksums': [ '751da668ba43ad15b53cdb0bfd4084bd4b07200db57b604a9a09aa99d8a3bc1b', # v0.21.0.tar.gz - '123c9aee92ae6e8567e381bef0a4a590f1f7898708b3df1911e41d5ac498cdb3', # ucx-py-setup-get_ucx_incpath.patch + 'faeb61c302ffb37e72221d18c83fc929e47a6c5cd84c4208b01c5a21f570f561', # ucx-py-setup-get_ucx_incpath.patch ], }), ] From 49699cdee0eb9aa9e05842c2c2778c61f21652c3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Sep 2021 10:42:26 +0200 Subject: [PATCH 1597/2365] add version to patch name --- easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb index 3c5750df67..514e47c1fa 100644 --- a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb @@ -26,7 +26,7 @@ exts_list = [ }), (name, version, { 'modulename': 'ucp', - 'patches': ['ucx-py-setup-get_ucx_incpath.patch'], + 'patches': ['ucx-py-%(version)s_setup-get-ucx-incpath.patch'], 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], 'sources': ['v%(version)s.tar.gz'], 'checksums': [ From 3556f3103b3a4eb3532b9372c7c34d6018f375ff Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 28 Sep 2021 10:42:59 +0200 Subject: [PATCH 1598/2365] Fix compilation of BWA on PPC --- easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb index 48f02d3037..b6825ba6a8 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb @@ -34,6 +34,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' moduleclass = 'bio' From 91fa5226f6199e66c247c1a43438e1d1168e252f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Sep 2021 10:57:42 +0200 Subject: [PATCH 1599/2365] update patch comment --- easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb index 514e47c1fa..ab94cdba53 100644 --- a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb @@ -31,7 +31,8 @@ exts_list = [ 'sources': ['v%(version)s.tar.gz'], 'checksums': [ '751da668ba43ad15b53cdb0bfd4084bd4b07200db57b604a9a09aa99d8a3bc1b', # v0.21.0.tar.gz - 'faeb61c302ffb37e72221d18c83fc929e47a6c5cd84c4208b01c5a21f570f561', # ucx-py-setup-get_ucx_incpath.patch + # ucx-py-0.21.0_setup-get-ucx-incpath.patch + 'faeb61c302ffb37e72221d18c83fc929e47a6c5cd84c4208b01c5a21f570f561', ], }), ] From f9003fb7b76eb50b562e575c7acad24b519d1a77 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 11:25:28 +0200 Subject: [PATCH 1600/2365] adding easyconfigs: MotionCor2-1.4.4-GCCcore-10.2.0.eb --- .../MotionCor2-1.4.4-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e040a5698e --- /dev/null +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ake Sandgren +# HPC2N +# Umea University + +name = 'MotionCor2' +version = '1.4.4' + +homepage = 'https://msg.ucsf.edu/' +description = """MotionCor2 correct anisotropic image motion at the +single pixel level across the whole frame, suitable for both single +particle and tomographic images. Iterative, patch-based motion detection +is combined with spatial and temporal constraints and dose weighting. + +Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, +Yifan Cheng and David A. Agard (2016) Anisotropic Correction of +Beam-induced Motion for Improved Single-particle Electron +Cryo-microscopy, Nature Methods, submitted. +BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [{ + 'filename': '%(name)s_%(version)s.zip', + 'extract_cmd': 'unzip -j %s' +}] +checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] + +# No longer directly downloadable, available from https://msg.ucsf.edu/software +# CUDA is a build dependency to make sure it gets installed. +# It's actually a runtime dependency, but that's handled in the wrapper to +# make sure it doesn't conflict with whatever toolchain happens to be loaded. +# Change CUDA version to match the latest one used in this version +# of MotionCor2 +builddependencies = [ + ('binutils', '2.35'), + ('CUDAcore', '11.1.1', '', True), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5'), + ('LibTIFF', '4.1.0'), +] +moduleclass = 'bio' From 088ff24b066382ed6ebad8882836e88f8545a742 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 16:21:41 +0200 Subject: [PATCH 1601/2365] adding easyconfigs: IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb --- ...-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb new file mode 100644 index 0000000000..1a94253258 --- /dev/null +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -0,0 +1,65 @@ +# Thomas Hofffmann, EMBL Heidelberg, structures-it@embl.de, 2021/09 +easyblock = 'Tarball' # there is no setup.py -> unpack tarball and move to site-packages in postinstall. + +name = 'IsoNet' +# There is no version tag available in github. Using commit and date instead. +local_commit = '674f67f1afb8aa1353c0d67ccb55263c1f20576f' +local_version = '0.1' +local_commit_date = '20210822' +local_commit_count = '04' +version = '%s_%s_%s_%s' % (local_version, local_commit_date, local_commit_count, local_commit[:7]) + +homepage = 'https://github.com/Heng-Z/IsoNet' +description = """IsoNet stands for for ISOtropic reconstructioN of Electron Tomography. It trains +deep convolutional neural networks to reconstruct meaningful contents in the mis +sing wedge for electron tomography, and to increase signal-to-noise ratio, +using the information learned from the original tomogram. The software requires +tomograms as input. Observing at about 30A resolution, the IsoNet generated +tomograms are largely isotropic.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/Heng-Z/IsoNet/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['dac1583bbab0d6b09496657b5d237b9c35c9a70ee9c0089a174e571b78892d49'] + +install_type = 'subdir' +postinstallcmds = [ + 'find %(installdir)s/isonet -name \'*.pyc\' -exec rm {} \\;' + '&& mv %(installdir)s/isonet %(installdir)s/lib/python%(pyshortver)s/site-packages/IsoNet' +] + +dependencies = [ + ('Python', '3.8.6'), + ('TensorFlow', '2.4.1'), + ('PyQt5', '5.15.1'), + ('SciPy-bundle', '2020.11'), + ('mrcfile', '1.3.0'), + ('tqdm', '4.60.0'), + ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! +] +sanity_pip_check = True +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('fire', '0.4.0', { + 'modulename': 'fire', + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], + 'use_pip': True, + 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], + }), +] + +modextrapaths = { + 'PATH': 'lib/python%(pyshortver)s/site-packages/IsoNet/bin', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/' +} +sanity_check_commands = [ + 'isonet.py check', + 'isonet.py --help', +] +sanity_check_paths = { + 'files': [], + 'dirs': ["lib/python%(pyshortver)s/site-packages/IsoNet"] +} + +moduleclass = 'bio' From a7c541ba4ecd6c1d6adebfe43d8cb9eb9f21da6d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 28 Sep 2021 16:35:39 +0200 Subject: [PATCH 1602/2365] Update IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb --- .../i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 1a94253258..6efea4b1db 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -38,7 +38,6 @@ dependencies = [ ('tqdm', '4.60.0'), ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] -sanity_pip_check = True exts_defaultclass = 'PythonPackage' exts_list = [ ('fire', '0.4.0', { From 808264b63d3d8c8e359624a6e711c84b67194a2d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 17:17:28 +0200 Subject: [PATCH 1603/2365] downgrade tqdm dep --- .../i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 6efea4b1db..05c2b7e472 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -35,7 +35,7 @@ dependencies = [ ('PyQt5', '5.15.1'), ('SciPy-bundle', '2020.11'), ('mrcfile', '1.3.0'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] exts_defaultclass = 'PythonPackage' From 063fc597013a024b96b3a6e3e107411728c7d794 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 17:42:55 +0200 Subject: [PATCH 1604/2365] exts_default_options --- .../IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 05c2b7e472..48e8d55811 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -38,12 +38,15 @@ dependencies = [ ('tqdm', '4.56.2'), ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} exts_defaultclass = 'PythonPackage' exts_list = [ ('fire', '0.4.0', { 'modulename': 'fire', 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], - 'use_pip': True, 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], }), ] From 2d342aba2dd1602d06a909f614923ac6ef6305bb Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 30 Sep 2021 11:20:17 +0100 Subject: [PATCH 1605/2365] adding easyconfigs: lifelines-0.26.3-fosscuda-2020b.eb --- .../lifelines-0.26.3-fosscuda-2020b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..3c8696a9d2 --- /dev/null +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb @@ -0,0 +1,45 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'lifelines' +version = '0.26.3' + +homepage = "https://lifelines.readthedocs.io/en/latest/" +description = """lifelines is a complete survival analysis library, written in pure Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('interface_meta', '1.2.4', { + 'checksums': ['4c7725dd4b80f97b7eecfb26023e1a8a7cdbb6d6a7207a8e93f9d4bfef9ee566'], + }), + ('autograd', '1.3', { + 'checksums': ['a15d147577e10de037de3740ca93bfa3b5a7cdfbc34cfb9105429c3580a33ec4'], + }), + ('autograd-gamma', '0.5.0', { + 'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'], + }), + ('formulaic', '0.2.4', { + 'checksums': ['15b71ea8972fb451f80684203cddd49620fc9ed5c2e35f31e0874e9c41910d1a'], + }), + (name, version, { + 'checksums': ['f3dc77601927b9dbebb77d1b4d6f5bd4e5e3e169f6e8d7c2beb31a9a36fcbe1b'], + }), +] + +moduleclass = 'data' From f1e7e7490a1821bc5db622bed582c7e3f37eaf9f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 30 Sep 2021 11:53:06 +0100 Subject: [PATCH 1606/2365] keep bio as the moduleclass --- .../easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb index 3c8696a9d2..2458724db7 100644 --- a/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb @@ -42,4 +42,4 @@ exts_list = [ }), ] -moduleclass = 'data' +moduleclass = 'bio' From 894ac8871b70f3ae33ce54409605b62b0a112b19 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 30 Sep 2021 15:17:20 +0200 Subject: [PATCH 1607/2365] add missing XZ dependency for recent LibTIFF versions --- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb index 43be2ea49e..13c0efa773 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -7,7 +7,7 @@ # $Id$ # # This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ +# https://hpcbios.readthedocs.org/en/latest/ ## easyblock = 'ConfigureMake' @@ -30,7 +30,8 @@ builddependencies = [('binutils', '2.35')] dependencies = [ ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.5') + ('libjpeg-turbo', '2.0.5'), + ('XZ', '5.2.5'), ] configopts = " --enable-ld-version-script " From 27005b19d2044dc8fbf7ff9f4ce77c4f2e7d8194 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 30 Sep 2021 21:54:21 +0200 Subject: [PATCH 1608/2365] also add jbigkit and zstd --- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb index 13c0efa773..c2e41230be 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -32,9 +32,12 @@ dependencies = [ ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.5'), ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('zstd', '1.4.5'), ] -configopts = " --enable-ld-version-script " +configopts = "--enable-ld-version-script " +configopts += '--disable-webp --disable-libdeflate ' sanity_check_paths = { 'files': ['bin/tiffinfo'], From f5f15d58883a71faeb16399b7c5164c47dea867e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Oct 2021 02:03:29 +0200 Subject: [PATCH 1609/2365] adding easyconfigs: PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb --- ...tric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 0000000000..b9d2000662 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '2.0.1' +local_pytorchver = '1.9.0' +versionsuffix = '-PyTorch-%s' % local_pytorchver + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', local_pytorchver), + ('scikit-learn', '0.23.2'), + ('scikit-image', '0.18.1'), + ('numba', '0.52.0'), + ('h5py', '3.1.0'), + ('tqdm', '4.56.2'), + ('RDFlib', '5.0.0'), + ('ASE', '3.20.1'), +] + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '0.7.4', { + 'checksums': ['9e9a18d22a3158fcd74df38761d43a7facc6df75126f2ab9f4e9a5d4d2188652'], + }), + ('torch_scatter', '2.0.8', { + 'checksums': ['d71aab489b5288a6c96e9f9a7c9e13c54774dcb55a99a40e6cd1aca8be9ef3e6'], + }), + ('torch_sparse', '0.6.12', { + 'checksums': ['85db85bd45855cde4be093c7e2413b962b21b31151ad7eacd19ca4e2808bced2'], + }), + ('torch_cluster', '1.5.9', { + 'checksums': ['96209e9f3f073c8e7fe91fbf7dd2cdd8655622d14dfc95a7618b4893a658dca5'], + }), + ('torch_spline_conv', '1.2.1', { + 'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'], + }), + ('python-louvain', '0.15', { + 'modulename': 'community.community_louvain', + 'checksums': ['2a856edfbe29952a60a5538a84bb78cca18f6884a88b9325e85a11c8dd4917eb'], + }), + ('torch_geometric', version, { + 'checksums': ['6ec91a407ca95959c1ca2009f6702983540ccafabc7f2553d56755ff8b393f4f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 1e6b8648588a8bd0f9301a483189f7c724b239a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Oct 2021 02:42:19 +0200 Subject: [PATCH 1610/2365] Update to newer numba --- .../PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb index b9d2000662..eabae5e96c 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -15,7 +15,7 @@ dependencies = [ ('PyTorch', local_pytorchver), ('scikit-learn', '0.23.2'), ('scikit-image', '0.18.1'), - ('numba', '0.52.0'), + ('numba', '0.53.1'), ('h5py', '3.1.0'), ('tqdm', '4.56.2'), ('RDFlib', '5.0.0'), From e82cc7a063785ef5deaf5012f30f71fc0016f204 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Oct 2021 16:21:10 +0200 Subject: [PATCH 1611/2365] Update easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb Co-authored-by: SebastianAchilles --- .../PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb index eabae5e96c..c3de9720e6 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -20,6 +20,7 @@ dependencies = [ ('tqdm', '4.56.2'), ('RDFlib', '5.0.0'), ('ASE', '3.20.1'), + ('YACS', '0.1.8'), ] use_pip = True From a60c28e97fcbf720f0fbcb74ab2013598ffe3006 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 3 Oct 2021 20:09:07 +0200 Subject: [PATCH 1612/2365] add missing header file --- easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb index 5d3338697b..cc565979b7 100644 --- a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb @@ -32,14 +32,14 @@ builddependencies = [ files_to_copy = [ (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), - (['libjbig/jbig85.h', 'libjbig/jbig.h'], 'include'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), ] sanity_check_paths = { 'files': ['lib/libjbig85.a', 'lib/libjbig.a', 'bin/pbmtojbg', 'bin/jbgtopbm', - 'include/jbig.h', + 'include/jbig.h', 'include/jbig_ar.h', ], 'dirs': ['bin', 'include', 'lib'] } From 499c6361a27b1ac14a595eff4e063320c4bae644 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Oct 2021 09:39:56 +0200 Subject: [PATCH 1613/2365] fix source URL for SUNDIALS 5.x --- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb | 4 ++-- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb | 2 +- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb index cf95385b96..f7e6418477 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb @@ -10,9 +10,9 @@ description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} -source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] +checksums = ['48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43'] builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb index 33df49c169..8bc61e3d1e 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb @@ -10,7 +10,7 @@ description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation toolchain = {'name': 'fosscuda', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} -source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb index 218050a770..2568c787c1 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb @@ -10,7 +10,7 @@ description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} -source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] From 50280ede60534390ad2f29c16b08d0d150ea9824 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 4 Oct 2021 08:51:44 +0100 Subject: [PATCH 1614/2365] Add Perl and Python runtime dependencies to Bowtie2 --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb index 2a3ee99cd4..90ac886ce2 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb @@ -28,9 +28,13 @@ checksums = ['4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e'] dependencies = [ ('tbb', '2020.3'), ('zlib', '1.2.11'), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), ] # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} +sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] + moduleclass = 'bio' From 9f12733dc65273b3c659f1536298b80edd995fad Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 4 Oct 2021 09:08:25 +0100 Subject: [PATCH 1615/2365] revert changes to GCC 9.3.0 and 10.2.0 versions due to pipeline failures --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb index 90ac886ce2..2a3ee99cd4 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb @@ -28,13 +28,9 @@ checksums = ['4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e'] dependencies = [ ('tbb', '2020.3'), ('zlib', '1.2.11'), - ('Perl', '5.32.0'), - ('Python', '3.8.6'), ] # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} -sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] - moduleclass = 'bio' From 4613e40e6452f03ad26db7e038157b606c4f1d35 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 4 Oct 2021 10:17:22 +0200 Subject: [PATCH 1616/2365] simple source specification with new easyblock. use CUDA/11.3.1 --- .../m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb index e040a5698e..ed127443bf 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb @@ -21,10 +21,7 @@ BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -sources = [{ - 'filename': '%(name)s_%(version)s.zip', - 'extract_cmd': 'unzip -j %s' -}] +sources = ['%(name)s_%(version)s.zip'] checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # No longer directly downloadable, available from https://msg.ucsf.edu/software @@ -35,7 +32,7 @@ checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # of MotionCor2 builddependencies = [ ('binutils', '2.35'), - ('CUDAcore', '11.1.1', '', True), + ('CUDA', '11.3.1', '', True), ] dependencies = [ From 7dcefa59308a9454c56e758b6fa530f908c4c69a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Oct 2021 10:26:47 +0200 Subject: [PATCH 1617/2365] add alternate valid checksum for SUNDIALS 5.7.0 source tarball (only PDF files in doc/ differ) --- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb | 5 ++++- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb | 5 ++++- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb index f7e6418477..51543acdb7 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb @@ -12,7 +12,10 @@ toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43'] +# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, +# other for new source tarball downloaded from GitHub +checksums = [('8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3', + '48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43')] builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb index 8bc61e3d1e..ccf4e47963 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb @@ -12,7 +12,10 @@ toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] +# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, +# other for new source tarball downloaded from GitHub +checksums = [('8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3', + '48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43')] builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb index 2568c787c1..5c283e4de3 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb @@ -12,7 +12,10 @@ toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] +# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, +# other for new source tarball downloaded from GitHub +checksums = [('8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3', + '48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43')] builddependencies = [('CMake', '3.18.4')] From b8d8974d5caa3fc1614cd66afbffc7f371554e5d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 4 Oct 2021 17:54:05 +0200 Subject: [PATCH 1618/2365] New download urls for SCOTCH 6.1.0 --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb | 6 +++--- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb index 4963e9ab5b..08a103b4d3 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb @@ -8,9 +8,9 @@ static mapping, and sparse matrix block ordering, and sequential mesh and hyperg toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'pic': True} -source_urls = ['https://gforge.inria.fr/frs/download.php/file/38352/'] -sources = ['%(namelower)s_%(version)s.tar.gz'] -checksums = ['a3bc3fa3b243fcb52f8d68de4272562a0328afb18a96f535724d284e36730485'] +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb index 2bded2513c..6e94531d82 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb @@ -8,9 +8,9 @@ static mapping, and sparse matrix block ordering, and sequential mesh and hyperg toolchain = {'name': 'iimpi', 'version': '2020b'} toolchainopts = {'pic': True} -source_urls = ['https://gforge.inria.fr/frs/download.php/file/38352/'] -sources = ['%(namelower)s_%(version)s.tar.gz'] -checksums = ['a3bc3fa3b243fcb52f8d68de4272562a0328afb18a96f535724d284e36730485'] +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] dependencies = [ ('zlib', '1.2.11'), From 08b02fc559439d08ffe766173c1c1ecfdff57981 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 5 Oct 2021 15:53:12 +0200 Subject: [PATCH 1619/2365] first installation of nanomax-analysis-utils into 2020b --- .../f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb | 26 ++++++++++++ ...nanomax-analysis-utils-0.4.3-foss-2020b.eb | 27 ++++++++++++ ...max-analysis-utils-0.4.3-fosscuda-2020b.eb | 27 ++++++++++++ .../PyOpenCL-2021.1.2-fosscuda-2020b.eb | 33 +++++++++++++++ .../s/silx/silx-0.14.0-fosscuda-2020b.eb | 41 +++++++++++++++++++ 5 files changed, 154 insertions(+) create mode 100644 easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..7126f817a8 --- /dev/null +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'FabIO' +version = '0.11.0' + +homepage = 'http://www.silx.org' +description = """FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. +FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), +for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers +(as a python dictionary) and datasets (as a numpy ndarray of integers or floats).""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1d2fcf58006c82548a16004e607d4518613d49e4a2f02a3797703eee2b39c6d8'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb new file mode 100644 index 0000000000..4affa74280 --- /dev/null +++ b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'nanomax-analysis-utils' +version = '0.4.3' + +github_account = 'maxiv-science' +homepage = "https://github.com/%(github_account)s/nanomax-analysis-utils" +description = """A set of tools for handling and analysing data at the NanoMAX beamline.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('silx', '0.14.0'), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['887874f9ab8ba42b31e47a51503aa85be7b215073151415d38b231f748072a42'] + +options = {'modulename': 'nmutils'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..738e464088 --- /dev/null +++ b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'nanomax-analysis-utils' +version = '0.4.3' + +github_account = 'maxiv-science' +homepage = "https://github.com/%(github_account)s/nanomax-analysis-utils" +description = """A set of tools for handling and analysing data at the NanoMAX beamline.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('silx', '0.14.0'), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['887874f9ab8ba42b31e47a51503aa85be7b215073151415d38b231f748072a42'] + +options = {'modulename': 'nmutils'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..cec1342f8e --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2021.1.2' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('pocl', '1.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.1', { + 'checksums': ['073ae22a0ae946e2db97164f2eb24a599cd3a51430384aa40859dffd73056c40'], + }), + ('pyopencl', version, { + 'checksums': ['18871bc80c5a94869521189cf2c04d72c88367a441a9a033f72f66792ac33d29'], + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..fc63b3528e --- /dev/null +++ b/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'silx' +version = '0.14.0' + +homepage = "http://www.silx.org/" +description = """The silx project provides a collection of Python packages to support the +development of data assessment, reduction and analysis applications at synchrotron radiation facilities.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('PyOpenGL', '3.1.5'), + ('matplotlib', '3.3.3'), + ('Mako', '1.1.3'), + ('Pillow', '8.0.1'), + ('FabIO', '0.11.0'), + ('Qtconsole', '5.0.2'), + ('PyOpenCL', '2021.1.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('hdf5plugin', '2.3.1', { + 'checksums': ['2f6d886012c37bf7e8e002173dd6b16e6879b8e0e9f7d2f2ef9f79db97ed28d2'], + }), + (name, version, { + 'checksums': ['17c595fe18c9eb3403a9d1f0ee6ea7b523607043c46c944573ecf406f6997866'], + }), +] + +modextrapaths = { + 'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins', +} + +moduleclass = 'vis' From affc8ca44431d38662f0d88dba041eea37331a27 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 5 Oct 2021 16:44:30 +0100 Subject: [PATCH 1620/2365] adding easyconfigs: NAMD-2.14-foss-2020b-mpi.eb, NAMD-2.14-fosscuda-2020b.eb --- .../n/NAMD/NAMD-2.14-foss-2020b-mpi.eb | 31 +++++++++++++++++ .../n/NAMD/NAMD-2.14-fosscuda-2020b.eb | 34 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb new file mode 100644 index 0000000000..7fd2267fc9 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb @@ -0,0 +1,31 @@ +name = 'NAMD' +version = '2.14' +versionsuffix = '-mpi' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] +sources = ['%(name)s_%(version)s_Source.tar.gz'] +patches = ['%(name)s-%(version)s-use_system_mremap_decl.patch'] +checksums = [ + '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz + 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch +] + +dependencies = [ + ('Tcl', '8.6.10'), +] + +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + +# Hard to make charm build the mpi version with gcc on POWER, so we don't currently try. +charm_arch = 'mpi-linux-x86_64' +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb new file mode 100644 index 0000000000..98aeeb12b8 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb @@ -0,0 +1,34 @@ +name = 'NAMD' +version = '2.14' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': False, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] +sources = [{'filename': 'NAMD_%(version)s_Source.tar.gz'}] +patches = [ + "%(name)s-%(version)s_Linux-POWER-cuda.patch", + "%(name)s-%(version)s-use_system_mremap_decl.patch" +] +checksums = [ + '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz + 'db4aeb482dfa805c859ea18940026395763169e0257401ee5341ca550029031c', # NAMD-2.14_Linux-POWER-cuda.patch + 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch +] + +# support for GCC 8+ on POWER +dependencies = [ + ('Tcl', '8.6.10'), +] + +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + +charm_arch = "multicore-linux-%(arch)s" +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' From dafd9283f8c1fbf2e958cbd99c7ab4cd291a7698 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 6 Oct 2021 11:42:38 +0200 Subject: [PATCH 1621/2365] Added pyFAI in foss and fosscuda --- .../p/pyFAI/pyFAI-0.20.0-foss-2020b.eb | 32 +++++++++++++++++++ .../p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb new file mode 100644 index 0000000000..0bff738d5d --- /dev/null +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pyFAI' +version = '0.20.0' +versionsuffix = '-Python-%(pyver)s' + +github_account = 'silx-kit' +homepage = "https://github.com/%(github_account)s/pyFAI" +description = """Python implementation of fast azimuthal integration.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('silx', '0.14.0'), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f39f56ff58868ab7f12d6fa5c7bf6b7d111b7fa687f3816c5d8d11cb75fa82f0'] + +options = {'modulename': 'pyFAI'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +modextravars = { + 'PYFAI_OPENCL': '0', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..a034f6b480 --- /dev/null +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pyFAI' +version = '0.20.0' +versionsuffix = '-Python-%(pyver)s' + +github_account = 'silx-kit' +homepage = "https://github.com/%(github_account)s/pyFAI" +description = """Python implementation of fast azimuthal integration.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('silx', '0.14.0'), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f39f56ff58868ab7f12d6fa5c7bf6b7d111b7fa687f3816c5d8d11cb75fa82f0'] + +options = {'modulename': 'pyFAI'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +modextravars = { + 'PYFAI_OPENCL': '0', +} + +moduleclass = 'data' From d5cc786edac781a2cdfcb4f9b01ad151211b2b9f Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 6 Oct 2021 14:47:17 +0200 Subject: [PATCH 1622/2365] added pyFAI (foss and fosscuda 2020b) as well as pmca for fosscuda 2020b --- .../p/pyFAI/pyFAI-0.20.0-foss-2020b.eb | 1 - .../p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb | 1 - .../p/pymca/pymca-5.6.3-fosscuda-2020b.eb | 35 +++++++++++++++++++ 3 files changed, 35 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb index 0bff738d5d..1a72ee67c6 100644 --- a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'pyFAI' version = '0.20.0' -versionsuffix = '-Python-%(pyver)s' github_account = 'silx-kit' homepage = "https://github.com/%(github_account)s/pyFAI" diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb index a034f6b480..c5766420e2 100644 --- a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'pyFAI' version = '0.20.0' -versionsuffix = '-Python-%(pyver)s' github_account = 'silx-kit' homepage = "https://github.com/%(github_account)s/pyFAI" diff --git a/easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..473c95d50e --- /dev/null +++ b/easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'pymca' +version = '5.6.3' + +github_account = 'vasole' +homepage = "https://github.com/%(github_account)s/pymca" +description = """The PyMca X-Ray Fluorescence Toolkit, including PyMca5 and fisx.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('silx', '0.14.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = { + 'source_urls': [GITHUB_SOURCE], + 'sources': ['v%(version)s.tar.gz'], +} + +exts_list = [ + ('fisx', '1.2.0', { + 'checksums': ['868642045725552126d43331cdec7d7a6a85251d54011b4a0360fc90b02041e4'], + }), + (name, version, { + 'checksums': ['36b37f51a550b1262346e853ec8d3f1e8dd45adfc1a80e3626dc35e197eadb8c'], + 'modulename': 'PyMca5', + }), +] + +moduleclass = 'data' From cebc491ce1ebc0636f50ccf9521c3d45e9fae1ee Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 6 Oct 2021 17:43:20 +0100 Subject: [PATCH 1623/2365] adding easyconfigs: SHAPEIT4-4.2.2-foss-2020b.eb, SHAPEIT4-4.2.2-foss-2021a.eb and patches: SHAPEIT4_4.2.2_use_EB_settings.patch --- .../s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb new file mode 100644 index 0000000000..e19de04e82 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = "MakeCp" + +name = 'SHAPEIT4' +version = '4.2.2' + +homepage = 'https://odelaneau.github.io/shapeit4/' +description = """ +SHAPEIT4 is a fast and accurate method for estimation of haplotypes +(aka phasing) for SNP array and high coverage sequencing data. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True, 'cstd': 'c++11'} + +github_account = 'odelaneau' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] +checksums = [ + '9f109e307b5cc22ab68e7bf77de2429a9bbb2212d66303386e6a3dd81a5bc556', # v4.2.2.tar.gz + '92ed45545bfcde7b1fbe079e6321ccae00865c8f0f66a924e872967d762df885', # SHAPEIT4_4.2.2_use_EB_settings.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('Boost', '1.74.0'), + ('HTSlib', '1.12'), +] + +buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts ' +buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options ' +buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS" ' + +files_to_copy = [(['bin/shapeit4.2'], 'bin'), 'maps'] + +sanity_check_paths = { + 'files': ["bin/shapeit4.2"], + 'dirs': ['maps'] +} + +sanity_check_commands = ['shapeit4.2 --help'] + +moduleclass = 'bio' From 835cdfea81ceb404d60aed2ec642a4ff0476f9f3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 6 Oct 2021 17:53:58 +0100 Subject: [PATCH 1624/2365] Use HTSlib 1.11 for 2020/b for consistency --- easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb index e19de04e82..c3694317b3 100644 --- a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb @@ -26,7 +26,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('XZ', '5.2.5'), ('Boost', '1.74.0'), - ('HTSlib', '1.12'), + ('HTSlib', '1.11'), ] buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts ' From 67ca183f4fcfbca584613883bf15887ee3fc9783 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 7 Oct 2021 18:02:45 +0200 Subject: [PATCH 1625/2365] adding easyconfigs: AlphaFold-2.0.1-foss-2020b.eb, AlphaFold-2.0.1-fosscuda-2020b.eb and patches: AlphaFold-2.0.1_data-dep-paths.patch, AlphaFold-2.0.1_setup_rm_tfcpu.patch --- .../a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb | 181 +++++++++++++++++ .../AlphaFold-2.0.1-fosscuda-2020b.eb | 185 ++++++++++++++++++ 2 files changed, 366 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb new file mode 100644 index 0000000000..8806522d26 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb @@ -0,0 +1,181 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.0.1' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.4.1'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.19'), # also provides absl-py +] + +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.0.1_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.0.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'b3dfdd3877343516f98bc49f8adbbb5101e8900524470816d4495a22ed986857', # v2.0.1.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '60c60abc254e713787843a1a53fcccefc56d242fa1cfa826701a5ff39227bd52', # AlphaFold-2.0.1_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + # source tarball on PyPI is missing requirements.txt, + # see https://github.com/deepmind/dm-haiku/issues/44 + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + 'modulename': 'haiku', + }), + ('dm-tree', '0.1.6', { + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + 'modulename': 'tree', + }), + ('websocket-client', '1.2.1', { + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + 'modulename': 'websocket', + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + # see https://github.com/google/ml_collections/issues/7 + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..5c6a924e87 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb @@ -0,0 +1,185 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.0.1' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.4.1'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.19'), # also provides absl-py +] +configopts = "-DCUDA_CUDA_LIBRARY=${EBROOTCUDA}/lib64/stubs/libcuda.so " +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.0.1_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.0.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'b3dfdd3877343516f98bc49f8adbbb5101e8900524470816d4495a22ed986857', # v2.0.1.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '60c60abc254e713787843a1a53fcccefc56d242fa1cfa826701a5ff39227bd52', # AlphaFold-2.0.1_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', +} + +moduleclass = 'bio' From 96b8fc92f21e23fb3634d0633a5a9cf947d0c76e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Oct 2021 20:31:59 +0200 Subject: [PATCH 1626/2365] adding easyconfigs: MMseqs2-13-45111-20211006-gompi-2020b.eb --- .../MMseqs2-13-45111-20211006-gompi-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211006-gompi-2020b.eb diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211006-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211006-gompi-2020b.eb new file mode 100644 index 0000000000..59646fc55e --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211006-gompi-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +local_commit = '49c2b70' +version = '13-45111-20211006' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['bb70cd38e6e27f136263250c0c6a9f045d1e4a883d2a93a54e708fb8e2ec4098'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [('bzip2', '1.0.8')] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' From bd26aee1c86df9e9ed40bbf6ae54046bf25f78a9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 8 Oct 2021 09:08:56 +0200 Subject: [PATCH 1627/2365] adding easyconfigs: swifter-1.0.9-foss-2020b.eb, swifter-1.0.9-fosscuda-2020b.eb --- .../s/swifter/swifter-1.0.9-foss-2020b.eb | 33 +++++++++++++++++++ .../s/swifter/swifter-1.0.9-fosscuda-2020b.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb new file mode 100644 index 0000000000..c379d2ef49 --- /dev/null +++ b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'swifter' +version = '1.0.9' + +homepage = 'https://github.com/jmcarpenter2/swifter' +description = """ +A package which efficiently applies any function to a pandas dataframe or +series in the fastest available manner.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('dask', '2021.2.0'), + ('tqdm', '4.56.2'), + ('IPython', '7.18.1'), +] + +exts_list = [ + ('modin', '0.8.2', { + 'checksums': ['0e224911e21e6a7134baa2a3162c91af2594bf75b9c2d7e39a3f0d10e38793a5'], + }), + (name, version, { + 'checksums': ['14cec10ff1ecdfbcfdd68985366b07add5f9b7bb77116720f47c88f29f048c3e'], + }), +] + +sanity_pip_check = True +use_pip = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb new file mode 100644 index 0000000000..083b6cf060 --- /dev/null +++ b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'swifter' +version = '1.0.9' + +homepage = 'https://github.com/jmcarpenter2/swifter' +description = """ +A package which efficiently applies any function to a pandas dataframe or +series in the fastest available manner.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('dask', '2021.2.0'), + ('tqdm', '4.56.2'), + ('IPython', '7.18.1'), +] + +exts_list = [ + ('modin', '0.8.2', { + 'checksums': ['0e224911e21e6a7134baa2a3162c91af2594bf75b9c2d7e39a3f0d10e38793a5'], + }), + (name, version, { + 'checksums': ['14cec10ff1ecdfbcfdd68985366b07add5f9b7bb77116720f47c88f29f048c3e'], + }), +] + +sanity_pip_check = True +use_pip = True + +moduleclass = 'data' From 033b0c57a777f2e92f0dae4b7d9af0a87d76a41f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 11 Oct 2021 11:50:30 +0200 Subject: [PATCH 1628/2365] {bio}[foss/2020b] QUAST 5.0.2 /w foss-2020b and Python 3 --- .../q/QUAST/QUAST-5.0.2-foss-2020b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb new file mode 100644 index 0000000000..c9d652ca8b --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'QUAST' +version = '5.0.2' + +homepage = 'https://github.com/ablab/%(namelower)s' +description = """QUAST evaluates genome assemblies by computing various metrics. +It works both with and without reference genomes. The tool accepts multiple +assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + + +dependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0'), + ('matplotlib', '3.3.3'), + ('Java', '11', '', True), + ('Boost', '1.74.0'), +] + +use_pip = True + +exts_list = [ + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + (name, version, { + 'install_target': 'install_full', + 'modulename': 'quast_libs', + 'patches': ['QUAST-%(version)s_fix-Python-3.8.patch'], + 'source_tmpl': 'quast_%(version)s.tar.gz', + 'source_urls': ['https://github.com/ablab/quast/archive/'], + 'checksums': [ + '9f30c03e0bfd261492fe6b72fb07645bdee5b29d741f75fc75857b6fa095d91d', # quast_5.0.2.tar.gz + '8ae7ebf45e5368ebc058fc208822a23d32ce1052bd53fd8c3aaa4ad14d3c95aa', # QUAST-5.0.2_fix-Python-3.8.patch + ], + }), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s quast.py quast"] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "wget quast.sf.net/test_data.tar.gz && " + "tar xzf test_data.tar.gz && " + "%(namelower)s.py --test && " + "rm ./test_data.tar.gz ./test_data -rf", + "%(namelower)s -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From bd5548be080adabb79cf36c8e1ceb7ba8b31be90 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 11 Oct 2021 12:17:32 +0200 Subject: [PATCH 1629/2365] rm switches should be before arguments --- easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb index c9d652ca8b..53e95a0065 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb @@ -50,7 +50,7 @@ sanity_check_commands = [ "wget quast.sf.net/test_data.tar.gz && " "tar xzf test_data.tar.gz && " "%(namelower)s.py --test && " - "rm ./test_data.tar.gz ./test_data -rf", + "rm -rf ./test_data.tar.gz ./test_data", "%(namelower)s -h", ] From cd72853232f4753b9bc201eec5c8f24c83b60623 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 12 Oct 2021 12:50:31 +0200 Subject: [PATCH 1630/2365] Dependencies of a commercial software (almost a bee) --- .../GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb | 58 +++++++++++++++++++ .../i/imkl/imkl-2020.4.304-NVHPC-21.2.eb | 39 +++++++++++++ .../OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 34 +++++++++++ .../q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb | 21 +++++++ .../UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb | 52 +++++++++++++++++ 5 files changed, 204 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb create mode 100644 easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb new file mode 100644 index 0000000000..4e78c65fb6 --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.1' +local_cudaversion = '11.2.1' +versionsuffix = '-CUDA-%s' % local_cudaversion + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cecc7dcc071107f77396f5553c9109790b6d2298ae29eb2dbbdd52b2a213e4ea'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CUDAcore', local_cudaversion, '', True), # needed by GDRCopy binaries, which are tools for testing + ('Check', '0.15.2'), +] + +# This easyconfig only installs the library and binaries of GDRCopy. Please +# keep in mind that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] + +local_envopts = "PREFIX=%(installdir)s CUDA=$EBROOTCUDACORE" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib exes %s" % local_envopts +installopts = local_envopts + +sanity_check_paths = { + 'files': ['bin/copybw', 'bin/copylat', 'bin/sanity', 'lib/libgdrapi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb new file mode 100644 index 0000000000..bf4b096ac1 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.4.304' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'NVHPC', 'version': '21.2'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb new file mode 100644 index 0000000000..8ef2dc343e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -0,0 +1,34 @@ +name = 'OpenMPI' +version = '4.0.5' +versionsuffix = '-CUDA-11.2.1' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'NVHPC', 'version': '21.2'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('libevent', '2.1.12'), + ('UCX', '1.9.0', versionsuffix), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), +] + +# disable MPI1 compatibility for now, see what breaks... +configopts = '--with-cuda=$EBROOTCUDACORE ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb b/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb new file mode 100644 index 0000000000..6fc8e3fd56 --- /dev/null +++ b/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'QD' +version = '2.3.17' +versionsuffix = '-20160110' +local_gitcommit = 'a5dbb61' + +homepage = 'https://github.com/scibuilder/QD' +description = "Quad Double computation package" + +toolchain = {'name': 'NVHPC', 'version': '21.2'} + +source_urls = ['https://github.com/scibuilder/QD/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_gitcommit, 'filename': SOURCE_TAR_GZ}] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['qdmod', 'qd']], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb new file mode 100644 index 0000000000..fd3d6e7b5d --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -0,0 +1,52 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.9.0' +local_cudaversion = '11.2.1' +versionsuffix = '-CUDA-%s' % local_cudaversion + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['a7a2c8841dc0d5444088a4373dc9b9cc68dbffcd917c1eba92ca8ed8e5e635fb'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('numactl', '2.0.13'), + ('CUDAcore', local_cudaversion, '', True), + ('GDRCopy', '2.1', versionsuffix), +] + +configure_cmd = "contrib/configure-release" +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' +configopts += '--with-cuda=$EBROOTCUDACORE --with-gdrcopy=$EBROOTGDRCOPY ' + +prebuildopts = 'unset CUDA_CFLAGS && unset LIBS && ' +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From a54855c75abdc1cb4370d2e991fb19e1ded825e9 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 12 Oct 2021 17:24:58 +0200 Subject: [PATCH 1631/2365] Dir with OSU MPI startup tests was missing from the PATH --- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb | 2 +- .../OSU-Micro-Benchmarks-5.7-gompi-2020b.eb | 2 +- .../OSU-Micro-Benchmarks-5.7-gompic-2020b.eb | 2 +- .../OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb index b13a760b9d..f66e7e0c42 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb @@ -14,7 +14,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb index 169f912486..a36a6b2ea0 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb @@ -14,7 +14,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb index f569964b49..36fcdf48c8 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb @@ -17,7 +17,7 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb index a3c2312f7d..45a7c6a32a 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb @@ -18,7 +18,7 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb index 0762e17f6c..8a01b3f40b 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb @@ -17,7 +17,7 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { From 4d8888212962a55cc9f46d67b9708add29f9ac4e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 12 Oct 2021 18:13:40 +0200 Subject: [PATCH 1632/2365] Added checksums to two eb files, fixed line that became too long --- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7-gompi-2020b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7-gompic-2020b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb | 4 +++- 5 files changed, 15 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb index f66e7e0c42..739dde4021 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb @@ -14,7 +14,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb index a36a6b2ea0..94f086b13d 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb @@ -14,7 +14,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb index 36fcdf48c8..7df7a5b835 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb @@ -17,7 +17,9 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb index 45a7c6a32a..1dd7a5a6e6 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb @@ -18,7 +18,9 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb index 8a01b3f40b..a1e5881a08 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb @@ -17,7 +17,9 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { From 3961dd05d49aa3ec05b1fcd66a68bd97a35bf125 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 13 Oct 2021 11:57:19 +0200 Subject: [PATCH 1633/2365] Update libGridXC-0.9.6-gompi-2020b.eb --- .../easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb index a46d4f4f17..4cfcff47e5 100644 --- a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb @@ -28,7 +28,7 @@ sanity_check_paths = { ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], - 'dirs': ['include'], + 'dirs': [], } moduleclass = 'phys' From d61dc0fbdb58105103adad804a02a038726304be Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 13 Oct 2021 11:57:32 +0200 Subject: [PATCH 1634/2365] Update libGridXC-0.9.6-iimpi-2020b.eb --- .../easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb index 3c9d3dbdce..e8ca5b5883 100644 --- a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb @@ -28,7 +28,7 @@ sanity_check_paths = { ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], - 'dirs': ['include'], + 'dirs': [], } moduleclass = 'phys' From c515d470820c49a2c4b97982b3e36a35e5cd218c Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 29 Jan 2021 16:13:28 +0100 Subject: [PATCH 1635/2365] Add xmlf90-1.5.4-GCC-10.2.0. --- .../x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..100e2c2696 --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'xmlf90' +version = '1.5.4' + +homepage = 'https://launchpad.net/xmlf90' +description = """xmlf90 is a basic XML parsing library written in Fortran.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0b1324ff224d5b5ad1127a6ad4f90979f6b127f1a517f98253eea377237bbe4'] + +sanity_check_paths = { + 'files': ['include/xmlf90_%s.mod' % x for x in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], + 'dirs': ['share/org.siesta-project'], +} + +moduleclass = 'data' From 899feb57da30166c3e42407d2d7eb4adfee25c60 Mon Sep 17 00:00:00 2001 From: alin m elena Date: Wed, 13 Oct 2021 11:38:04 +0100 Subject: [PATCH 1636/2365] change version to indicate is serial --- .../libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb new file mode 100644 index 0000000000..80974c5155 --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +version_suffix = 'serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'usempi': False} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +preconfigopts = 'unset MPIFC && unset MPICC && ' +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', ('lib/libfdf.a', 'lib64/libfdf.a')], + 'dirs': [''], +} + +moduleclass = 'data' From c6e818103f56f66a5bd692fa561e482551441eeb Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 13 Oct 2021 14:00:53 +0200 Subject: [PATCH 1637/2365] Add missing scripts from utils and analysis_scripts to bin --- .../cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index 5d9c5f8d47..a8269f3c48 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -47,9 +47,26 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/zhonge/cryodrgn/archive'], 'checksums': ['1efecc2a0add2392411076082c122039a490f5ddf3e01f1da38aea1a81592077'], + 'postinstallcmds': [ + "sed -i '1s|^|#!/usr/bin/env python\\n|' utils/* analysis_scripts/*", + 'cp utils/* analysis_scripts/* %(installdir)s/bin', + 'chmod +x %(installdir)s/bin/*.py' + ] }), ] -sanity_check_commands = ["%(namelower)s --help"] +local_scripts = [ + 'add_psize', 'filter_mrcs', 'filter_pkl', 'filter_star', 'flip_hand', 'fsc', 'invert_contrast', 'kmeans', + 'phase_flip', 'plotfsc', 'plot_loss', 'plot_z1', 'plot_z2', 'plot_z_pca', 'run_umap', 'translate_stack', 'tsne', + 'view_header', 'view_stack', 'write_starfile' +] + +sanity_check_paths = { + 'files': ['bin/%s.py' % x for x in local_scripts], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s --help'] +sanity_check_commands += ['%s.py -h' % x for x in local_scripts] moduleclass = 'chem' From c340f1bbe1e805553c7bb6c3c0c945a1b313faa1 Mon Sep 17 00:00:00 2001 From: alin m elena Date: Wed, 13 Oct 2021 14:06:43 +0100 Subject: [PATCH 1638/2365] inject checksum --- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb | 2 +- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb index 149f34fc77..107a697104 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] +checksums = ['0f9ee2c69dfc2fd085127aae4b3b794fad20ef5c2dad6c89728ce5fbf300eb75'] builddependencies = [ ('CMake', '3.18.4') diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb index 32d0079345..56558c5277 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'intel', 'version': '2020b'} source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] +checksums = ['0f9ee2c69dfc2fd085127aae4b3b794fad20ef5c2dad6c89728ce5fbf300eb75'] builddependencies = [ ('CMake', '3.18.4') From 0fabd550a4e4c3ad0357bdaee1c795cdb74f28ea Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Oct 2021 00:59:59 +0200 Subject: [PATCH 1639/2365] remove format mapping from homepage of Subread easyconfigs --- easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb index 17cdbfec0d..cb9042bbb7 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb @@ -7,7 +7,7 @@ name = 'Subread' version = '2.0.2' # HTTPS is not valid -homepage = 'http://%(namelower)s.sourceforge.net/' +homepage = 'http://subread.sourceforge.net/' description = """High performance read alignment, quantification and mutation discovery""" toolchain = {'name': 'GCC', 'version': '10.2.0'} From accd7ff3b40d179d988f646ce0ed1d7c422212f5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Oct 2021 01:38:50 +0200 Subject: [PATCH 1640/2365] replace sed with fix_python_shebang_for in cryoDRGN v0.3.2 --- .../c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index a8269f3c48..2a47fefb4a 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -48,13 +48,14 @@ exts_list = [ 'source_urls': ['https://github.com/zhonge/cryodrgn/archive'], 'checksums': ['1efecc2a0add2392411076082c122039a490f5ddf3e01f1da38aea1a81592077'], 'postinstallcmds': [ - "sed -i '1s|^|#!/usr/bin/env python\\n|' utils/* analysis_scripts/*", - 'cp utils/* analysis_scripts/* %(installdir)s/bin', - 'chmod +x %(installdir)s/bin/*.py' - ] + 'cp utils/* analysis_scripts/* %(installdir)s/bin', + 'chmod +x %(installdir)s/bin/*.py', + ], }), ] +fix_python_shebang_for = ['bin/*.py'] + local_scripts = [ 'add_psize', 'filter_mrcs', 'filter_pkl', 'filter_star', 'flip_hand', 'fsc', 'invert_contrast', 'kmeans', 'phase_flip', 'plotfsc', 'plot_loss', 'plot_z1', 'plot_z2', 'plot_z_pca', 'run_umap', 'translate_stack', 'tsne', From 95aeb13bb15b838309e90c2aca08cb06a3bcd0c4 Mon Sep 17 00:00:00 2001 From: alin m elena Date: Thu, 14 Oct 2021 08:12:55 +0100 Subject: [PATCH 1641/2365] address the comments --- .../easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb index 80974c5155..a7fbdaa174 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb @@ -2,23 +2,21 @@ easyblock = 'ConfigureMake' name = 'libfdf' version = '0.2.2' -version_suffix = 'serial' +versionsuffix = 'serial' homepage = 'https://launchpad.net/libfdf' description = """LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF).""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -toolchainopts = {'usempi': False} source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] sources = ['libfdf-%(version)s.tar.gz'] checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] -preconfigopts = 'unset MPIFC && unset MPICC && ' configopts = ' --without-mpi ' sanity_check_paths = { - 'files': ['include/fdf.mod', ('lib/libfdf.a', 'lib64/libfdf.a')], + 'files': ['include/fdf.mod', 'lib/libfdf.a'], 'dirs': [''], } From d1ee710e3e404c0ef24c6d622e247ac6f264ee7f Mon Sep 17 00:00:00 2001 From: alin m elena Date: Thu, 14 Oct 2021 08:16:21 +0100 Subject: [PATCH 1642/2365] address the comments --- .../easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb index 93bb74df60..87e76b10a6 100644 --- a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb @@ -8,16 +8,16 @@ description = """libpspio is a library to read and write pseudopotentials in mul toolchain = {'name': 'GCC', 'version': '10.2.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://gitlab.e-cam2020.eu/esl/pspio/uploads/7efa924be97bd46354237ca3fb89495e/'] -checksums = ['740861617e1feb50a9e00609769b12d8'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cb3d51ffa6b822305bb943edc7ddfaf1cfc1b928f0594330d732330bfc081850'] configopts = ' --enable-gsl --enable-fortran ' dependencies = [('GSL', '2.6')] sanity_check_paths = { - 'files': ['include/pspiof_m.mod', 'include/pspio.h'] + [('lib/libpspiof.a', 'lib64/libpspiof.a')], + 'files': ['include/pspiof_m.mod', 'include/pspio.h', 'lib/libpspiof.a'], 'dirs': [], } From a91b48b649f9a79144b99278cb944b337507cd45 Mon Sep 17 00:00:00 2001 From: alin m elena Date: Thu, 14 Oct 2021 08:34:58 +0100 Subject: [PATCH 1643/2365] keep style happy --- .../easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb index a7fbdaa174..71cbe3216a 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'libfdf' version = '0.2.2' -versionsuffix = 'serial' +versionsuffix = '-serial' homepage = 'https://launchpad.net/libfdf' description = """LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF).""" From b84ad709f5eefd0089b9521c70a970be911206e3 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 10:23:31 +0200 Subject: [PATCH 1644/2365] Update libmbd-0.10.4-foss-2020b.eb --- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb index 107a697104..94410426c2 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -35,16 +35,15 @@ local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" parallel = 1 -# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# make sure that built libraries (libmbd.so) in build directory are picked when running tests # this is required when RPATH linking is used pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " runtest = 'test' sanity_check_paths = { - 'files': ['lib/libmbd.so'] + - ['lib64/libmbd.so'], + 'files': ['lib/libmbd.%s' % SHLIB_EXT], 'dirs': ['include', 'lib/cmake/mbd'], } -moduleclass = 'chem' +moduleclass = 'phys' From 0b3c3508c004c824ce7c5ffc87e55501064c9eed Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 10:25:30 +0200 Subject: [PATCH 1645/2365] Update libmbd-0.10.4-foss-2020b.eb --- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb index 94410426c2..f9a79031af 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -42,8 +42,8 @@ pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PAT runtest = 'test' sanity_check_paths = { - 'files': ['lib/libmbd.%s' % SHLIB_EXT], - 'dirs': ['include', 'lib/cmake/mbd'], + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd.h', 'include/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], } moduleclass = 'phys' From bbb285e0d4dfc6dbbc900c3af7d31cdfd2c731af Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 10:27:03 +0200 Subject: [PATCH 1646/2365] Update libmbd-0.10.4-intel-2020b.eb --- .../easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb index 56558c5277..f33ad17bec 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -35,16 +35,15 @@ local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" parallel = 1 -# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# make sure that built libraries (libmbd.so) in build directory are picked when running tests # this is required when RPATH linking is used pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " runtest = 'test' sanity_check_paths = { - 'files': ['lib/libmbd.so'] + - ['lib64/libmbd.so'], - 'dirs': ['include', 'lib/cmake/mbd'], + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd.h', 'include/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], } -moduleclass = 'chem' +moduleclass = 'phys' From 42b3e6015fb8bd1e4519434e253852c490c3a5af Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 10:38:39 +0200 Subject: [PATCH 1647/2365] Explicitly set compiler and compilation flags --- easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb index d4ec2b5be5..7551ae8627 100644 --- a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb @@ -14,6 +14,9 @@ source_urls = ['https://github.com/zerothi/fdict/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] +# Create file that sets the compiler (and compilation flags) to use +prebuildopts = 'echo FC=$FC > setup.make && echo FFLAGS=$FFLAGS >> setup.make &&' + files_to_copy = [(['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), (['settings.bash'], 'bin')] sanity_check_paths = { From 3c1cfc3b4672e9ae3f36800d086273173386f59f Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 13 Oct 2021 16:14:26 +0200 Subject: [PATCH 1648/2365] Add ELSI-RCI v0.1.0 for foss/2020b and intel/2020b. --- .../e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb | 41 +++++++++++++++++++ .../e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb | 40 ++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb new file mode 100644 index 0000000000..1416d14559 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + + +# Compilation of tests seem to be broken, so are disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb new file mode 100644 index 0000000000..1c578e61e1 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +# Compilation of tests seem to be broken, so are disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' From e8730ecc707fd9e62b26100450e53e27a5d1f58f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 14:26:52 +0200 Subject: [PATCH 1649/2365] add SHA256 checksum for QD 2.3.17 --- easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb b/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb index 6fc8e3fd56..5d803a7d74 100644 --- a/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb +++ b/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'NVHPC', 'version': '21.2'} source_urls = ['https://github.com/scibuilder/QD/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_gitcommit, 'filename': SOURCE_TAR_GZ}] +checksums = ['1e5949b7d20434193d496c28070d8f2fb6406a7688a86080dfdac57fbe730624'] sanity_check_paths = { 'files': ['lib/lib%s.a' % x for x in ['qdmod', 'qd']], From e7a4f0bbb2f045adc0523a19d974029010c22fdc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 14:30:59 +0200 Subject: [PATCH 1650/2365] skip mkl_fused_batch_norm_op_test test for TensorFlow 2.5.0 (broken on AMD EPYC systems) --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 2 ++ .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index b8e0b20e47..a394921436 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -203,6 +203,8 @@ exts_list = [ # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 '-//tensorflow/core/common_runtime:mkl_layout_pass_test', '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", 'with_xla': True, diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 7c571141ea..9794ccd903 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -218,6 +218,8 @@ exts_list = [ # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 '-//tensorflow/core/common_runtime:mkl_layout_pass_test', '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + From f87c98db616e8dbd3d3c7b77524fc087c9e9eb3a Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 17:57:30 +0200 Subject: [PATCH 1651/2365] Make sure to set up the makefile and use Lua as a dep --- .../f/flook/flook-0.8.1-GCC-10.2.0.eb | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb index 6b9f747a77..8ddf6098dd 100644 --- a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb @@ -14,7 +14,21 @@ source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] sources = ['v%(version)s/flook-%(version)s.tar.gz'] checksums = ['beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'] -dependencies = [('libreadline', '8.0')] +dependencies = [('Lua', '5.4.2')] + +# Construct the 'setup.make' file +prebuildopts = 'echo CC = $CC > setup.make &&' +prebuildopts += 'echo FC = "$FC" >> setup.make &&' +prebuildopts += 'echo CFLAGS = "$CFLAGS" >> setup.make &&' +prebuildopts += 'echo FFLAGS = "$FFLAGS" >> setup.make &&' +prebuildopts += 'echo ".f90.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo ".F90.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo ".c.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(CC) -c \$(CFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo "LUA_DIR = $EBROOTLUA" >> setup.make &&' +prebuildopts += 'echo "INC += -I\$(LUA_DIR)/include" >> setup.make &&' buildopts = ' liball ' parallel = 1 From 9ed76caccd8055101effa2cb777f03195cffb060 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 20:33:25 +0200 Subject: [PATCH 1652/2365] strip out extracting of examples in imkl easyconfig, now done by imkl easyblock --- .../i/imkl/imkl-2020.4.304-NVHPC-21.2.eb | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb index bf4b096ac1..75ac380269 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb @@ -23,17 +23,4 @@ license_file = HOME + '/licenses/intel/license.lic' interfaces = True -postinstallcmds = [ - # extract the examples - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', -] - -modextravars = { - 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', -} - moduleclass = 'numlib' From 2e642e1789ae09ef9f5f682244880e613aea1e43 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 20:48:19 +0200 Subject: [PATCH 1653/2365] add missing patch for OpenMPI 4.0.5, add back commented out configure option to re-enable MPI-1 --- .../o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb index 8ef2dc343e..949050f89e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -10,7 +10,12 @@ toolchainopts = {'pic': True} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] builddependencies = [ ('pkg-config', '0.29.2'), @@ -25,9 +30,11 @@ dependencies = [ ('PMIx', '3.1.5'), ] -# disable MPI1 compatibility for now, see what breaks... configopts = '--with-cuda=$EBROOTCUDACORE ' +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + # to enable SLURM integration (site-specific) # configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' From 083378b2d3945190ac3cba629a4001b3be616b74 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 15 Oct 2021 09:09:07 +0200 Subject: [PATCH 1654/2365] Update ELSI-RCI-0.1.0-foss-2020b.eb --- easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb index 1416d14559..24ee50dfb9 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb @@ -25,7 +25,7 @@ builddependencies = [ ] -# Compilation of tests seem to be broken, so are disable it +# Compilation of tests seem to be broken, so disable it configopts = [ "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" From bd41c7210a5aac9504647ecd2d18424fb71021bb Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 15 Oct 2021 09:09:30 +0200 Subject: [PATCH 1655/2365] Update ELSI-RCI-0.1.0-intel-2020b.eb --- easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb index 1c578e61e1..8e5e7166b3 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb @@ -24,7 +24,7 @@ builddependencies = [ ('CMake', '3.18.4'), ] -# Compilation of tests seem to be broken, so are disable it +# Compilation of tests seem to be broken, so disable it configopts = [ "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" From 894bb395011608969ddce6d995ebe219191d9513 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 29 Jan 2021 16:34:26 +0100 Subject: [PATCH 1656/2365] Add NTPoly-2.5.1-foss-2020b.eb. --- .../n/NTPoly/NTPoly-2.5.1-foss-2020b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb new file mode 100644 index 0000000000..148464f5a7 --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.5.1' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5d1abd3dc3286167caf0c326ef14838ac8360aa1e912bd7bd6d212259fbff1ac'] + +configopts = ['-DBUILD_SHARED_LIBS=on'] + +builddependencies = [('CMake', '3.18.4')] + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From b3875605a68b22fc6d3161a146b1d68236baf004 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 9 Jun 2021 15:23:59 +0200 Subject: [PATCH 1657/2365] Add Bison-3.5.3-GCCcore-10.2.0.eb. This is required to compile ELSI-2.6.4, as it does not seem to work with newer versions of Bison. --- .../b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c20e3f3948 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.5.3' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['34e201d963156618a0ea5bc87220f660a1e08403dd3c7c7903d4f38db3f40039'] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.35', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' From 200e5551723b2639ba977a47b65371853353d4df Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 9 Jun 2021 17:40:24 +0200 Subject: [PATCH 1658/2365] Add ELSI-2.6.4-intel-2020b and NTPoly-2.5.1-intel-2020b. --- .../n/NTPoly/NTPoly-2.5.1-intel-2020b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb new file mode 100644 index 0000000000..38ed055e46 --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.5.1' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5d1abd3dc3286167caf0c326ef14838ac8360aa1e912bd7bd6d212259fbff1ac'] + +configopts = ['-DBUILD_SHARED_LIBS=on'] + +builddependencies = [('CMake', '3.18.4')] + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From ea410896a6afc673c3470398322e5a587ab55120 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 15 Oct 2021 11:56:55 +0200 Subject: [PATCH 1659/2365] Added a version suffix to ELSI-2.6.4-intel-2020b and ELSI-2.6.4-foss-2020b to make it consistent with older easyconfigs. --- .../e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 40 +++++++++++++++++++ .../e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb | 38 ++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb new file mode 100644 index 0000000000..9faa87a5f8 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -0,0 +1,40 @@ +name = 'ELSI' +version = '2.6.4' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['pexsi-1.2.0-mpi30.patch'] +checksums = [ + 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz + 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.5.3'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('ELPA', '2020.11.001'), + ('NTPoly', '2.5.1'), +] + +build_internal_pexsi = True + +configopts = "-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS='-fallow-argument-mismatch' -DCMAKE_CXX_FLAGS='-std=c++11'" + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb new file mode 100644 index 0000000000..48b7ddd05d --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb @@ -0,0 +1,38 @@ +name = 'ELSI' +version = '2.6.4' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.5.3'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('ELPA', '2020.11.001'), + ('NTPoly', '2.5.1'), +] + +build_internal_pexsi = True + +configopts = "-DENABLEBSEPACK=ON" + +runtest = True + +moduleclass = 'math' From 32a206e7a8ac9e6ad9cd4ab1740c8533c0ad9a44 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 15 Oct 2021 11:57:27 +0200 Subject: [PATCH 1660/2365] Make sure not to overwrite the Fortran flags set by EasyBuild. --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 9faa87a5f8..a09b2e0f5c 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -33,7 +33,7 @@ dependencies = [ build_internal_pexsi = True -configopts = "-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS='-fallow-argument-mismatch' -DCMAKE_CXX_FLAGS='-std=c++11'" +configopts = "-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS='-fallow-argument-mismatch $FFLAGS' -DCMAKE_CXX_FLAGS='-std=c++11'" runtest = True From 9eb0fc6a0b6db910a446026679528c14bb9393da Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 15 Oct 2021 12:00:55 +0200 Subject: [PATCH 1661/2365] Fix quotes. --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index a09b2e0f5c..6e3fbc632a 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -33,7 +33,7 @@ dependencies = [ build_internal_pexsi = True -configopts = "-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS='-fallow-argument-mismatch $FFLAGS' -DCMAKE_CXX_FLAGS='-std=c++11'" +configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" -DCMAKE_CXX_FLAGS="-std=c++11"' runtest = True From ad71492a4e07accf57b0ebd2d0ee75da023b37ef Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 15 Oct 2021 13:47:01 +0200 Subject: [PATCH 1662/2365] adding easyconfigs: XCrySDen-1.6.2-foss-2020b.eb, Togl-2.0-GCCcore-10.2.0.eb, bwidget-1.9.14-GCCcore-10.2.0.eb --- .../bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb | 26 ++++++++++ .../t/Togl/Togl-2.0-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ .../x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb | 34 ++++++++++++++ 3 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..14d2aeee87 --- /dev/null +++ b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'bwidget' +version = '1.9.14' + +homepage = 'https://core.tcl-lang.org/bwidget/home' +description = 'The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://downloads.sourceforge.net/project/tcllib/BWidget/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8e9692140167161877601445e7a5b9da5bb738ce8d08ee99b016629bc784a672'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Tk', '8.6.10')] + +modextrapaths = {'TCLLIBPATH': '.'} + +sanity_check_paths = { + 'files': ['button.tcl'], + 'dirs': ['BWman'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7392a7e7e1 --- /dev/null +++ b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'Togl' +version = '2.0' + +homepage = 'https://sourceforge.net/projects/togl/' +description = """A Tcl/Tk widget for OpenGL rendering.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://downloads.sourceforge.net/project/togl/Togl/2.0/'] +sources = ['%(name)s%(version)s-src.tar.gz'] +patches = [ + 'Togl-2.0_configure.patch', + 'Togl-2.0_decl.patch', +] +checksums = [ + 'b7d4a90bbad3aca618d505ee99e7fd8fb04c829f63231dda2360f557ba3f7610', # Togl2.0-src.tar.gz + 'da97f36b60cd107444cd92453809135b14dc1e8775146b3ba0731da8002e6f9f', # Togl-2.0_configure.patch + '05db6b3ca5139f60616d074903883a3070fcfb1eb8c965b0938779b4f9a6ec6a', # Togl-2.0_decl.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Mesa', '20.2.1'), + ('Tk', '8.6.10'), + ('Tcl', '8.6.10'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -DTOGL_USE_FONTS=0" && ' + +configopts = "--prefix=%(installdir)s --exec-prefix=%(installdir)s " +configopts += "--with-tcl=$EBROOTTCL/lib --with-tk=$EBROOTTK/lib" + +modextrapaths = { + 'LD_LIBRARY_PATH': 'lib/Togl%(version)s', + 'LIBRARY_PATH': 'lib/Togl%(version)s', +} + + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb new file mode 100644 index 0000000000..65d2188148 --- /dev/null +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb @@ -0,0 +1,34 @@ +name = 'XCrySDen' +version = '1.6.2' + +homepage = "http://www.xcrysden.org/" +description = """XCrySDen is a crystalline and molecular structure visualisation program aiming + at display of isosurfaces and contours, which can be superimposed on crystalline structures and + interactively rotated and manipulated.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'vectorize': False} + +source_urls = ["http://www.xcrysden.org/download/"] +sources = [SOURCELOWER_TAR_GZ] +patches = ['XCrySDen-1.6.2_no-bwidget.patch'] +checksums = [ + '811736ee598bec1a5b427fd10e4e063a30dd7cadae96a43a50b36ce90a4f503f', # xcrysden-1.6.2.tar.gz + '85f23723f67e1a4af2575d403154f9cf8194369a0ff6ed96437a51f2ea81a220', # XCrySDen-1.6.2_no-bwidget.patch +] + +prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" + +local_tcltk_ver = '8.6.10' +dependencies = [ + ('Tcl', local_tcltk_ver), + ('Tk', local_tcltk_ver), + ('Togl', '2.0'), + ('X11', '20201008'), + ('libGLU', '9.0.1'), + ('bwidget', '1.9.14'), +] + +parallel = 1 + +moduleclass = 'vis' From aae104dad45da1f81e482dd36f2ead9e1cdb26dd Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 15 Oct 2021 13:25:07 +0100 Subject: [PATCH 1663/2365] [fdict] enable intel toolchain --- .../fdict/fdict-0.8.0-iccifort-2020.4.304.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..2b92b32e4e --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ + A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. + """ + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +# Create file that sets the compiler (and compilation flags) to use +prebuildopts = 'echo FC=$FC > setup.make && echo FFLAGS=$FFLAGS >> setup.make &&' + +files_to_copy = [(['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), (['settings.bash'], 'bin')] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['bin'], +} + +moduleclass = 'data' From fb0eb995f1e7611d4aa1bc306d18c25e57dd5270 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 15 Oct 2021 13:29:50 +0100 Subject: [PATCH 1664/2365] [flook] add intel toolchain --- .../flook/flook-0.8.1-iccifort-2020.4.304.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..6ef6d3bf5e --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """ + The fortran-Lua-hook library. + """ + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +checksums = ['beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'] + +dependencies = [('Lua', '5.4.2')] + +# Construct the 'setup.make' file +prebuildopts = 'echo CC = $CC > setup.make &&' +prebuildopts += 'echo FC = "$FC" >> setup.make &&' +prebuildopts += 'echo CFLAGS = "$CFLAGS" >> setup.make &&' +prebuildopts += 'echo FFLAGS = "$FFLAGS" >> setup.make &&' +prebuildopts += 'echo ".f90.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo ".F90.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo ".c.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(CC) -c \$(CFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo "LUA_DIR = $EBROOTLUA" >> setup.make &&' +prebuildopts += 'echo "INC += -I\$(LUA_DIR)/include" >> setup.make &&' + +buildopts = ' liball ' +parallel = 1 + +files_to_copy = [(['libflookall.a', 'libflook.a'], 'lib'), (['flook.mod'], 'include')] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' From 533b3ff091f563a65256bddd7f22e0aba6a54d47 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 15 Oct 2021 15:41:31 +0200 Subject: [PATCH 1665/2365] Break long line. --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 6e3fbc632a..0ffc96295a 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -33,7 +33,8 @@ dependencies = [ build_internal_pexsi = True -configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" -DCMAKE_CXX_FLAGS="-std=c++11"' +configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' +configopts += '-DCMAKE_CXX_FLAGS="-std=c++11"' runtest = True From a221e26697b5a910966ace37e0f6c2db28d3340b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 15 Oct 2021 23:50:50 +0200 Subject: [PATCH 1666/2365] extirp setup.make out of easyconfig flook-0.8.1-iccifort-2020.4.304.eb --- .../f/flook/flook-0.8.1-GCC-10.2.0.eb | 33 ++++++++----------- .../flook/flook-0.8.1-iccifort-2020.4.304.eb | 33 ++++++++----------- 2 files changed, 26 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb index 8ddf6098dd..fc27032402 100644 --- a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb @@ -4,36 +4,29 @@ name = 'flook' version = '0.8.1' homepage = 'https://github.com/ElectronicStructureLibrary/flook' -description = """ - The fortran-Lua-hook library. - """ +description = """The fortran-Lua-hook library.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] sources = ['v%(version)s/flook-%(version)s.tar.gz'] -checksums = ['beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] dependencies = [('Lua', '5.4.2')] -# Construct the 'setup.make' file -prebuildopts = 'echo CC = $CC > setup.make &&' -prebuildopts += 'echo FC = "$FC" >> setup.make &&' -prebuildopts += 'echo CFLAGS = "$CFLAGS" >> setup.make &&' -prebuildopts += 'echo FFLAGS = "$FFLAGS" >> setup.make &&' -prebuildopts += 'echo ".f90.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo ".F90.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo ".c.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(CC) -c \$(CFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo "LUA_DIR = $EBROOTLUA" >> setup.make &&' -prebuildopts += 'echo "INC += -I\$(LUA_DIR)/include" >> setup.make &&' - -buildopts = ' liball ' parallel = 1 -files_to_copy = [(['libflookall.a', 'libflook.a'], 'lib'), (['flook.mod'], 'include')] +local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] sanity_check_paths = { 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb index 6ef6d3bf5e..ffd6dc3cff 100644 --- a/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb @@ -4,36 +4,29 @@ name = 'flook' version = '0.8.1' homepage = 'https://github.com/ElectronicStructureLibrary/flook' -description = """ - The fortran-Lua-hook library. - """ +description = """The fortran-Lua-hook library.""" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] sources = ['v%(version)s/flook-%(version)s.tar.gz'] -checksums = ['beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] dependencies = [('Lua', '5.4.2')] -# Construct the 'setup.make' file -prebuildopts = 'echo CC = $CC > setup.make &&' -prebuildopts += 'echo FC = "$FC" >> setup.make &&' -prebuildopts += 'echo CFLAGS = "$CFLAGS" >> setup.make &&' -prebuildopts += 'echo FFLAGS = "$FFLAGS" >> setup.make &&' -prebuildopts += 'echo ".f90.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo ".F90.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo ".c.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(CC) -c \$(CFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo "LUA_DIR = $EBROOTLUA" >> setup.make &&' -prebuildopts += 'echo "INC += -I\$(LUA_DIR)/include" >> setup.make &&' - -buildopts = ' liball ' parallel = 1 -files_to_copy = [(['libflookall.a', 'libflook.a'], 'lib'), (['flook.mod'], 'include')] +local_comp_flags = 'VENDOR="intel" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] sanity_check_paths = { 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], From c3af3580a88d9b2866a5db42769ee52c60064e24 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 16 Oct 2021 00:17:24 +0200 Subject: [PATCH 1667/2365] use intel vendor settings with EB flags in fdict-0.8.0-iccifort-2020.4.304.eb --- .../easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb | 13 ++++++++----- .../f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb | 13 ++++++++----- 2 files changed, 16 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb index 7551ae8627..3c66280563 100644 --- a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb @@ -5,8 +5,8 @@ version = '0.8.0' homepage = 'https://github.com/zerothi/fdict' description = """ - A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. - """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" toolchain = {'name': 'GCC', 'version': '10.2.0'} @@ -14,10 +14,13 @@ source_urls = ['https://github.com/zerothi/fdict/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] -# Create file that sets the compiler (and compilation flags) to use -prebuildopts = 'echo FC=$FC > setup.make && echo FFLAGS=$FFLAGS >> setup.make &&' +buildopts = 'VENDOR="gnu" FFLAGS="$FFLAGS"' -files_to_copy = [(['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), (['settings.bash'], 'bin')] +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'bin'), +] sanity_check_paths = { 'files': ['include/dictionary.mod', 'lib/libfdict.a'], diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb index 2b92b32e4e..62851d38d0 100644 --- a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb @@ -5,8 +5,8 @@ version = '0.8.0' homepage = 'https://github.com/zerothi/fdict' description = """ - A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. - """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} @@ -14,10 +14,13 @@ source_urls = ['https://github.com/zerothi/fdict/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] -# Create file that sets the compiler (and compilation flags) to use -prebuildopts = 'echo FC=$FC > setup.make && echo FFLAGS=$FFLAGS >> setup.make &&' +buildopts = 'VENDOR="intel" FFLAGS="$FFLAGS" FPP="$FC -E -P"' -files_to_copy = [(['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), (['settings.bash'], 'bin')] +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'bin'), +] sanity_check_paths = { 'files': ['include/dictionary.mod', 'lib/libfdict.a'], From eda14436708b883fbee39fde64f371a8cd45575c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 16 Oct 2021 00:18:17 +0200 Subject: [PATCH 1668/2365] install settings.bash in share dir of fdict-0.8.0-iccifort-2020.4.304.eb --- easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb | 4 ++-- .../easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb index 3c66280563..bfae886c93 100644 --- a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb @@ -19,12 +19,12 @@ buildopts = 'VENDOR="gnu" FFLAGS="$FFLAGS"' files_to_copy = [ (['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), - (['settings.bash'], 'bin'), + (['settings.bash'], 'share'), ] sanity_check_paths = { 'files': ['include/dictionary.mod', 'lib/libfdict.a'], - 'dirs': ['bin'], + 'dirs': ['share'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb index 62851d38d0..1158369a84 100644 --- a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb @@ -19,12 +19,12 @@ buildopts = 'VENDOR="intel" FFLAGS="$FFLAGS" FPP="$FC -E -P"' files_to_copy = [ (['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), - (['settings.bash'], 'bin'), + (['settings.bash'], 'share'), ] sanity_check_paths = { 'files': ['include/dictionary.mod', 'lib/libfdict.a'], - 'dirs': ['bin'], + 'dirs': ['share'], } moduleclass = 'data' From 1327067f478a329065883c2f4561d9cb3ccb5fcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 Oct 2021 13:12:44 +0200 Subject: [PATCH 1669/2365] remove duplicate empty line --- easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb index 7392a7e7e1..b764b7ccc1 100644 --- a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb @@ -38,7 +38,6 @@ modextrapaths = { 'LIBRARY_PATH': 'lib/Togl%(version)s', } - sanity_check_paths = { 'files': [], 'dirs': ['include', 'lib'], From 0d9481baf943b4c7ef29119628401cd3abe71fbd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 Oct 2021 13:13:15 +0200 Subject: [PATCH 1670/2365] move down prebuildopts in XCrySDen easyconfig --- easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb index 65d2188148..207a525546 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb @@ -17,8 +17,6 @@ checksums = [ '85f23723f67e1a4af2575d403154f9cf8194369a0ff6ed96437a51f2ea81a220', # XCrySDen-1.6.2_no-bwidget.patch ] -prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" - local_tcltk_ver = '8.6.10' dependencies = [ ('Tcl', local_tcltk_ver), @@ -31,4 +29,6 @@ dependencies = [ parallel = 1 +prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" + moduleclass = 'vis' From 5936bc83ed031366222c9d0c6e23f5aee6ce625f Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 18 Oct 2021 11:12:18 +0200 Subject: [PATCH 1671/2365] Make sure not to overwrite the C++ flags set by EasyBuild. --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 0ffc96295a..f0577f3105 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -34,7 +34,7 @@ dependencies = [ build_internal_pexsi = True configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' -configopts += '-DCMAKE_CXX_FLAGS="-std=c++11"' +configopts += '-DCMAKE_CXX_FLAGS="-std=c++11 $CXXFLAGS"' runtest = True From 2bca8282583181445fdefbac2fbee1f47e6d9e41 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 18 Oct 2021 15:45:51 +0000 Subject: [PATCH 1672/2365] Version bump. Improvements on JAX etc --- ...-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..66d8b4e92b --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.23.0' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-{}'.format(local_tf_version) + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('flatbuffers', '1.12.0'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('TensorFlow', local_tf_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 76a60f23a4e1561e43a3b6c7630187402cbec5bf Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Tue, 19 Oct 2021 10:26:58 +0100 Subject: [PATCH 1673/2365] [libpsml][xmlf90] build them with intel toolchain --- .../xmlf90-1.5.4-iccifort-2020.4.304.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..1e938b9be2 --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'xmlf90' +version = '1.5.4' + +homepage = 'https://launchpad.net/xmlf90' +description = """xmlf90 is a basic XML parsing library written in Fortran.""" + +# can't move down to GCCcore and combine with Intel, gfortran modules are incompatible with ifort +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0b1324ff224d5b5ad1127a6ad4f90979f6b127f1a517f98253eea377237bbe4'] + +sanity_check_paths = { + 'files': ['include/xmlf90_%s.mod' % x for x in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], + 'dirs': ['share/org.siesta-project'], +} + +moduleclass = 'data' From e93951c5438f5f884a7fc7c460e1ca59904c9b98 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Tue, 19 Oct 2021 11:04:29 +0100 Subject: [PATCH 1674/2365] [libpspio] add intel forctoolchain --- .../libpspio-0.2.4-iccifort-2020.4.304.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..6b551f2ed9 --- /dev/null +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-iccifort-2020.4.304.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpspio' +version = '0.2.4' + +homepage = 'https://gitlab.e-cam2020.eu/esl/pspio/' +description = """libpspio is a library to read and write pseudopotentials in multiple formats.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://gitlab.e-cam2020.eu/esl/pspio/uploads/7efa924be97bd46354237ca3fb89495e/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cb3d51ffa6b822305bb943edc7ddfaf1cfc1b928f0594330d732330bfc081850'] + +configopts = ' --enable-gsl --enable-fortran ' + +dependencies = [('GSL', '2.6')] + +sanity_check_paths = { + 'files': ['include/pspiof_m.mod', 'include/pspio.h', 'lib/libpspiof.a'], + 'dirs': [], +} + +moduleclass = 'phys' From adc708f4bf159e1c1dec5ff0fc02cdb5e80c42e6 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Tue, 19 Oct 2021 11:49:53 +0100 Subject: [PATCH 1675/2365] [libfdf] add intel toolchain --- ...libfdf-0.2.2-iccifort-2020.4.304-serial.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb new file mode 100644 index 0000000000..bb206d03e6 --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +versionsuffix = '-serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' From 6201574f0c00f049d7e96123e49e7450004ba704 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 14:58:26 +0200 Subject: [PATCH 1676/2365] Use toolchainopts to set C++ standard --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index f0577f3105..8c30a9e232 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -10,7 +10,7 @@ description = """ELSI provides and enhances scalable, open-source software libra """ toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True, 'pic': True} +toolchainopts = {'usempi': True, 'pic': True, , 'cstd': 'c++11'} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] sources = [SOURCELOWER_TAR_GZ] @@ -34,7 +34,6 @@ dependencies = [ build_internal_pexsi = True configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' -configopts += '-DCMAKE_CXX_FLAGS="-std=c++11 $CXXFLAGS"' runtest = True From 4ad79d18cd5a567f1915aad093b1e3eb69c60430 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 14:59:51 +0200 Subject: [PATCH 1677/2365] Typo --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 8c30a9e232..3534b95faa 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -10,7 +10,7 @@ description = """ELSI provides and enhances scalable, open-source software libra """ toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True, 'pic': True, , 'cstd': 'c++11'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11'} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] sources = [SOURCELOWER_TAR_GZ] From d88464a721fd76f32c9da56b013077a9e3d1f144 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 15:23:14 +0200 Subject: [PATCH 1678/2365] Rename ESL-Bundle-0.6.0-foss-2020b.eb to ESL-Bundle-0.6.1-foss-2020b.eb --- .../ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb new file mode 100644 index 0000000000..d0bffc67f0 --- /dev/null +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'ESL-Bundle' +version = '0.6.1' + +homepage = 'https://esl.cecam.org' + +description = """ + The ESL Bundle is a collection of libraries and utilities broadly used in + electronic structure calculations, put together to make their use easier by + researchers and scientific software developers. ESL stands for Electronic + Structure Library, an initiative which distributes quality software and + promotes open standards for high-performance computing applications in the + field of electronic structure calculations. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('ELSI-RCI', '0.1.0'), + ('fdict', '0.8.0'), + ('flook', '0.8.1'), + ('libfdf', '0.2.2', '-serial'), + ('libmbd', '0.10.4'), + ('libpsml', '1.1.10'), + ('libpspio', '0.2.4'), + ('libxc', '4.3.4'), + ('libGridXC', '0.9.6'), + ('libvdwxc', '0.4.0'), + ('PSolver', '1.8.3'), + ('ELSI', '2.6.4'), + ('spglib', '1.16.1'), + ('Wannier90', '3.1.0'), +] + +moduleclass = 'phys' From f07a734e368c93cc822309b8f936a7994e4bf614 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 15:23:38 +0200 Subject: [PATCH 1679/2365] Rename ESL-Bundle-0.6.0-intel-2020b.eb to ESL-Bundle-0.6.1-intel-2020b.eb --- .../ESL-Bundle-0.6.1-intel-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb new file mode 100644 index 0000000000..354cab5b34 --- /dev/null +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'ESL-Bundle' +version = '0.6.1' + +homepage = 'https://esl.cecam.org' + +description = """ + The ESL Bundle is a collection of libraries and utilities broadly used in + electronic structure calculations, put together to make their use easier by + researchers and scientific software developers. ESL stands for Electronic + Structure Library, an initiative which distributes quality software and + promotes open standards for high-performance computing applications in the + field of electronic structure calculations. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('ELSI-RCI', '0.1.0'), + ('fdict', '0.8.0'), + ('flook', '0.8.1'), + ('libfdf', '0.2.2', '-serial'), + ('libmbd', '0.10.4'), + ('libpsml', '1.1.10'), + ('libpspio', '0.2.4'), + ('libxc', '4.3.4'), + ('libGridXC', '0.9.6'), + ('libvdwxc', '0.4.0'), + ('PSolver', '1.8.3'), + ('ELSI', '2.6.4'), + ('spglib', '1.16.1'), + ('Wannier90', '3.1.0'), +] + +moduleclass = 'phys' From 0ceb6b36aca5f4eb32ba61f5f778ae648cd5cf57 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 16:16:42 +0200 Subject: [PATCH 1680/2365] Delete ESL-Bundle-0.6.1-intel-2020b.eb --- .../ESL-Bundle-0.6.1-intel-2020b.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb deleted file mode 100644 index 354cab5b34..0000000000 --- a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'Bundle' - -name = 'ESL-Bundle' -version = '0.6.1' - -homepage = 'https://esl.cecam.org' - -description = """ - The ESL Bundle is a collection of libraries and utilities broadly used in - electronic structure calculations, put together to make their use easier by - researchers and scientific software developers. ESL stands for Electronic - Structure Library, an initiative which distributes quality software and - promotes open standards for high-performance computing applications in the - field of electronic structure calculations. -""" - -toolchain = {'name': 'intel', 'version': '2020b'} - -dependencies = [ - ('ELSI-RCI', '0.1.0'), - ('fdict', '0.8.0'), - ('flook', '0.8.1'), - ('libfdf', '0.2.2', '-serial'), - ('libmbd', '0.10.4'), - ('libpsml', '1.1.10'), - ('libpspio', '0.2.4'), - ('libxc', '4.3.4'), - ('libGridXC', '0.9.6'), - ('libvdwxc', '0.4.0'), - ('PSolver', '1.8.3'), - ('ELSI', '2.6.4'), - ('spglib', '1.16.1'), - ('Wannier90', '3.1.0'), -] - -moduleclass = 'phys' From c3f0e5f4cb4740d462d8ada8b947ee3a984b4272 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 16:17:14 +0200 Subject: [PATCH 1681/2365] Update ESL-Bundle-0.6.1-foss-2020b.eb --- .../easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb index d0bffc67f0..640410c954 100644 --- a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb @@ -28,7 +28,7 @@ dependencies = [ ('libGridXC', '0.9.6'), ('libvdwxc', '0.4.0'), ('PSolver', '1.8.3'), - ('ELSI', '2.6.4'), + ('ELSI', '2.6.4', '-PEXSI'), ('spglib', '1.16.1'), ('Wannier90', '3.1.0'), ] From c896f1ac9638c3a10e7f54a9592454a3c0c49d93 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Tue, 19 Oct 2021 13:41:37 +0100 Subject: [PATCH 1682/2365] [libcdwxc] activate intel toolchain --- .../l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb new file mode 100644 index 0000000000..2662d04e13 --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.org' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC &&' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +dependencies = [ + ('FFTW', '3.3.8') +] + +moduleclass = 'chem' From 1b7ddedf0dc1b97702a351cff6fe68191ca0758c Mon Sep 17 00:00:00 2001 From: alin m elena Date: Tue, 19 Oct 2021 20:30:53 +0100 Subject: [PATCH 1683/2365] keep linter happy --- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb index 2662d04e13..7a947276f3 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -21,7 +21,7 @@ sanity_check_paths = { 'libvdwxc_q0test', 'libvdwxc_q0test2']] + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include'], + 'dirs': ['include'], } dependencies = [ From de46542cc3ecf3e925646e8ac5ba2098c3289f5b Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 20 Oct 2021 11:02:31 +0200 Subject: [PATCH 1684/2365] Update libvdwxc-0.4.0-intel-2020b.eb --- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb index 7a947276f3..751488a072 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -24,6 +24,7 @@ sanity_check_paths = { 'dirs': ['include'], } +# MKL FFTW does not have all the features of fftw3 and libvdwxc is using them dependencies = [ ('FFTW', '3.3.8') ] From 912cfef5f9d6c4c958bb2789d31a5a437dd96b9b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Oct 2021 12:37:22 +0200 Subject: [PATCH 1685/2365] Fix PMIx detection as per OpenMPI issue 8823 --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 6 +++++- .../o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 6 +++++- .../easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb | 6 +++++- .../o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb | 6 +++++- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 4 +++- 5 files changed, 23 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb index de69437e30..110d6438af 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb index 949050f89e..503f955baf 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -10,11 +10,15 @@ toolchainopts = {'pic': True} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb index 245532a13e..12093c5a84 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'gcccuda', 'version': '2020b'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb index 6083f480cd..d33ec82375 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'iccifort', 'version': '2020.4.304'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index fda533d6ab..084adbc63f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -10,7 +10,8 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', - 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', ] checksums = [ '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a', # openmpi-4.1.0.tar.gz @@ -18,6 +19,7 @@ checksums = [ 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ From 6f2222a17fd922922d4f8455a0ebb3ff67979996 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 20 Oct 2021 13:20:58 +0200 Subject: [PATCH 1686/2365] Add ESL-Bundle-0.6.1 for intel/2020b. --- .../ESL-Bundle-0.6.1-intel-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb new file mode 100644 index 0000000000..e060b31d21 --- /dev/null +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'ESL-Bundle' +version = '0.6.1' + +homepage = 'https://esl.cecam.org' + +description = """ + The ESL Bundle is a collection of libraries and utilities broadly used in + electronic structure calculations, put together to make their use easier by + researchers and scientific software developers. ESL stands for Electronic + Structure Library, an initiative which distributes quality software and + promotes open standards for high-performance computing applications in the + field of electronic structure calculations. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('ELSI-RCI', '0.1.0'), + ('fdict', '0.8.0'), + ('flook', '0.8.1'), + ('libfdf', '0.2.2', '-serial'), + ('libmbd', '0.10.4'), + ('libpsml', '1.1.10'), + ('libpspio', '0.2.4'), + ('libxc', '4.3.4'), + ('libGridXC', '0.9.6'), + ('libvdwxc', '0.4.0'), + ('PSolver', '1.8.3'), + ('ELSI', '2.6.4', '-PEXSI'), + ('spglib', '1.16.1'), + ('Wannier90', '3.1.0'), +] + +moduleclass = 'phys' From c9990565077ce2fc69f7c1900f17e93e2832b8f9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Oct 2021 16:43:02 +0200 Subject: [PATCH 1687/2365] Update ELSI-2.6.4 to use the Bison compat patch and the correct Bison version for the toolchain. --- .../easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 10 +++++++--- .../easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb | 10 ++++++++-- 2 files changed, 15 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 3534b95faa..332df2352b 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -14,15 +14,19 @@ toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11'} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['pexsi-1.2.0-mpi30.patch'] +patches = [ + 'pexsi-1.2.0-mpi30.patch', + 'ELSI-2.7.1_bison_3.7_compat.patch', +] checksums = [ 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.5.3'), + ('Bison', '3.7.1'), ('CMake', '3.18.4'), ] @@ -33,7 +37,7 @@ dependencies = [ build_internal_pexsi = True -configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' +configopts = '-DENABLE_BSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' runtest = True diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb index 48b7ddd05d..800d33b16d 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb @@ -14,13 +14,19 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'pexsi-1.2.0-mpi30.patch', + 'ELSI-2.7.1_bison_3.7_compat.patch', +] checksums = [ 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz + 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.5.3'), + ('Bison', '3.7.1'), ('CMake', '3.18.4'), ] @@ -31,7 +37,7 @@ dependencies = [ build_internal_pexsi = True -configopts = "-DENABLEBSEPACK=ON" +configopts = "-DENABLE_BSEPACK=ON" runtest = True From 103847665a9380a0279eaa9e777ab0a3adcd3515 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Oct 2021 20:36:50 +0200 Subject: [PATCH 1688/2365] use proper tqdm dependency in artic-ncov2019 easyconfig --- .../a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 9aedc07f20..c499524697 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -40,6 +40,7 @@ dependencies = [ ('nanopolish', '0.13.3'), ('seqtk', '1.3'), ('BCFtools', '1.11'), + ('tqdm', '4.56.2'), ] use_pip = True @@ -56,9 +57,6 @@ exts_list = [ 'modulename': 'vcf', 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], }), - ('tqdm', '4.62.2', { - 'checksums': ['a4d6d112e507ef98513ac119ead1159d286deab17dffedd96921412c2d236ff5'], - }), ('fieldbioinformatics', '1.2.1', { 'modulename': 'artic', 'source_tmpl': '%(version)s.tar.gz', From d95eca47402e62e333f73354a455c4ac37884ad0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Oct 2021 10:20:42 +0200 Subject: [PATCH 1689/2365] adding easyconfigs: GTDB-Tk-1.7.0-intel-2020b.eb --- .../g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb new file mode 100644 index 0000000000..2e0232fed4 --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'GTDB-Tk' +version = '1.7.0' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/g/gtdbtk'] +sources = ['gtdbtk-%(version)s.tar.gz'] +checksums = ['36b65074845e7edef4d7aeead286c770fb9a03ddbff63946533fa2e1934e8f26'] + +dependencies = [ + ('Python', '3.8.6'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.3.3'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.56.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From b26877c41a490a84857765b2a67f05c7b6ab70ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Oct 2021 21:45:14 +0200 Subject: [PATCH 1690/2365] add compiler/parallel/tcltk R libraries included in base installation to extensions in R 4.x easyconfigs using foss toolchain --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 6 ++++++ 3 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index d8bbd8572a..3226ee0f4b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -74,15 +74,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 10 Nov 2020 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index e3dbbcb551..26d6cbdb27 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -81,15 +81,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 08 Mar 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index d1f3feab30..febdb0ca5e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -78,15 +78,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 07 Apr 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { From f7c4ffc3a6406cf6e54099f566565d090a6479b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Oct 2021 08:36:15 +0200 Subject: [PATCH 1691/2365] add compiler/parallel/tcltk R libraries included in base installation to extensions in R easyconfigs using fosscuda toolchain --- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 6 ++++++ 3 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 9e5053e29b..d35824d64b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -83,15 +83,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 10 Nov 2020 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 9d9ad1166d..9c612d32b9 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -85,15 +85,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 08 Mar 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 2f1b150a61..d1e5430a10 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -88,15 +88,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 07 Apr 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { From 83287667c4d68a4611d48a4ac6c0ab7a0a346ca1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 22 Oct 2021 16:20:00 +0100 Subject: [PATCH 1692/2365] adding easyconfigs: pygraphviz-1.7-foss-2020b.eb, pygraphviz-1.7-foss-2021a.eb --- .../p/pygraphviz/pygraphviz-1.7-foss-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb new file mode 100644 index 0000000000..d42c422ae7 --- /dev/null +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pygraphviz' +version = '1.7' + +homepage = 'https://pygraphviz.github.io/' +description = """PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. +With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz +graph data structure and layout algorithms.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_ZIP] +checksums = ['a7bec6609f37cf1e64898c59f075afd659106cf9356c5f387cecaa2e0cdb2304'] + +dependencies = [ + ('Python', '3.8.6'), + ('Graphviz', '2.47.0', '-Java-11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 4db2047c2ef13ae5d113db1eb704fcbe97dfaabe Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Oct 2021 17:26:07 +0100 Subject: [PATCH 1693/2365] Fix spatstat.* downloads for Seurat/4.0.1 --- .../easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb index bddbf11b5e..be3f28cdb2 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb @@ -25,18 +25,21 @@ exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} exts_list = [ ('spatstat.utils', '2.1-0', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.utils'], 'checksums': ['ed3569fea295b62396c49cdcfe476414b0b0f3e52044175532f316a402d3f8a1'], }), ('spatstat.data', '2.1-0', { 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], }), ('spatstat.geom', '2.0-1', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'], 'checksums': ['70ebfe115e733b2e6778baf6e2935861472154c0dd21f15a84ec2a61e0a3f6e4'], }), ('spatstat.sparse', '2.0-0', { 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], }), ('spatstat.core', '2.0-0', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'], 'checksums': ['fde9a91bd32b7a3c8b25e802a16d470dcc919c24da5715149e1d91eeec119ba7'], }), (name, version, { From ac63e4fc5d82735c42a311c48fa12e71f2bd5889 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Oct 2021 12:02:45 +0200 Subject: [PATCH 1694/2365] Add description to patch. --- .../a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb index bbc631dca5..5ed303535e 100644 --- a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb @@ -19,7 +19,7 @@ patches = [ checksums = [ '503e7775f9764cf8298cbd2d06c4a36a9c83efbd84d58721eee638adfd1e626e', # abtem-1.0.0b24.tar.gz # abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch - '49eee97f444ff16b45745adcd70dbbf63d5ddb842d7d6539ec303f388b4293da', + '7aa081d6543bbec7024e2f4f166b9ea6ba62624fae465db04d231cce207b9b21', '0d4a0500e4947e4967858e6644969796d5bd76bc556a9c09fdc80461dcbcaed6', # abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch ] From 3e9e9068e62ad4c79009b70b47e7ab26fb5c40d0 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 26 Oct 2021 13:01:38 +0200 Subject: [PATCH 1695/2365] updating per review --- .../s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..abdce7f539 --- /dev/null +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb @@ -0,0 +1,78 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +## + +easyblock = 'MakeCp' + +name = 'SMV' # SmokeView +version = '6.7.17' + +homepage = 'https://github.com/firemodels/smv' +description = """Smokeview is a visualization program that displays output of FDS and CFAST simulations.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/firemodels/%(name)s/archive/refs/tags/'] +sources = ['%(name)s%(version)s.tar.gz'] +patches = [ + 'SMV-%(version)s_missing-includes.patch', + ('example.smv', '.'), # example file for sanity check +] +checksums = [ + '2e718af991e48228bf374fdefcce00d2e8b5827cc29ae2138ae267fda896f127', # SMV6.7.17.tar.gz + '2b287f3e6ff368422684bd887568a369b9db3426a94efefcccc7680392b742ab', # SMV-6.7.17_missing-includes.patch + '1adf7dcc5293ec7a5f7ec01a828dec88b4ddd025505167b4e361d9450f66ea59', # example.smv +] + +dependencies = [ + ('libgd', '2.3.0'), + ('freeglut', '3.2.1'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('Lua', '5.4.2'), + ('lpeg', '1.0.2'), + ('libGLU', '9.0.1'), + ('glew', '2.1.0'), + ('Xvfb', '1.20.9'), +] + +local_compiler_lib_append = '/compilers_and_libraries_$EBVERSIONICCIFORT/linux/compiler/lib/intel64_lin/' + +local_buildopts = ' -lglui -lglut -lfreeglut -lGLU -lGL -llibgd ' +local_buildopts += ' LDFLAGS=" -L%(installdir)s -L$EBROOTFREEGLUT/lib -L$EBROOTLIBGD/lib " ' +local_buildopts += ' IFLAGS=" -I$EBROOTFREEGLUT/include/GL -I%(builddir)s/smv-SMV%(version)s/Source/glui_v2_1_beta/ ' +local_buildopts += ' -I%(builddir)s/smv-SMV%(version)s/Source/glui_gl/GL/glut.h "' +local_buildopts += ' EB_L_PATH=%(installdir)s ' +local_buildopts += ' CFLAGS="-Dpp_LINUX" ' + +prebuildopts = "cd %(builddir)s/smv-SMV%(version)s/Build/LIBS/intel_linux_64/ && " +prebuildopts += " make all -f make_LIBS.make " +prebuildopts += "SRCDIR=%(builddir)s/smv-SMV%(version)s/Source/ LIBDIR=%(installdir)s && " +prebuildopts += "cd %(builddir)s/smv-SMV%(version)s/Build/smokeview/ && " +prebuildopts += "export IFORT_COMPILER_LIB=$EBROOTICCIFORT%s && " % local_compiler_lib_append + +buildopts = ' intel_linux_64 ' + local_buildopts +buildopts += ' && make -j %(parallel)s intel_linux_64_db ' + local_buildopts + +files_to_copy = [ + (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*"], 'bin'), +] + +postinstallcmds = [ + 'ln -s %(installdir)s/bin/smokeview_linux_64 %(installdir)s/bin/smokeview' +] + +modextrapaths = {'PATH': ['bin']} + +sanity_check_commands = [ + "cd %(builddir)s/smv-SMV%(version)s && timeout 10 xvfb-run smokeview example 2>&1 | grep 'Terminated' ", +] + +sanity_check_paths = { + 'files': ["bin/smokeview"], + 'dirs': ["bin"], +} + +moduleclass = 'bio' From f606413153ffcf534c714b681e445651216032ce Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Oct 2021 15:57:31 +0200 Subject: [PATCH 1696/2365] Add version suffix because of ASE dependency. --- .../pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb | 44 +++++++++++++++++++ ...pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb | 44 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb create mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..2e18fed82c --- /dev/null +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb @@ -0,0 +1,44 @@ +easyblock = "PythonPackage" + +name = 'pyqstem' +version = '1.0.3' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/PyQSTEM' +description = """QSTEM is a program for quantitative image simulation in electron +microscopy, including TEM, STEM and CBED image simulation. + +This project interfaces the QSTEM code with Python and the Atomic +Simulation Environment (ASE) to provide a single environment for +building models, simulating and analysing images.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), +] +checksums = [ + '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz + # pyqstem-1.0.3-Remove-unused-scipy-import.patch + 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', +] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-image', '0.18.1'), + ('ASE', _aseversion), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..b6a80dcfb0 --- /dev/null +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb @@ -0,0 +1,44 @@ +easyblock = "PythonPackage" + +name = 'pyqstem' +version = '1.0.3' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/PyQSTEM' +description = """QSTEM is a program for quantitative image simulation in electron +microscopy, including TEM, STEM and CBED image simulation. + +This project interfaces the QSTEM code with Python and the Atomic +Simulation Environment (ASE) to provide a single environment for +building models, simulating and analysing images.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), +] +checksums = [ + '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz + # pyqstem-1.0.3-Remove-unused-scipy-import.patch + 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', +] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-image', '0.18.1'), + ('ASE', _aseversion), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' From 1ed98c95d19b3210a56d37a586cf47f6d4f6d500 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 26 Oct 2021 17:06:08 +0200 Subject: [PATCH 1697/2365] adding easyconfigs: panaroo-1.2.8-foss-2020b.eb, MAFFT-7.475-GCC-10.2.0-with-extensions.eb, PRANK-170427-GCC-10.2.0.eb --- .../MAFFT-7.475-GCC-10.2.0-with-extensions.eb | 48 ++++++++++++++ .../p/PRANK/PRANK-170427-GCC-10.2.0.eb | 34 ++++++++++ .../p/panaroo/panaroo-1.2.8-foss-2020b.eb | 64 +++++++++++++++++++ 3 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-GCC-10.2.0-with-extensions.eb create mode 100644 easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-GCC-10.2.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-GCC-10.2.0-with-extensions.eb new file mode 100644 index 0000000000..70eb55dda6 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-GCC-10.2.0-with-extensions.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) +# 7.305 modified by: +# Adam Huffman (The Francis Crick Institute) +# 7.453 switch to Bundle by: +# Alex Domingo (Vrije Universiteit Brussel) + +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.475' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['bb6973ae089ea18cfbd3861a5b9d2c8b7e1543a1fdc78ac2d7cd8dbe3443f319'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb new file mode 100644 index 0000000000..fccd68f173 --- /dev/null +++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'PRANK' +version = '170427' + +homepage = 'http://wasabiapp.org/software/prank/' +description = """ PRANK is a probabilistic multiple alignment program for DNA, + codon and amino-acid sequences. PRANK is based on a novel algorithm that treats + insertions correctly and avoids over-estimation of the number of deletion events.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://wasabiapp.org/download/prank/'] +sources = ['%(namelower)s.source.%(version)s.tgz'] +checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859'] + +# PRANK uses MAFFT as external tool to contruct guide tree +dependencies = [('MAFFT', '7.475', '-with-extensions')] + +start_dir = 'src' + +files_to_copy = [(['prank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/prank'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb new file mode 100644 index 0000000000..1fcc48802c --- /dev/null +++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb @@ -0,0 +1,64 @@ +# Author: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'panaroo' +version = '1.2.8' + +homepage = 'https://gtonkinhill.github.io/panaroo/' +description = "A pangenome analysis pipeline." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('CD-HIT', '4.8.1'), + ('PRANK', '170427'), + ('Biopython', '1.78'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), + ('edlib', '1.3.9'), + ('tqdm', '4.60.0'), + ('matplotlib', '3.3.3'), + ('scikit-learn', '0.23.2'), + ('plotly.py', '4.14.3'), + ('DendroPy', '4.5.2'), + ('pyfaidx', '0.5.9.5'), + ('prokka', '1.14.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} + +exts_list = [ + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), + ('argcomplete', '1.12.3', { + 'checksums': ['2c7dbffd8c045ea534921e63b0be6fe65e88599990d8dc408ac8c542b72a5445'], + }), + ('argh', '0.26.2', { + 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], + }), + ('gffutils', '0.10.1', { + 'checksums': ['a8fc39006d7aa353147238160640e2210b168f7849cb99896be3fc9441e351cb'], + }), + ('intbitset', '2.4.1', { + 'checksums': ['44bca80b8cc702d5a56f0686f2bb5e028ab4d0c2c1761941589d46b7fa2c701c'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/gtonkinhill/panaroo/archive/'], + 'checksums': ['af56fae581908a93b843a90471dc80d4ff7299afc9e66e22510233d1a76d00c5'], + }), +] + +sanity_check_commands = [ + "panaroo --version" +] + +moduleclass = 'bio' From 7a5bc8fde13fecbbd9b6330d6c5684060434659d Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 26 Oct 2021 17:40:23 +0200 Subject: [PATCH 1698/2365] Fixed issues --- easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb index 1fcc48802c..733968e101 100644 --- a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb +++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb @@ -18,7 +18,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('networkx', '2.5'), ('edlib', '1.3.9'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('matplotlib', '3.3.3'), ('scikit-learn', '0.23.2'), ('plotly.py', '4.14.3'), @@ -30,10 +30,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - exts_list = [ ('sklearn', '0.0', { 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], From 076b2fdb40f7f5d5bf5f63d7b22be7edb1445f04 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 27 Oct 2021 12:01:18 +0200 Subject: [PATCH 1699/2365] add sanity_check_command for PRANK --- easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb index fccd68f173..ee59ac1eae 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['prank -help'] + moduleclass = 'bio' From 65b1519b0e41a5398178fcc75ff40ffcdf390e6e Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 27 Oct 2021 12:45:39 +0200 Subject: [PATCH 1700/2365] adding easyconfigs: abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb, abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb and patches: abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch --- .../abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb | 39 +++++++++++++++++++ ...bTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb create mode 100644 easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..58040804ad --- /dev/null +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'abTEM' +version = '1.0.0b26' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/abTEM' +description = """abTEM provides a Python API for running simulations +of Transmission Electron Microscopy images.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch', +] +checksums = [ + '8a40b7ff5caeb5997924f43e981d5158159e521bda2abd4093c6f555661a4294', # abtem-1.0.0b26.tar.gz + # abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch + 'd0532bdde462591fe1a5202fc79ec7decef10207d3e622fa4b605b09ffe55adf', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('h5py', '3.1.0'), + ('numba', '0.53.1'), + ('pyFFTW', '0.12.0'), + ('tqdm', '4.56.2'), + ('imageio', '2.9.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..24cc2f9f1f --- /dev/null +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'abTEM' +version = '1.0.0b26' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/abTEM' +description = """abTEM provides a Python API for running simulations +of Transmission Electron Microscopy images.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch', +] +checksums = [ + '8a40b7ff5caeb5997924f43e981d5158159e521bda2abd4093c6f555661a4294', # abtem-1.0.0b26.tar.gz + # abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch + 'd0532bdde462591fe1a5202fc79ec7decef10207d3e622fa4b605b09ffe55adf', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('h5py', '3.1.0'), + ('numba', '0.53.1'), + ('pyFFTW', '0.12.0'), + ('tqdm', '4.56.2'), + ('imageio', '2.9.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 5a4935c802c18e2765d6c94a2dfbca92e27c5eeb Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 27 Oct 2021 13:23:50 +0200 Subject: [PATCH 1701/2365] Add dependencies. --- .../i/imageio/imageio-2.9.0-foss-2020b.eb | 25 +++++++++++++++++++ .../p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb create mode 100755 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb new file mode 100644 index 0000000000..51d59be8f6 --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.9.0' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow', '8.0.1'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb new file mode 100755 index 0000000000..09b5d4fc47 --- /dev/null +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pyFFTW' +version = '0.12.0' + +homepage = 'https://github.com/pyFFTW/pyFFTW' +description = """A pythonic wrapper around FFTW, the FFT library, presenting a unified interface + for all the supported transforms.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['60988e823ca75808a26fd79d88dbae1de3699e72a293f812aa4534f8a0a58cb0'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('FFTW', '3.3.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 10fe7bd7f5846c2cc9ee56a181a30a17a7d2826f Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Wed, 27 Oct 2021 17:46:52 +0100 Subject: [PATCH 1702/2365] Create PyTables-3.5.2-foss-2020b-Python-2.7.18.eb New version for foss 2020b + Python 2.7.18. --- ...PyTables-3.5.2-foss-2020b-Python-2.7.18.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..ce4f3ad63b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.5.2' +# This is the last version to support Python 2.7. +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-libs.patch'] +checksums = [ + 'e4fc6f1194f02a8b10ff923e77364fb70710592f620d7de35f4d4e064dc70e91', # v3.5.2.tar.gz + '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.5.2-fix-libs.patch +] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', versionsuffix), # provides numexpr. + ('HDF5', '1.10.7'), + ('LZO', '2.10'), + ('Blosc', '1.21.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bins = ['pt2to3', 'ptdump', 'ptrepack'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ['%s --help' % x for x in local_bins] + +moduleclass = 'data' From 82cf85d48be6c78db37c095bf2a8f1048ae72663 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Thu, 28 Oct 2021 16:16:34 +0100 Subject: [PATCH 1703/2365] Rename Pillow-6.2.2-foss-2020b-Python-2.7.18 to Pillow-6.2.2-foss-2020b-Python-2.7.18.eb --- .../Pillow-6.2.2-foss-2020b-Python-2.7.18.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..a8a8a9dd9f --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '6.2.2' +# This is the last Pillow version to support Python 2.7. +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['db9ff0c251ed066d367f53b64827cc9e18ccea001b986d08c265e53625dab950'] + +dependencies = [ + ('Python', '2.7.18'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.1.0'), + ('freetype', '2.10.3') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From cc55266c949079a260fc922153a1ccba0d7e43ae Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 29 Oct 2021 20:48:14 +1050 Subject: [PATCH 1704/2365] adding easyconfigs: CapnProto-0.9.1-GCCcore-10.2.0.eb --- .../CapnProto-0.9.1-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5f3f76e2e2 --- /dev/null +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to 0.9.1 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'CapnProto' +version = '0.9.1' + +homepage = 'https://capnproto.org' +description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" +# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." +# (only on Intel Skylake?) +toolchainopts = {'cstd': 'c++17', 'lowopt': True} + +source_urls = ['https://capnproto.org/'] +sources = ['capnproto-c++-%(version)s.tar.gz'] +checksums = ['83680aaef8c192b884e38eab418b8482d321af6ae7ab7befa3a9370b8e716aad'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/capnp', 'bin/capnpc', 'bin/capnpc-c++', 'bin/capnpc-capnp'], + 'dirs': ['include/capnp', 'include/kj', 'lib'], +} + +moduleclass = 'bio' From de19fedb9e0ab3ed5a49aed6c3ff9f41b0d6cee1 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 29 Oct 2021 15:06:54 +0200 Subject: [PATCH 1705/2365] adding easyconfigs: Highway-0.12.2-GCCcore-10.2.0.eb, zopfli-1.0.3-foss-2020b.eb, zlib-ng-2.0.5-foss-2020b.eb, liblzma-5.2.5-foss-2020b.eb, liblzf-3.4-GCCcore-10.2.0.eb, libjxl-0.5-GCCcore-10.2.0.eb, libavif-0.9.0-foss-2020b.eb --- .../Highway/Highway-0.12.2-GCCcore-10.2.0.eb | 31 +++++++++++++++ .../l/libavif/libavif-0.9.0-foss-2020b.eb | 39 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5111d10fd4 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Highway' +version = '0.12.2' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e1d47ce510429fdcf31f41697ca74fb0dcd59d933196e531a86d51751a56f4cc'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb new file mode 100644 index 0000000000..23a8645f59 --- /dev/null +++ b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libavif' +version = '0.9.0' + +homepage = 'https://github.com/AOMediaCodec/libavif' +description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format, +as described here: https://aomediacodec.github.io/av1-avif/ +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('NASM', '2.15.05'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('Rust', '1.52.1'), +] + +# TODO FIX THIS - NEED THOSE +# configopts = ' -DAVIF_CODEC_AOM=ON -DAVIF_CODEC_DAV1D=ON -DAVIF_CODEC_LIBGAV1=ON -DAVIF_CODEC_RAV1E=ON ' +sanity_check_paths = { + 'files': ['lib/libavif.so.10.0.0', 'include/avif/avif.h'], + 'dirs': ['lib/', 'include/avif/'] +} + +sanity_check_commands = [ +] + +moduleclass = 'tools' From d6bab5cfb08b89cbc5818b26754111c585846604 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 29 Oct 2021 15:11:58 +0200 Subject: [PATCH 1706/2365] adding easyconfigs: libaec-1.0.6-foss-2020b.eb, lerc-3.0-foss-2020b.eb, jxrlib-1.1-foss-2020b.eb, CFITSIO-3.49-GCCcore-10.2.0.eb, brunsli-0.1-foss-2020b.eb, Blosc2-2.0.3-GCCcore-10.2.0.eb, imagecodecs-2021.8.26-foss-2020b.eb --- .../b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb | 29 +++++++ .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb | 37 +++++++++ .../imagecodecs-2021.8.26-foss-2020b.eb | 82 +++++++++++++++++++ 3 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cc97656d2c --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.0.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3d4e1b6d40 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.49' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] + +# curl for HTTPs support +dependencies = [('cURL', '7.72.0')] + +builddependencies = [('binutils', '2.35')] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = '&& make shared && make testprog' + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb new file mode 100644 index 0000000000..c75dc12b18 --- /dev/null +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -0,0 +1,82 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'imagecodecs' +version = '2021.8.26' + +homepage = 'https://www.lfd.uci.edu/~gohlke/' +description = """ +Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, +compression, and decompression functions for use in the tifffile, czifile, zarr, and other +scientific image input/output modules. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +# changing src line endings +local_extract_cmd = ' tar -xvf %s ' +local_extract_cmd += ' && find . -type f -print0 | xargs -0 dos2unix ' + +sources = [{ + 'source_urls': PYPI_SOURCE, + 'filename': SOURCE_TAR_GZ, + 'extract_cmd': local_extract_cmd, +}] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('SciPy-bundle', '2020.11'), + ('Brotli', '1.0.9'), + ('bzip2', '1.0.8'), + ('Blosc', '1.21.0'), + ('Blosc2', '2.0.3'), + ('CFITSIO', '3.49'), + ('CharLS', '2.2.0'), + ('giflib', '5.2.1'), + ('jxrlib', '1.1'), + ('LittleCMS', '2.11'), + ('lerc', '3.0'), + ('libaec', '1.0.6'), + ('libavif', '0.9.0'), + ('libdeflate', '1.7'), + ('libjpeg-turbo', '2.0.5'), + ('libjxl', '0.5'), + ('liblzf', '3.4'), + ('libpng', '1.6.37'), + ('liblzma', '5.2.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('libwebp', '1.1.0'), + ('lz4', '1.9.2'), + ('OpenJPEG', '2.4.0'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), + ('zlib-ng', '2.0.5'), + ('zopfli', '1.0.3'), + ('zfp', '0.5.5'), + ('zstd', '1.4.5'), + ('brunsli', '0.1'), + ('HDF5', '1.10.7'), + ('h5py', '3.1.0'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'use_pip': True, + 'download_dep_fail': True, +} + +exts_list = [ + ('bitshuffle', '0.3.5', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'] + }), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From af6c49341409ec1dff6431c38d7f97be37ea717f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 29 Oct 2021 15:13:57 +0200 Subject: [PATCH 1707/2365] adding easyconfigs: tifffile-2021.8.30-foss-2020b.eb, unittest2-1.1.0-foss-2020b.eb, SimpleITK-2.1.0-foss-2020b.eb, requests-2.26.0-foss-2020b.eb, batchgenerators-0.23-foss-2020b.eb, Lua-5.3.5-GCCcore-10.2.0.eb --- .../l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb | 30 +++++++++++ .../s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb | 53 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..125417a6c6 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +name = 'Lua' +version = '5.3.5' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0c2eed3f960446e1a3e4b9a1ca2f3ff893b6ce41942cf54d5dd59ab4b3b058ac'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('libreadline', '8.0'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb new file mode 100644 index 0000000000..0b1009560a --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'SimpleITK' +version = '2.1.0' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/s/simpleitk/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d5d3b805863b9dfcffeebec69a1b79b5709fc814b12cb9ab759ccbd3e4746839'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Lua', '5.3.5'), + ('ITK', '5.2.1'), + ('scikit-build', '0.11.1'), +] +start_dir = 'SimpleITK' + +configopts = '-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF -DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF ' + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_pyinstpath = "%(installdir)s/lib/python%(pyshortver)s/site-packages" +postinstallcmds = [ + "mkdir -p %s " % local_pyinstpath + + " && cd %(builddir)s/easybuild_obj/Wrapping/Python " + + " && export PYTHONPATH=%s:$PYTHONPATH " % local_pyinstpath + + " && pip install --prefix=%(installdir)s . " +] +separate_build_dir = True + +# todo make nicer dir path +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/']} + +sanity_check_paths = { + 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'include/%(name)s-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(name)s'")] + +moduleclass = 'tools' From 67b81b6591d46e90538154b5e8800cc26a165455 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 17:04:36 +0200 Subject: [PATCH 1708/2365] adding easyconfigs: SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb --- ...0.2.0-20210620-foss-2020b-Python-2.7.18.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..861f11bb8c --- /dev/null +++ b/easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonPackage' + +name = 'SRST2' +local_commit = '73f885f' +version = '0.2.0-20210620' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://katholt.github.io/srst2' +description = "Short Read Sequence Typing for Bacterial Pathogens" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/katholt/srst2/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['04b383bae7450b89945053fbd1945ecf7234a78cfd374f90c7ef427d84571d20'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', versionsuffix), + ('Bowtie2', '2.4.2'), + ('SAMtools', '1.11'), +] + +download_dep_fail = True +use_pip = True + +# inject Bowtie2/SAMtools version in scripts that check for known version +preinstallopts = """sed -i "s@,'2.2.9'@,'2.2.9', '$EBVERSIONBOWTIE2'@g" scripts/qsub_srst2.py && """ +preinstallopts += """sed -i "s@,'2.2.9'@,'2.2.9', '$EBVERSIONBOWTIE2'@g" scripts/slurm_srst2.py && """ +preinstallopts += """sed -i "s@,'2.2.9'@,'2.2.9', '$EBVERSIONBOWTIE2'@g" scripts/srst2.py && """ +preinstallopts += """sed -i "s@'0.1.18',@'$EBVERSIONSAMTOOLS', '0.1.18',@g" scripts/qsub_srst2.py && """ +preinstallopts += """sed -i "s@'0.1.18',@'$EBVERSIONSAMTOOLS', '0.1.18',@g" scripts/slurm_srst2.py && """ +preinstallopts += """sed -i "s@'0.1.18',@'$EBVERSIONSAMTOOLS', '0.1.18',@g" scripts/srst2.py && """ + +fix_python_shebang_for = ['bin/*.py'] + +postinstallcmds = ["cp -a data %(installdir)s"] + +sanity_check_paths = { + 'files': ['bin/getmlst.py', 'bin/slurm_srst2.py', 'bin/srst2'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "srst2 --version", + "getmlst.py -h", + "slurm_srst2.py -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From cdbc4dbdb47dd20066955c2b7a6d032e0ff7fd71 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 17:31:12 +0200 Subject: [PATCH 1709/2365] adding easyconfigs: Megalodon-2.3.5-foss-2020b.eb --- .../m/Megalodon/Megalodon-2.3.5-foss-2020b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb new file mode 100644 index 0000000000..b4801f257c --- /dev/null +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'Megalodon' +version = '2.3.5' + +homepage = 'https://github.com/nanoporetech/megalodon' +description = """Megalodon is a research command line tool to extract high accuracy modified base and sequence variant +calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference +genome/transriptome.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('scikit-learn', '0.23.2'), + ('tqdm', '4.60.0'), + ('Pysam', '0.16.0.1'), + ('Seaborn', '0.11.1'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '4.0.0', { + 'checksums': ['a249813104439bfe3d4e346bb560756e23217655273410c60b9bade205eb3e66'], + }), + ('mappy', '2.22', { + 'checksums': ['219c93ab7f8d5d7c26face512a9e738a7306f3376ebfa3017eac70676ba97840'], + }), + ('ont_pyguppy_client_lib', '5.0.16', { + 'modulename': 'pyguppy_client_lib', + 'sources': ['ont_pyguppy_client_lib-%(version)s-cp38-cp38-manylinux2010_x86_64.whl'], + 'checksums': ['6e89cccb2d3943ee5d6e9a6cd55e1cc8700656201d1a411b638919560bbb0772'], + }), + ('megalodon', version, { + 'checksums': ['0ae6c6dcaf599f98ca421d1f4df616cf0a4cf3436b305553220a479dc41f3426'], + }), +] + +sanity_check_paths = { + 'files': ['bin/megalodon'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "megalodon -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 5223561a909944ef416469d02fd8d28d6bf19ab9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 17:56:13 +0200 Subject: [PATCH 1710/2365] stick to tqdm 4.56.2 dependency in Megalodon easyconfig using foss/2020b toolchain --- easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb index b4801f257c..f71e6ef6e2 100644 --- a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb @@ -15,7 +15,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('h5py', '3.1.0'), ('scikit-learn', '0.23.2'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('Pysam', '0.16.0.1'), ('Seaborn', '0.11.1'), ] From 47c6890f37f71a059970a1321c6a4e9521119078 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 18:00:50 +0200 Subject: [PATCH 1711/2365] adding easyconfigs: Megalodon-2.3.5-fosscuda-2020b.eb --- .../Megalodon-2.3.5-fosscuda-2020b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..0561598001 --- /dev/null +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'Megalodon' +version = '2.3.5' + +homepage = 'https://github.com/nanoporetech/megalodon' +description = """Megalodon is a research command line tool to extract high accuracy modified base and sequence variant +calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference +genome/transriptome.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('scikit-learn', '0.23.2'), + ('tqdm', '4.56.2'), + ('Pysam', '0.16.0.1'), + ('Seaborn', '0.11.1'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '4.0.0', { + 'checksums': ['a249813104439bfe3d4e346bb560756e23217655273410c60b9bade205eb3e66'], + }), + ('mappy', '2.22', { + 'checksums': ['219c93ab7f8d5d7c26face512a9e738a7306f3376ebfa3017eac70676ba97840'], + }), + ('ont_pyguppy_client_lib', '5.0.16', { + 'modulename': 'pyguppy_client_lib', + 'sources': ['ont_pyguppy_client_lib-%(version)s-cp38-cp38-manylinux2010_x86_64.whl'], + 'checksums': ['6e89cccb2d3943ee5d6e9a6cd55e1cc8700656201d1a411b638919560bbb0772'], + }), + ('megalodon', version, { + 'checksums': ['0ae6c6dcaf599f98ca421d1f4df616cf0a4cf3436b305553220a479dc41f3426'], + }), +] + +sanity_check_paths = { + 'files': ['bin/megalodon'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "megalodon -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 4b592eee9d6851a95b6be8bdd84d8930ee8b9697 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 18:39:47 +0200 Subject: [PATCH 1712/2365] adding easyconfigs: SimNIBS-3.2.4-foss-2020b.eb, FMM3D-20211018-foss-2020b.eb --- .../f/FMM3D/FMM3D-20211018-foss-2020b.eb | 45 +++++++++++++++++++ .../s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb | 41 +++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb b/easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb new file mode 100644 index 0000000000..32ce0d7089 --- /dev/null +++ b/easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'FMM3D' +local_commit = '7ba20d6' +version = '20211018' + +homepage = 'https://fmm3d.readthedocs.io' +description = """Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-body +interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a +multi-core shared-memory machine.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/flatironinstitute/FMM3D/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['e6cd07f2a31159ce41705a117771a0bab819b192075e24a28b0cf8c5ca9f5ba5'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +skipsteps = ['configure', 'build'] + +installopts = 'FAST_KER=ON PREFIX="%(installdir)s/lib" && ' +installopts += 'export FMM_FLIBS="%(installdir)s/lib/libfmm3d.a $FFLAGS" && ' +# also install Python bindings +installopts += "make python-dist && pip install --no-deps --ignore-installed --prefix %(installdir)s python/dist/*.whl" + +sanity_check_paths = { + 'files': ['lib/libfmm3d.a', 'lib/libfmm3d.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cd %(builddir)s/FMM3D-* && make test", + "python -c 'import fmm3dpy'", + "cd %(builddir)s/FMM3D-* && python python/test/test_hfmm.py", + "cd %(builddir)s/FMM3D-* && python python/test/test_lfmm.py", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb b/easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb new file mode 100644 index 0000000000..88e82bb578 --- /dev/null +++ b/easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'SimNIBS' +version = '3.2.4' + +homepage = 'https://simnibs.github.io/simnibs' +description = "SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('NiBabel', '3.2.1'), + ('FMM3D', '20211018'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/simnibs/simnibs/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['ad4482b4cdd306d4356757b4d065d844ea698dab2530aa09fb59219d2a982219'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/headreco', 'bin/simnibs'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "headreco --help", + "simnibs --help", +] + +moduleclass = 'bio' From 0ad0f5a2f3d915c6d7c7621e98919f5c5a86adb4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 15:26:01 +0100 Subject: [PATCH 1713/2365] style fixes + correct moduleclass for lpeg + change name to LPeg --- .../l/LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ .../s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb | 2 +- 2 files changed, 39 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d0801000f6 --- /dev/null +++ b/easybuild/easyconfigs/l/LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +## + +easyblock = 'MakeCp' + +name = 'LPeg' +version = '1.0.2' + +homepage = 'http://www.inf.puc-rio.br/~roberto/lpeg/' +description = """LPeg is a new pattern-matching library for Lua, based on Parsing Expression Grammars (PEGs).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://www.inf.puc-rio.br/~roberto/lpeg/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48d66576051b6c78388faad09b70493093264588fcd0f258ddaab1cdd4a15ffe'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Lua', '5.4.2'), +] + +files_to_copy = [ + (['lpeg.%s' % SHLIB_EXT], 'lib'), + (['*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/lpeg.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb index abdce7f539..01a46d62af 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb @@ -32,7 +32,7 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), ('Lua', '5.4.2'), - ('lpeg', '1.0.2'), + ('LPeg', '1.0.2'), ('libGLU', '9.0.1'), ('glew', '2.1.0'), ('Xvfb', '1.20.9'), From 6282b08745b90dbf21a3aee21494c56a32381bcf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 16:01:18 +0100 Subject: [PATCH 1714/2365] trivially simplify SMV easyconfig + fix moduleclass --- .../s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb index 01a46d62af..484357754e 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb @@ -38,8 +38,6 @@ dependencies = [ ('Xvfb', '1.20.9'), ] -local_compiler_lib_append = '/compilers_and_libraries_$EBVERSIONICCIFORT/linux/compiler/lib/intel64_lin/' - local_buildopts = ' -lglui -lglut -lfreeglut -lGLU -lGL -llibgd ' local_buildopts += ' LDFLAGS=" -L%(installdir)s -L$EBROOTFREEGLUT/lib -L$EBROOTLIBGD/lib " ' local_buildopts += ' IFLAGS=" -I$EBROOTFREEGLUT/include/GL -I%(builddir)s/smv-SMV%(version)s/Source/glui_v2_1_beta/ ' @@ -51,10 +49,9 @@ prebuildopts = "cd %(builddir)s/smv-SMV%(version)s/Build/LIBS/intel_linux_64/ && prebuildopts += " make all -f make_LIBS.make " prebuildopts += "SRCDIR=%(builddir)s/smv-SMV%(version)s/Source/ LIBDIR=%(installdir)s && " prebuildopts += "cd %(builddir)s/smv-SMV%(version)s/Build/smokeview/ && " -prebuildopts += "export IFORT_COMPILER_LIB=$EBROOTICCIFORT%s && " % local_compiler_lib_append +prebuildopts += "export IFORT_COMPILER_LIB=$EBROOTICCIFORT/lib64/intel64/ && " buildopts = ' intel_linux_64 ' + local_buildopts -buildopts += ' && make -j %(parallel)s intel_linux_64_db ' + local_buildopts files_to_copy = [ (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*"], 'bin'), @@ -64,15 +61,13 @@ postinstallcmds = [ 'ln -s %(installdir)s/bin/smokeview_linux_64 %(installdir)s/bin/smokeview' ] -modextrapaths = {'PATH': ['bin']} - sanity_check_commands = [ "cd %(builddir)s/smv-SMV%(version)s && timeout 10 xvfb-run smokeview example 2>&1 | grep 'Terminated' ", ] sanity_check_paths = { - 'files': ["bin/smokeview"], - 'dirs': ["bin"], + 'files': ['bin/smokeview'], + 'dirs': [], } -moduleclass = 'bio' +moduleclass = 'vis' From 6ce6f82ad5bf3b80379b776b76620efed803dee7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 19:34:54 +0100 Subject: [PATCH 1715/2365] adding easyconfigs: MMseqs2-13-45111-20211019-gompi-2020b.eb --- .../MMseqs2-13-45111-20211019-gompi-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211019-gompi-2020b.eb diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211019-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211019-gompi-2020b.eb new file mode 100644 index 0000000000..0277029f5d --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211019-gompi-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +local_commit = '9cc89aa' +version = '13-45111-20211019' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['b1b89aa2b5ccd97411000d8ba7d296f6134818f475b47e3d7672b071b9ff47f3'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [('bzip2', '1.0.8')] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' From e37c7dc3069cb86ab9754dd8368a1aece42fff39 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 08:16:53 +0000 Subject: [PATCH 1716/2365] Specify EB Python and fix URL in comment for Arrow 0.17.1 --- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 4 ++-- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 8fbcaf8468..92f2b7bc74 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -39,9 +39,9 @@ dependencies = [ separate_build_dir = True start_dir = 'cpp' -# see https://arrow.apache.org/docs/python/development.html +# see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index ee3c044110..7982ce4dd0 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -35,9 +35,9 @@ dependencies = [ separate_build_dir = True start_dir = 'cpp' -# see https://arrow.apache.org/docs/python/development.html +# see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " From 860cac129d189150d49583b5c37d976126fc3de3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 08:18:48 +0000 Subject: [PATCH 1717/2365] remove separate_build_dir --- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 1 - easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 92f2b7bc74..e2b5ef35e8 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -36,7 +36,6 @@ dependencies = [ ('Boost', '1.74.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index 7982ce4dd0..0b26d1ec45 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -32,7 +32,6 @@ dependencies = [ ('Boost', '1.74.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html From f0eba899b6e7217fb9b1e86d4692fc09934fb693 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 08:59:01 +0000 Subject: [PATCH 1718/2365] also specify the EB built Python during pyarrow build --- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 1 + easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index e2b5ef35e8..8f577b4f44 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -46,6 +46,7 @@ configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index 0b26d1ec45..101f92aa06 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -43,6 +43,7 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] From 821586ed08b94bb9fe4b05e70a1fa41d6b044c61 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 1 Nov 2021 16:31:14 +0200 Subject: [PATCH 1719/2365] updating for review --- .../l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb | 29 +++++++++ .../l/libavif/libavif-0.9.0-foss-2020b.eb | 2 +- .../l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 60 +++++++++++++++++++ .../z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 29 +++++++++ .../z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb | 29 +++++++++ 5 files changed, 148 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c477cf445c --- /dev/null +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'LibLZF' +version = '3.4' + +homepage = 'http://oldhome.schmorp.de/marc/liblzf.html' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] +sources = ['liblzf-%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_commands = ['lzf -h'] + +sanity_check_paths = { + 'files': ['bin/lzf'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb index 23a8645f59..5ef2dc0e96 100644 --- a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ # TODO FIX THIS - NEED THOSE # configopts = ' -DAVIF_CODEC_AOM=ON -DAVIF_CODEC_DAV1D=ON -DAVIF_CODEC_LIBGAV1=ON -DAVIF_CODEC_RAV1E=ON ' sanity_check_paths = { - 'files': ['lib/libavif.so.10.0.0', 'include/avif/avif.h'], + 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], 'dirs': ['lib/', 'include/avif/'] } diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d9f77d0267 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libjxl' +version = '0.6.1' +local_lodepng_version = "48e5364" + +homepage = 'https://github.com/libjxl/libjxl' +description = "JPEG XL image format reference implementation" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'optarch': False} # optarch causes some test failures + +github_account = 'libjxl' +source_urls = [GITHUB_SOURCE] +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, + 'download_filename': local_lodepng_version, + 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], + 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, +] +patches = [ + 'libjxl-0.3.7_external_lcms2.patch', + 'libjxl-%(version)s_remove-broken-test.patch', +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('googletest', '1.10.0'), + ('pkg-config', '0.29.2'), + ('Highway', '0.12.2'), # Highway only has a static library +] + +dependencies = [ + ('LittleCMS', '2.11'), + ('Brotli', '1.0.9'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('giflib', '5.2.1'), + ('libwebp', '1.1.0'), + ('OpenEXR', '2.5.5'), + ('gperftools', '2.9.1'), +] + +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' +# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) +configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..25cec87e17 --- /dev/null +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Zopfli' +version = '1.0.3' + +homepage = 'https://github.com/google/zopfli' +description = """Zopfli Compression Algorithm is a compression library programmed in C to perform +very good, but slow, deflate or zlib compression.""" + +# toolchain = {'name': 'foss', 'version': '2020b'} +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/', 'include/'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..44717cae45 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'zlib-ng' +version = '2.0.5' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_commands = [ +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/', 'include/'], +} + +moduleclass = 'tools' From c2f8b5446d968dce07ff6af00ebd1b4c5dd28ab3 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 1 Nov 2021 20:46:05 +0200 Subject: [PATCH 1720/2365] updating for tests --- easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb | 1 + .../easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 6 ++++++ .../easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 1 + .../easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb | 1 + 5 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb index c477cf445c..01e7faabd9 100644 --- a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] sources = ['liblzf-%(version)s.tar.gz'] +checksums = ['ec62974877b4b85f6e37db97e71678c7abfe83091b57d32ec69fa37b2c3c9499'] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb index 5ef2dc0e96..d92567651e 100644 --- a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['ea1603fc18e7dd20cf01f0b405156576886ecb5df84db8c0e87187cd2f8a00f4'] builddependencies = [ ('CMake', '3.18.4'), diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index d9f77d0267..21392e1cad 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -25,6 +25,12 @@ patches = [ 'libjxl-0.3.7_external_lcms2.patch', 'libjxl-%(version)s_remove-broken-test.patch', ] +checksums = [ + 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz + 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz + 'a430237fdef24c07f2187e079dad3041f124d5dc00ec713dba4eb308d78712f6', # libjxl-0.3.7_external_lcms2.patch + '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb index 25cec87e17..280d70f476 100644 --- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -15,6 +15,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd'] builddependencies = [ ('CMake', '3.18.4'), diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb index 44717cae45..ebe8e39426 100644 --- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['eca3fe72aea7036c31d00ca120493923c4d5b99fe02e6d3322f7c88dbdcd0085'] builddependencies = [ ('CMake', '3.18.4'), From 9d185b7cfae103a9dd8ed158ad25f1eff52dc37e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 1 Nov 2021 22:34:21 +0200 Subject: [PATCH 1721/2365] updating for tests --- .../b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb | 30 +++++++++++ .../b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 50 +++++++++++++++++++ .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb | 41 +++++++++++++++ .../z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 35 +++++++++++++ 4 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d41c44db0f --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.0.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e964d5ced892c7c6afbfdd50511d5087a04c2d60bfd6798feccf813ba27389ff'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3fc7cbf9e5 --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brunsli-0.1_wrong_paths.patch'] +checksums = [ + '62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc', # v0.1.tar.gz + '34795a1adba1ec208033922eaf27b3b3a23535a2e09201f93f9098666dd7319d', # Brunsli-0.1_wrong_paths.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '0.12.2'), +] + +configopts = ' -DCMAKE_BUILD_TYPE=Release ' +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon "' + +postinstallcmds = [ + 'mkdir %(installdir)s/bin ', + 'cp dbrunsli %(installdir)s/bin ', + 'cp *.a %(installdir)s/lib64 ', + 'cp *.so %(installdir)s/lib64 ', + ] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['bin'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e49ddd7b1d --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.49' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + '5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3', # cfitsio-3.49.tar.gz + 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch +] + +# curl for HTTPs support +dependencies = [('cURL', '7.72.0')] + +builddependencies = [('binutils', '2.35')] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = '&& make shared && make testprog' + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c0eee77907 --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'MakeCp' + +name = 'zfp' +version = '0.5.5' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. +zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and +write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['6a7f4934489087d9c117a4af327fd6495ea757924f4df467b9c537abf8bd86c4'] + +separate_build_dir = True + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +files_to_copy = ['bin', 'lib', 'include'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From c3fbfb440bb9b594fb9e512514c1142b5186d622 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 20:37:13 +0000 Subject: [PATCH 1722/2365] Delete CFITSIO-3.49-GCCcore-10.2.0.eb accidentally added --- .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb deleted file mode 100644 index e49ddd7b1d..0000000000 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'ConfigureMake' - -name = 'CFITSIO' -version = '3.49' - -homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' -description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in -FITS (Flexible Image Transport System) data format.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] -sources = ['%%(namelower)s-%s.tar.gz' % version] -patches = ['CFITSIO-3.48_install_test_data.patch'] -checksums = [ - '5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3', # cfitsio-3.49.tar.gz - 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch -] - -# curl for HTTPs support -dependencies = [('cURL', '7.72.0')] - -builddependencies = [('binutils', '2.35')] - -# make would create just static libcfitsio.a. -# Let's create dynamic lib and testprog too. -buildopts = '&& make shared && make testprog' - -sanity_check_paths = { - 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -sanity_check_commands = [ - ('cd %(installdir)s/share && testprog'), -] - -moduleclass = 'lib' From 436d1f29d01b9636e284927f2fd12cff2eb70e0f Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 20:37:28 +0000 Subject: [PATCH 1723/2365] Delete Brunsli-0.1-GCCcore-10.2.0.eb accidentally added --- .../b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb deleted file mode 100644 index 3fc7cbf9e5..0000000000 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ /dev/null @@ -1,50 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'Brunsli' -version = '0.1' - -homepage = 'https://github.com/google/brunsli/' -description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files -and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still -written in portable C.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = ['https://github.com/google/brunsli/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['Brunsli-0.1_wrong_paths.patch'] -checksums = [ - '62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc', # v0.1.tar.gz - '34795a1adba1ec208033922eaf27b3b3a23535a2e09201f93f9098666dd7319d', # Brunsli-0.1_wrong_paths.patch -] - -builddependencies = [ - ('CMake', '3.18.4'), - ('binutils', '2.35'), -] - -dependencies = [ - ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), -] - -configopts = ' -DCMAKE_BUILD_TYPE=Release ' -configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon "' - -postinstallcmds = [ - 'mkdir %(installdir)s/bin ', - 'cp dbrunsli %(installdir)s/bin ', - 'cp *.a %(installdir)s/lib64 ', - 'cp *.so %(installdir)s/lib64 ', - ] - -sanity_check_paths = { - 'files': ['bin/dbrunsli'], - 'dirs': ['bin'], -} - -sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] - -moduleclass = 'lib' From 924b80e0ee49c542d7432a6f7838bec1f0d6ae65 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 20:37:42 +0000 Subject: [PATCH 1724/2365] Delete Blosc2-2.0.3-GCCcore-10.2.0.eb accidentally added --- .../b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb deleted file mode 100644 index d41c44db0f..0000000000 --- a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'Blosc2' -version = '2.0.3' - -homepage = 'https://www.blosc.org/' - -description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['e964d5ced892c7c6afbfdd50511d5087a04c2d60bfd6798feccf813ba27389ff'] - -builddependencies = [ - ('binutils', '2.35'), - ('CMake', '3.18.4'), -] - -sanity_check_paths = { - 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', - 'lib/libblosc2.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' From 0062ce588c579640853a62aa462bedfa58849523 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 1 Nov 2021 23:32:21 +0200 Subject: [PATCH 1725/2365] fix for tests --- .../l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 65 +++++++++++++++++++ .../z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 33 ++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..be0ec4a4a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -0,0 +1,65 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libjxl' +version = '0.6.1' +local_lodepng_version = "48e5364" + +homepage = 'https://github.com/libjxl/libjxl' +description = "JPEG XL image format reference implementation" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'optarch': False} # optarch causes some test failures + +github_account = 'libjxl' +source_urls = [GITHUB_SOURCE] +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, + 'download_filename': local_lodepng_version, + 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], + 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, +] +patches = [ + 'libjxl-0.6.1_external_lcms2.patch', + 'libjxl-%(version)s_remove-broken-test.patch', +] +checksums = [ + 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz + 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz + '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('googletest', '1.10.0'), + ('pkg-config', '0.29.2'), + ('Highway', '0.12.2'), # Highway only has a static library +] + +dependencies = [ + ('LittleCMS', '2.11'), + ('Brotli', '1.0.9'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('giflib', '5.2.1'), + ('libwebp', '1.1.0'), + ('OpenEXR', '2.5.5'), + ('gperftools', '2.9.1'), +] + +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' +# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) +configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..80e3ed2438 --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'MakeCp' + +name = 'zfp' +version = '0.5.5' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. +zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and +write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['6a7f4934489087d9c117a4af327fd6495ea757924f4df467b9c537abf8bd86c4'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +files_to_copy = ['bin', 'lib', 'include'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From 3ca67176b402069bfca09b73431444c6cd89582f Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 21:33:51 +0000 Subject: [PATCH 1726/2365] Delete zfp-0.5.5-GCCcore-10.2.0.eb added accidentaly --- .../z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb deleted file mode 100644 index 80e3ed2438..0000000000 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'MakeCp' - -name = 'zfp' -version = '0.5.5' - -homepage = 'https://github.com/LLNL/zfp' -description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. -zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. -zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and -write large data sets to and from disk.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/LLNL/zfp/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['6a7f4934489087d9c117a4af327fd6495ea757924f4df467b9c537abf8bd86c4'] - -builddependencies = [ - ('CMake', '3.18.4'), - ('binutils', '2.35'), -] - -files_to_copy = ['bin', 'lib', 'include'] - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'include', 'lib'], -} - -moduleclass = 'lib' From a86640f6351f2c5a749c2eb2b6b2c2635bdf9c3b Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 21:34:11 +0000 Subject: [PATCH 1727/2365] Delete libjxl-0.6.1-GCCcore-10.2.0.eb added accidentaly --- .../l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 65 ------------------- 1 file changed, 65 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb deleted file mode 100644 index be0ec4a4a1..0000000000 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ /dev/null @@ -1,65 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'libjxl' -version = '0.6.1' -local_lodepng_version = "48e5364" - -homepage = 'https://github.com/libjxl/libjxl' -description = "JPEG XL image format reference implementation" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'optarch': False} # optarch causes some test failures - -github_account = 'libjxl' -source_urls = [GITHUB_SOURCE] -sources = [ - 'v%(version)s.tar.gz', - {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, - 'download_filename': local_lodepng_version, - 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], - 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, -] -patches = [ - 'libjxl-0.6.1_external_lcms2.patch', - 'libjxl-%(version)s_remove-broken-test.patch', -] -checksums = [ - 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz - 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch -] - -builddependencies = [ - ('binutils', '2.35'), - ('CMake', '3.18.4'), - ('googletest', '1.10.0'), - ('pkg-config', '0.29.2'), - ('Highway', '0.12.2'), # Highway only has a static library -] - -dependencies = [ - ('LittleCMS', '2.11'), - ('Brotli', '1.0.9'), - ('libjpeg-turbo', '2.0.5'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), - ('giflib', '5.2.1'), - ('libwebp', '1.1.0'), - ('OpenEXR', '2.5.5'), - ('gperftools', '2.9.1'), -] - -configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' -# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) -configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' - -runtest = "test" - -sanity_check_paths = { - 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'lib' From 9cc9852c5410b88d6a178809c5aa2489bfc2217c Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 1 Nov 2021 23:34:54 +0200 Subject: [PATCH 1728/2365] fix for tests --- easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 3 +-- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 2 -- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index 21392e1cad..be0ec4a4a1 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -22,13 +22,12 @@ sources = [ 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, ] patches = [ - 'libjxl-0.3.7_external_lcms2.patch', + 'libjxl-0.6.1_external_lcms2.patch', 'libjxl-%(version)s_remove-broken-test.patch', ] checksums = [ 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - 'a430237fdef24c07f2187e079dad3041f124d5dc00ec713dba4eb308d78712f6', # libjxl-0.3.7_external_lcms2.patch '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch ] diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index c0eee77907..80e3ed2438 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -18,8 +18,6 @@ source_urls = ['https://github.com/LLNL/zfp/archive'] sources = ['%(version)s.tar.gz'] checksums = ['6a7f4934489087d9c117a4af327fd6495ea757924f4df467b9c537abf8bd86c4'] -separate_build_dir = True - builddependencies = [ ('CMake', '3.18.4'), ('binutils', '2.35'), From 968b8b88ea1c93ec2e625902998aaa735d03d0a4 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 2 Nov 2021 11:37:44 +0200 Subject: [PATCH 1729/2365] tests --- easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index be0ec4a4a1..f1a925dd52 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -28,6 +28,7 @@ patches = [ checksums = [ 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz + 'a430237fdef24c07f2187e079dad3041f124d5dc00ec713dba4eb308d78712f6', # libjxl-0.6.1_external_lcms2.patch '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch ] From 0fef230365e51efb658b71ec04477c31a45d3c9f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 2 Nov 2021 12:58:05 +0200 Subject: [PATCH 1730/2365] style checks --- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index 80e3ed2438..efd4f45522 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -7,9 +7,9 @@ version = '0.5.5' homepage = 'https://github.com/LLNL/zfp' description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. -zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. -zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and -write large data sets to and from disk.""" +zfp provides compressed-array classes that support high throughput read and write random access to individual array +elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications +that read and write large data sets to and from disk.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} From 102cb5500108a7c7a558a5a9e85806dceea3af7f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 2 Nov 2021 15:59:44 +0200 Subject: [PATCH 1731/2365] fix for tests --- .../b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb | 1 + .../b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 48 +++++++++++++++++++ .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb | 4 ++ .../imagecodecs-2021.8.26-foss-2020b.eb | 20 ++++---- .../l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb | 34 +++++++++++++ 5 files changed, 95 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb index cc97656d2c..d41c44db0f 100644 --- a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb @@ -14,6 +14,7 @@ toolchainopts = {'pic': True, 'cstd': 'c++11'} source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['e964d5ced892c7c6afbfdd50511d5087a04c2d60bfd6798feccf813ba27389ff'] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fce89e11c4 --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brunsli-0.1_wrong_paths.patch'] +checksums = [ + '62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc', # v0.1.tar.gz + '34795a1adba1ec208033922eaf27b3b3a23535a2e09201f93f9098666dd7319d', # Brunsli-0.1_wrong_paths.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '0.12.2'), +] + +configopts = ' -DCMAKE_BUILD_TYPE=Release ' +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon "' + +postinstallcmds = [ + 'mkdir %(installdir)s/bin ', + 'cp dbrunsli %(installdir)s/bin ', + 'cp *.a %(installdir)s/lib64 ', + 'cp *.so %(installdir)s/lib64 ', + ] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['bin'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb index 3d4e1b6d40..e49ddd7b1d 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb @@ -15,6 +15,10 @@ toolchainopts = {'pic': True} source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s-%s.tar.gz' % version] patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + '5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3', # cfitsio-3.49.tar.gz + 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch +] # curl for HTTPs support dependencies = [('cURL', '7.72.0')] diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index c75dc12b18..e16110f851 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -1,6 +1,6 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'imagecodecs' version = '2021.8.26' @@ -18,12 +18,6 @@ toolchain = {'name': 'foss', 'version': '2020b'} local_extract_cmd = ' tar -xvf %s ' local_extract_cmd += ' && find . -type f -print0 | xargs -0 dos2unix ' -sources = [{ - 'source_urls': PYPI_SOURCE, - 'filename': SOURCE_TAR_GZ, - 'extract_cmd': local_extract_cmd, -}] - dependencies = [ ('Python', '3.8.6'), ('matplotlib', '3.3.3'), @@ -45,7 +39,7 @@ dependencies = [ ('libjxl', '0.5'), ('liblzf', '3.4'), ('libpng', '1.6.37'), - ('liblzma', '5.2.5'), + ('XZ', '5.2.5'), ('libpng', '1.6.37'), ('LibTIFF', '4.1.0'), ('libwebp', '1.1.0'), @@ -66,6 +60,7 @@ exts_defaultclass = 'PythonPackage' exts_default_options = { 'use_pip': True, 'download_dep_fail': True, + 'sanity_pip_check': True } exts_list = [ @@ -73,10 +68,11 @@ exts_list = [ 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'] }), + (name, version, { + 'source_urls': PYPI_SOURCE, + 'filename': SOURCE_TAR_GZ, + 'extract_cmd': local_extract_cmd, + }), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6a3ff1593c --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s' ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/aec', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['bin/', 'lib/', 'include/'] +} + +sanity_check_commands = [ + 'aec --help', +] + +moduleclass = 'tools' From 261a78ff3de03f4950295643c9a3463f1bf2413d Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 2 Nov 2021 15:49:37 +0000 Subject: [PATCH 1732/2365] Update imagecodecs-2021.8.26-foss-2020b.eb adding checksums --- .../i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index e16110f851..0b6499d704 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -66,12 +66,14 @@ exts_default_options = { exts_list = [ ('bitshuffle', '0.3.5', { 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'] + 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'], + 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], }), (name, version, { 'source_urls': PYPI_SOURCE, 'filename': SOURCE_TAR_GZ, 'extract_cmd': local_extract_cmd, + 'checksums': ['e87994d918ea951a589ec46648c24d9c7e56b7b5c2466d93f3b07883f0ecea19'], }), ] From f0587ce5b798c2c7fcdcc8ecc0c5b4c8cb2eb6a4 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 3 Nov 2021 11:17:13 +0200 Subject: [PATCH 1733/2365] changes for tests --- easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index fce89e11c4..caadf4deda 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -36,7 +36,7 @@ postinstallcmds = [ 'cp dbrunsli %(installdir)s/bin ', 'cp *.a %(installdir)s/lib64 ', 'cp *.so %(installdir)s/lib64 ', - ] +] sanity_check_paths = { 'files': ['bin/dbrunsli'], diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb index 6a3ff1593c..b29e2d0401 100644 --- a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ are not directly supported, they can also be efficiently coded by grouping expon toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s' ] +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] From 6ef03102c04c27186d151347584c12b414aa3ebd Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 3 Nov 2021 12:04:10 +0200 Subject: [PATCH 1734/2365] changes for tests --- .../imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index 0b6499d704..8440baa649 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -31,13 +31,13 @@ dependencies = [ ('giflib', '5.2.1'), ('jxrlib', '1.1'), ('LittleCMS', '2.11'), - ('lerc', '3.0'), + ('LERC', '3.0'), ('libaec', '1.0.6'), ('libavif', '0.9.0'), ('libdeflate', '1.7'), ('libjpeg-turbo', '2.0.5'), ('libjxl', '0.5'), - ('liblzf', '3.4'), + ('LibLZF', '3.4'), ('libpng', '1.6.37'), ('XZ', '5.2.5'), ('libpng', '1.6.37'), @@ -51,7 +51,7 @@ dependencies = [ ('zopfli', '1.0.3'), ('zfp', '0.5.5'), ('zstd', '1.4.5'), - ('brunsli', '0.1'), + ('Brunsli', '0.1'), ('HDF5', '1.10.7'), ('h5py', '3.1.0'), ] @@ -70,9 +70,9 @@ exts_list = [ 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], }), (name, version, { - 'source_urls': PYPI_SOURCE, - 'filename': SOURCE_TAR_GZ, - 'extract_cmd': local_extract_cmd, + 'extract_cmd': " tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix ", + 'filename': '%(name)s-%(version)s.tar.gz', + 'source_urls': 'https://pypi.python.org/packages/source/%(nameletter)s/%(name)s', 'checksums': ['e87994d918ea951a589ec46648c24d9c7e56b7b5c2466d93f3b07883f0ecea19'], }), ] From fbc7aedbe240fdc42701e0cb2970298149872864 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 3 Nov 2021 16:24:36 +0200 Subject: [PATCH 1735/2365] fix for tests --- .../dicom2nifti-2.3.0-foss-2020b.eb | 35 ++++++++ .../m/MedPy/MedPy-0.4.0-foss-2020b.eb | 28 ++++++ .../n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb | 85 +++++++++++++++++++ .../s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb | 14 +-- 4 files changed, 157 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb new file mode 100644 index 0000000000..4692d2a37e --- /dev/null +++ b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'dicom2nifti' +version = '2.3.0' + +homepage = 'https://github.com/icometrix/dicom2nifti' +description = "Python library for converting dicom files to nifti" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['808c4ddbcffd492d41ff20a2837b5e2a3cbe2058d43512fe97b99d678a758bfd'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('pydicom', '2.1.2'), + ('NiBabel', '3.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/dicom2nifti'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb new file mode 100644 index 0000000000..07a664b8e8 --- /dev/null +++ b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb @@ -0,0 +1,28 @@ +# This easyconfig was created by James Carpenter of the BEAR Software team at the University of Birmingham. +# updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'MedPy' +version = '0.4.0' + +homepage = 'https://pypi.org/project/MedPy/' +description = """MedPy is a library and script collection for medical image processing in Python, providing basic + functionalities for reading, writing and manipulating large images of arbitrary dimensionality. Its main + contributions are n-dimensional versions of popular image filters, a collection of image feature extractors, ready + to be used with scikit-learn, and an exhaustive n-dimensional graph-cut package.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f8a94937dbb947ab069e767862dc6b86896b153c41ce8ed9369c7d79c0033a88'] + +dependencies = [ + ('Python', '3.8.6'), + ('SimpleITK', '2.1.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb new file mode 100644 index 0000000000..0cd1960361 --- /dev/null +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb @@ -0,0 +1,85 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'nnU-Net' +version = '1.7.0' + +homepage = 'https://github.com/MIC-DKFZ/nnUNet' +description = """ +nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain. +It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset. +""" +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://files.pythonhosted.org/packages/8e/cf/0e5a45faba472c1df80da8d3fcb8d90b31a2258e48fdbc47cd2e30c16233/'] +sources = ['nnunet-%(version)s.tar.gz'] +checksums = ['7ad3d5b89af389fa86cea58f409bd2353b511a746587f37d26c00a756849f356'] + +builddependencies = [ + ('Bazel', '3.7.2') +] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), + ('dicom2nifti', '2.3.0'), + ('scikit-image', '0.18.1'), + ('TensorFlow', '2.5.0'), + ('SciPy-bundle', '2020.11'), + ('batchgenerators', '0.23'), + ('scikit-learn', '0.23.2'), + ('requests', '2.26.0'), + ('NiBabel', '3.2.1'), + ('SimpleITK', '2.1.0'), + ('tifffile', '2021.8.30'), + ('MedPy', '0.4.0'), + ('jax', '0.2.19') +] + +# sklearn is incorrect package name +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('absl-py', '0.15.0', { + 'modulename': 'absl', + 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['5faa387ad6b522516283cbe45adbc4c46bedcf501c82db2f9174945f3ec2ea7d'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'nnunet'} + +sanity_check_commands = ['nnUNet_train --help'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb index 0b1009560a..956b38dd32 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb @@ -28,15 +28,19 @@ dependencies = [ ] start_dir = 'SimpleITK' -configopts = '-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF -DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF ' +configopts = '-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF ' +configopts += ' -DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF ' preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_pyinstpath = "%(installdir)s/lib/python%(pyshortver)s/site-packages" + +local_postinstall_cmds = "mkdir -p %s " % local_pyinstpath +local_postinstall_cmds += " && cd %(builddir)s/easybuild_obj/Wrapping/Python " +local_postinstall_cmds += " && export PYTHONPATH=%s:$PYTHONPATH " % local_pyinstpath +local_postinstall_cmds += " && pip install --prefix=%(installdir)s . " + postinstallcmds = [ - "mkdir -p %s " % local_pyinstpath - + " && cd %(builddir)s/easybuild_obj/Wrapping/Python " - + " && export PYTHONPATH=%s:$PYTHONPATH " % local_pyinstpath - + " && pip install --prefix=%(installdir)s . " + local_postinstall_cmds ] separate_build_dir = True From 49b53c45f4253769a6ffb9f3533adda59749aaf7 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 3 Nov 2021 19:50:58 +0100 Subject: [PATCH 1736/2365] Adding dependent libraries order patch for imread --- .../s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb index 3169f709e7..7b0b41a3f5 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb @@ -25,7 +25,11 @@ exts_list = [ 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], }), ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + 'patches': ['imread-0.7.4_shlibs_order.patch'], + 'checksums': [ + '0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f', # imread-0.7.4.tar.gz + '887cca0c4d8161d16fc0637ff06716d99cb3fd90ba800c92b6fbe3709c142b16', # imread-0.7.4_shlibs_order.patch + ], }), ('pooch', '1.3.0', { 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], From 26079710e9561813e55db2d34aa5c07f637b8545 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 4 Nov 2021 15:18:30 +0200 Subject: [PATCH 1737/2365] adding ITK --- .../easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb new file mode 100644 index 0000000000..bb09e67391 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb @@ -0,0 +1,62 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.2.1' # 5.1.2 + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + + +builddependencies = [ + ('CMake', '3.18.4'), + ('Bison', '3.7.1'), + ('Eigen', '3.3.8'), +] + +dependencies = [ + ('double-conversion', '3.1.5'), + ('expat', '2.2.9'), + ('HDF5', '1.10.7'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('VTK', '9.0.1'), + ('zlib', '1.2.11'), +] + +local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +# local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' +configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' \ No newline at end of file From 96839ffc835f350027402b89b25812df3a92a638 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 4 Nov 2021 15:53:13 +0200 Subject: [PATCH 1738/2365] fix for tests --- easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb | 6 +++--- easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb | 5 ++++- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb index bb09e67391..69753b7704 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb @@ -6,7 +6,7 @@ easyblock = 'CMakeMake' name = 'ITK' -version = '5.2.1' # 5.1.2 +version = '5.2.1' homepage = 'https://itk.org' description = """Insight Segmentation and Registration Toolkit (ITK) provides @@ -19,7 +19,7 @@ toolchainopts = {'pic': True, 'cstd': 'c++11'} github_account = 'InsightSoftwareConsortium' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] - +checksums = ['6022b2b64624b8bcec3333fe48d5f74ff6ebceb3bdf98258ba7d7fbbc76b99ab'] builddependencies = [ ('CMake', '3.18.4'), @@ -59,4 +59,4 @@ sanity_check_paths = { 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], } -moduleclass = 'data' \ No newline at end of file +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb index 0cd1960361..64574eb1e4 100644 --- a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb @@ -12,7 +12,10 @@ It condenses and automates the keys decisions for designing a successful segment """ toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = ['https://files.pythonhosted.org/packages/8e/cf/0e5a45faba472c1df80da8d3fcb8d90b31a2258e48fdbc47cd2e30c16233/'] +source_urls = [ + 'https://files.pythonhosted.org/packages/8e/cf/0e5a45faba472c1df80da8d3fcb8d90b31a2258e48fdbc47cd2e30c16233/' +] + sources = ['nnunet-%(version)s.tar.gz'] checksums = ['7ad3d5b89af389fa86cea58f409bd2353b511a746587f37d26c00a756849f356'] From e991d5f56c1fffcb78a2c58fb6f4d7147a94eb9b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Nov 2021 10:14:48 +0100 Subject: [PATCH 1739/2365] {cae}[foss/2020b] OpenFOAM 8-20210316 --- .../OpenFOAM-8-foss-2020b-20210316.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b-20210316.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b-20210316.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b-20210316.eb new file mode 100644 index 0000000000..4d4dd88545 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b-20210316.eb @@ -0,0 +1,45 @@ +name = 'OpenFOAM' +local_commit = '1c9b587' +version = '8' +versionsuffix = '-20210316' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': 'OpenFOAM-%(version)s%(versionsuffix)s.tar.gz', +}] +patches = [ + 'OpenFOAM-%(version)s-cleanup.patch', +] +checksums = [ + '2fef19014b408e4ea42062d5bf204419af086cbfa56a21a96676007f926b48f2', # OpenFOAM-8-20210316.tar.gz + 'e3fac8049611ee109f07eb5b0ed4b1526782a21b3f12435e03529d56c8483b9f', # OpenFOAM-8-cleanup.patch +] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('CGAL', '5.2'), + ('ParaView', '5.8.1', '-mpi'), + ('gnuplot', '5.4.1'), +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' From f6b8fe20566a126a35ed670e59ff27bc23ff70b6 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 5 Nov 2021 12:57:45 +0200 Subject: [PATCH 1740/2365] update to 2.1.1 --- .../AlphaFold-2.1.1-fosscuda-2020b.eb | 189 ++++++++++++++++++ 1 file changed, 189 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..e32c730e44 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -0,0 +1,189 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.1' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.4.1'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.19'), # also provides absl-py +] +configopts = "-DCUDA_CUDA_LIBRARY=${EBROOTCUDA}/lib64/stubs/libcuda.so " +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'http://two.embl.de/AlphaFold-2.1.0_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'http://two.embl.de/AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'http://two.embl.de/AlphaFold-2.0.1_relax_gpu.patch' + ], + 'checksums': [ + '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '0f0b9a7913898176b7e7878c0818fd60f7c5f527ec2bc84cd81d96a503f432c2', # AlphaFold-2.1.0_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +moduleclass = 'bio' From 26d0147ce099367e447d961551779f79ad24d647 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 5 Nov 2021 13:10:17 +0200 Subject: [PATCH 1741/2365] fix checksum --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index e32c730e44..267562d051 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -85,7 +85,7 @@ components = [ '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '0f0b9a7913898176b7e7878c0818fd60f7c5f527ec2bc84cd81d96a503f432c2', # AlphaFold-2.1.0_data-dep-paths.patch + '4d5f53486d7c16ad0c93d17c89c04d3ae1310de0adad6bca4dd7ea249bf030d1', # AlphaFold-2.1.0_data-dep-paths.patch 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch From 1ad4ca4b93d95ab2ad58fdf53b6b37cd1eb9d23c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 5 Nov 2021 13:22:09 +0200 Subject: [PATCH 1742/2365] fix patch urls --- .../a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index 267562d051..3598983c8f 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -75,11 +75,11 @@ components = [ ], 'patches': [ 'AlphaFold-2.0.0_fix-packages.patch', - 'http://two.embl.de/AlphaFold-2.1.0_data-dep-paths.patch', + 'AlphaFold-2.1.0_data-dep-paths.patch', 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', - 'http://two.embl.de/AlphaFold-2.0.1_setup_rm_tfcpu.patch', - 'http://two.embl.de/AlphaFold-2.0.1_relax_gpu.patch' + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.0.1_relax_gpu.patch' ], 'checksums': [ '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz From 65fd97be5099f4bc8f2cc9bc2a273ee4d643c5cd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Nov 2021 13:03:05 +0100 Subject: [PATCH 1743/2365] {chem}[foss/2020b] CP2K 5.1 --- .../easyconfigs/c/CP2K/CP2K-5.1-foss-2020b.eb | 49 +++++++++++++++++++ .../l/Libint/Libint-1.1.6-foss-2020b.eb | 32 ++++++++++++ .../l/libxc/libxc-3.0.1-foss-2020b.eb | 33 +++++++++++++ 3 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020b.eb new file mode 100644 index 0000000000..8bc41a594e --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020b.eb @@ -0,0 +1,49 @@ +name = 'CP2K' +version = '5.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] +checksums = [ + 'e23613b593354fa82e0b8410e17d94c607a0b8c6d9b5d843528403ab09904412', # cp2k-5.1.tar.bz2 + '02475cbe24c8d4ba27037c826adf8a534cad634c3c4e02c21d743f5284516bda', # CP2K-2.4.0-fix_compile_date_lastsvn.patch +] + +dependencies = [ + ('Libint', '1.1.6'), + ('libxc', '3.0.1'), + ('libxsmm', '1.16.1'), + ('FFTW', '3.3.8'), + ('PLUMED', '2.6.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.1'), +] + +# values to use here are +1 those used for building Libint +# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT +extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" + +# regression test reports failures +ignore_regtest_fails = True + +# You might want to set OMP_NUM_THREADS, otherwise OpenBLAS will start (by default) +# the number of accessible CPUcores OpenMP threads. Since it is a MPI only version (popt), +# the performance will be copletely bad, as on N CPU cores N^2 threads will run. +# intel toolchain versions do not have this problem. YOU HAVE BEEN WARNED! +# modextravars = {'OMP_NUM_THREADS': '1'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020b.eb new file mode 100644 index 0000000000..b85944e7d7 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020b.eb @@ -0,0 +1,32 @@ +name = 'Libint' +version = '1.1.6' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/evaleev/libint/archive/'] +sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] +checksums = ['f201b0c621df678cfe8bdf3990796b8976ff194aba357ae398f2f29b0e2985a6'] + +builddependencies = [('Autotools', '20200321')] + +preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && " + +# these are important for CP2K +# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT +configopts = "--with-libint-max-am=5 --with-libderiv-max-am1=4 " + +configopts += " --enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb new file mode 100644 index 0000000000..e9d1b83c72 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '3.0.1' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] +checksums = [ + '836692f2ab60ec3aca0cca105ed5d0baa7d182be07cc9d0daa7b80ee1362caf7', # libxc-3.0.1.tar.gz + '27338d9f63ce33386a6241e7bd8edde66ac8684d103acf0e6cbb5bde011730b9', # libxc-3.0_no-longdouble.patch +] + +configopts = '--enable-static --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' From 4f36af96cca0566d51959e2761b4d0351db38ee6 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 5 Nov 2021 17:20:59 +0200 Subject: [PATCH 1744/2365] adding easyconfigs: STACEY-1.2.5-GCC-10.2.0.eb --- .../s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb new file mode 100644 index 0000000000..e6fffcbcc2 --- /dev/null +++ b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'Tarball' + +name = 'STACEY' +version = '1.2.5' + +homepage = 'http://www.indriid.com/software.html' +description = """The BEAST2 package STACEY can be used for species delimitation and species tree estimation, +based on the multispecies coalescent model.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://www.indriid.com/2019/'] +sources = ['%(name)s.addon.v%(version)s.zip'] +checksums = ['a6ce3ce83ddafe3505622961c7d90e696e11b2b51246f7447d820e1b3e717b58'] + +builddependencies = [ + ('Xvfb', '1.20.9'), +] +dependencies = [ + ('Beast', '2.6.4'), +] + +# we need to link installdir to hardcoded package directory of Beast (~/.beast/2.6/) +postinstallcmds = [ + # if package dir doesnt exist yet, initial run of `beauti` creates it + 'timeout 10 xvfb-run beauti 2>&1 | grep "Terminated"', + # now we can link our installdir to the package dir + 'ln -s %(installdir)s ~/.beast/2.6/STACEY ', +] + +sanity_check_paths = { + 'files': ['stacey.src.jar'], + 'dirs': ['lib/', 'templates/', 'examples'], +} + +moduleclass = 'data' From 60e413dd5b2c7709f673e7b886e0925146c2e389 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 8 Nov 2021 13:12:55 +0000 Subject: [PATCH 1745/2365] Update easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit removing trash Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb index 280d70f476..505836bb08 100644 --- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -9,7 +9,6 @@ homepage = 'https://github.com/google/zopfli' description = """Zopfli Compression Algorithm is a compression library programmed in C to perform very good, but slow, deflate or zlib compression.""" -# toolchain = {'name': 'foss', 'version': '2020b'} toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} From b3465507f1c2e6d4a04fcf52b8292a5164e563fc Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 8 Nov 2021 13:13:27 +0000 Subject: [PATCH 1746/2365] Update easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit flags for zopfli Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb index 505836bb08..3950b08a0b 100644 --- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('CMake', '3.18.4'), ('binutils', '2.35'), ] - +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] sanity_check_paths = { 'files': [], 'dirs': ['lib/', 'include/'], From 48a2cf794da32a0f4a039df75d9137abf8a0374d Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 8 Nov 2021 13:13:44 +0000 Subject: [PATCH 1747/2365] Update easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit better sanity check for zopfli Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb index 3950b08a0b..ee2b65fa1c 100644 --- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -22,8 +22,8 @@ builddependencies = [ ] configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] sanity_check_paths = { - 'files': [], - 'dirs': ['lib/', 'include/'], + 'files': ['bin/zopfli', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT, 'include/zopfli.h'], + 'dirs': [], } moduleclass = 'tools' From 33253d4954d07b8714772aedaa3da900baa874b6 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 8 Nov 2021 15:39:13 +0200 Subject: [PATCH 1748/2365] remove cuda stubs; update AlphaFold-2.1.0_data-dep-paths.patch: 1. correct mgy_clusters_2018_12.fa, 2. correct treatment of default parameter --model_preset=monomer --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index 3598983c8f..d7f3a32793 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -28,7 +28,6 @@ dependencies = [ ('Kalign', '3.3.1'), ('jax', '0.2.19'), # also provides absl-py ] -configopts = "-DCUDA_CUDA_LIBRARY=${EBROOTCUDA}/lib64/stubs/libcuda.so " local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " @@ -85,7 +84,7 @@ components = [ '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '4d5f53486d7c16ad0c93d17c89c04d3ae1310de0adad6bca4dd7ea249bf030d1', # AlphaFold-2.1.0_data-dep-paths.patch + 'ecd1b240fdcd30110879dc4a88880405ae3fafb0f93f95f14fe30f6562148e13', # AlphaFold-2.1.0_data-dep-paths.patch 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch From d0ce2e197674f90d4cc611433a55dc206e7b3de9 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 8 Nov 2021 16:20:30 +0200 Subject: [PATCH 1749/2365] review fixes --- .../easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 9 ++++++++- .../z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb | 5 ++--- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb index 01e7faabd9..7b980f3eae 100644 --- a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ sanity_check_commands = ['lzf -h'] sanity_check_paths = { - 'files': ['bin/lzf'], + 'files': ['bin/lzf', 'lib/liblzf.a'], 'dirs': ['bin', 'lib'], } diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index efd4f45522..befa00aab2 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -23,10 +23,17 @@ builddependencies = [ ('binutils', '2.35'), ] +configopts = ' -DZFP_WITH_OPENMP ' + +buildopts = ' && make test ' + files_to_copy = ['bin', 'lib', 'include'] +sanity_check_commands = ['zfp --version'] +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + sanity_check_paths = { - 'files': [], + 'files': ['bin/zfp', 'bin/testzfp', 'lib/libzfp.a'], 'dirs': ['bin', 'include', 'lib'], } diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb index ebe8e39426..061cbd1104 100644 --- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb @@ -19,11 +19,10 @@ builddependencies = [ ('binutils', '2.35'), ] -sanity_check_commands = [ -] +configopts = ' -DZLIB_ENABLE_TESTS=True ' sanity_check_paths = { - 'files': [], + 'files': ['lib/libz-ng.%s' % SHLIB_EXT, 'include/zlib-ng.h', 'include/zconf-ng.h'], 'dirs': ['lib/', 'include/'], } From 920f55690f44ce374d9f9484a98ec18c1b151eed Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 8 Nov 2021 17:18:11 +0200 Subject: [PATCH 1750/2365] review fixes --- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index befa00aab2..73d372020a 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -29,7 +29,6 @@ buildopts = ' && make test ' files_to_copy = ['bin', 'lib', 'include'] -sanity_check_commands = ['zfp --version'] sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] sanity_check_paths = { From 2dbde4125fff9678fb01c8b573148f8bd0cfb9b3 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 8 Nov 2021 17:49:05 +0200 Subject: [PATCH 1751/2365] review fixes --- easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index f1a925dd52..2b161ae705 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -28,7 +28,7 @@ patches = [ checksums = [ 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - 'a430237fdef24c07f2187e079dad3041f124d5dc00ec713dba4eb308d78712f6', # libjxl-0.6.1_external_lcms2.patch + '1948d2527c658637939327eec093301539b164714f5bf146ed2e0dcadffadf00', # libjxl-0.6.1_external_lcms2.patch '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch ] From 79b1e5333379f178261d28449893840a145accd9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 10:39:41 +0100 Subject: [PATCH 1752/2365] cleanup in libavif easyconfig --- .../easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb index d92567651e..6e46d36eea 100644 --- a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb @@ -27,14 +27,9 @@ dependencies = [ ('Rust', '1.52.1'), ] -# TODO FIX THIS - NEED THOSE -# configopts = ' -DAVIF_CODEC_AOM=ON -DAVIF_CODEC_DAV1D=ON -DAVIF_CODEC_LIBGAV1=ON -DAVIF_CODEC_RAV1E=ON ' sanity_check_paths = { 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], - 'dirs': ['lib/', 'include/avif/'] + 'dirs': [], } -sanity_check_commands = [ -] - moduleclass = 'tools' From cfb997a03be5c1d7d98c345cfabc4f4773ae1b84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 10:46:51 +0100 Subject: [PATCH 1753/2365] refine sanity check for jxl 0.6.1 --- .../easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index 2b161ae705..5f5052289c 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -60,7 +60,12 @@ runtest = "test" sanity_check_paths = { 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], - 'dirs': ['include'], + 'dirs': ['include/jxl'], } +sanity_check_commands = [ + "cjxl --help", + "djxl --help", +] + moduleclass = 'lib' From bb88d81190372438cb68a7d3c42d7b6fa71c22bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 10:48:33 +0100 Subject: [PATCH 1754/2365] preserve description in patch for libjxl 0.6.1 --- easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index 5f5052289c..4bd51b12d1 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -29,7 +29,7 @@ checksums = [ 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz '1948d2527c658637939327eec093301539b164714f5bf146ed2e0dcadffadf00', # libjxl-0.6.1_external_lcms2.patch - '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch + '11b7cf639049afd9acd1c362287a743cdbe1a6f55e6f9d42b6eaa75ac6a0e6da', # libjxl-0.6.1_remove-broken-test.patch ] builddependencies = [ From e94d1461c877bd341cd1d585361dd28d2b691cef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 11:04:49 +0100 Subject: [PATCH 1755/2365] add sanity check command for Zopfli --- .../z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb index ee2b65fa1c..d65bafa85e 100644 --- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -20,10 +20,17 @@ builddependencies = [ ('CMake', '3.18.4'), ('binutils', '2.35'), ] -configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF', +] + sanity_check_paths = { - 'files': ['bin/zopfli', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT, 'include/zopfli.h'], + 'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT], 'dirs': [], } +sanity_check_commands = ["zopfli --help"] + moduleclass = 'tools' From 123c44038f4ae9fe8cfeb41b10bb405662ed66f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 11:07:41 +0100 Subject: [PATCH 1756/2365] minor tweak to sanity check paths for zfp --- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index 73d372020a..16947a10f4 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -29,11 +29,11 @@ buildopts = ' && make test ' files_to_copy = ['bin', 'lib', 'include'] -sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] - sanity_check_paths = { - 'files': ['bin/zfp', 'bin/testzfp', 'lib/libzfp.a'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], + 'dirs': ['include/zfp'], } +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + moduleclass = 'lib' From aaa5fbba32715cb258c2df5d039de00dabeaefb6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 11:10:16 +0100 Subject: [PATCH 1757/2365] also check for static zlib-ng library --- .../easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb index 061cbd1104..bf962cbf1d 100644 --- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb @@ -22,8 +22,8 @@ builddependencies = [ configopts = ' -DZLIB_ENABLE_TESTS=True ' sanity_check_paths = { - 'files': ['lib/libz-ng.%s' % SHLIB_EXT, 'include/zlib-ng.h', 'include/zconf-ng.h'], - 'dirs': ['lib/', 'include/'], + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], } moduleclass = 'tools' From 3b2a48cfea6527cc91fa7944e02f889a84f227ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 12:52:43 +0100 Subject: [PATCH 1758/2365] use compiler options controlled by EasyBuild for building zfp --- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index 16947a10f4..860d74ceb2 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -19,15 +19,15 @@ sources = ['%(version)s.tar.gz'] checksums = ['6a7f4934489087d9c117a4af327fd6495ea757924f4df467b9c537abf8bd86c4'] builddependencies = [ - ('CMake', '3.18.4'), ('binutils', '2.35'), ] -configopts = ' -DZFP_WITH_OPENMP ' +prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " +buildopts = 'ZFP_WITH_OPENMP=1' -buildopts = ' && make test ' +runtest = 'test' -files_to_copy = ['bin', 'lib', 'include'] +files_to_copy = ['bin', 'include', 'lib'] sanity_check_paths = { 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], From cad9210c0ced07cba3d5fd8c8833baf1061eded2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 15:12:25 +0100 Subject: [PATCH 1759/2365] fix name/version for imagecodecs dependencies: libjxl and Zopfli --- .../i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index 8440baa649..26470172bd 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -36,7 +36,7 @@ dependencies = [ ('libavif', '0.9.0'), ('libdeflate', '1.7'), ('libjpeg-turbo', '2.0.5'), - ('libjxl', '0.5'), + ('libjxl', '0.6.1'), ('LibLZF', '3.4'), ('libpng', '1.6.37'), ('XZ', '5.2.5'), @@ -48,7 +48,7 @@ dependencies = [ ('snappy', '1.1.8'), ('zlib', '1.2.11'), ('zlib-ng', '2.0.5'), - ('zopfli', '1.0.3'), + ('Zopfli', '1.0.3'), ('zfp', '0.5.5'), ('zstd', '1.4.5'), ('Brunsli', '0.1'), From 5fe2a9d1dd815ffb270593e13442d9358518d5df Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 16:08:41 +0100 Subject: [PATCH 1760/2365] avoid need for patch in Brunsli easyconfig --- .../b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 25 ++++++++++--------- 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index caadf4deda..f90442fc54 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -12,11 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/google/brunsli/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['Brunsli-0.1_wrong_paths.patch'] -checksums = [ - '62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc', # v0.1.tar.gz - '34795a1adba1ec208033922eaf27b3b3a23535a2e09201f93f9098666dd7319d', # Brunsli-0.1_wrong_paths.patch -] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] builddependencies = [ ('CMake', '3.18.4'), @@ -28,19 +24,24 @@ dependencies = [ ('Highway', '0.12.2'), ] -configopts = ' -DCMAKE_BUILD_TYPE=Release ' -configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon "' +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" +# also install dbrunsli binary and missing libraries postinstallcmds = [ - 'mkdir %(installdir)s/bin ', - 'cp dbrunsli %(installdir)s/bin ', - 'cp *.a %(installdir)s/lib64 ', - 'cp *.so %(installdir)s/lib64 ', + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib*/", + "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, ] sanity_check_paths = { 'files': ['bin/dbrunsli'], - 'dirs': ['bin'], + 'dirs': ['include/brunsli', 'lib'], } sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] From a6d389b54f85c964ab353a56bc548ae531f292b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 16:09:47 +0100 Subject: [PATCH 1761/2365] remove duplicate libpng dependency in imagecodecs easyconfig --- .../i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index 26470172bd..129dc5ac16 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -40,7 +40,6 @@ dependencies = [ ('LibLZF', '3.4'), ('libpng', '1.6.37'), ('XZ', '5.2.5'), - ('libpng', '1.6.37'), ('LibTIFF', '4.1.0'), ('libwebp', '1.1.0'), ('lz4', '1.9.2'), From 5b99d8d4aad5c269380b54d020cf3b36356f0faa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 19:59:08 +0100 Subject: [PATCH 1762/2365] extend/clean up sanity check for libaec --- .../l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb index b29e2d0401..d5fc64c036 100644 --- a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb @@ -23,12 +23,10 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['bin/aec', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], - 'dirs': ['bin/', 'lib/', 'include/'] + 'files': ['bin/aec', 'include/libaec.h', 'include/szlib.h', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['share/man'], } -sanity_check_commands = [ - 'aec --help', -] +sanity_check_commands = ["aec --help"] -moduleclass = 'tools' +moduleclass = 'lib' From 19cc72040dffe9df0d308f03af959be7da62b545 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:09:39 +0100 Subject: [PATCH 1763/2365] cleanup in imagecodecs easyconfig + make sure that openjpeg.h is found --- .../imagecodecs-2021.8.26-foss-2020b.eb | 36 +++++++---------- .../j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 2 files changed, 53 insertions(+), 22 deletions(-) create mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index 129dc5ac16..acd6766b2c 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -5,23 +5,18 @@ easyblock = 'PythonBundle' name = 'imagecodecs' version = '2021.8.26' -homepage = 'https://www.lfd.uci.edu/~gohlke/' -description = """ -Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, +homepage = 'https://github.com/cgohlke/imagecodecs' +description = """Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in the tifffile, czifile, zarr, and other -scientific image input/output modules. -""" +scientific image input/output modules.""" toolchain = {'name': 'foss', 'version': '2020b'} -# changing src line endings -local_extract_cmd = ' tar -xvf %s ' -local_extract_cmd += ' && find . -type f -print0 | xargs -0 dos2unix ' - +local_openjpeg_maj_min = '2.4' dependencies = [ ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy ('matplotlib', '3.3.3'), - ('SciPy-bundle', '2020.11'), ('Brotli', '1.0.9'), ('bzip2', '1.0.8'), ('Blosc', '1.21.0'), @@ -43,7 +38,7 @@ dependencies = [ ('LibTIFF', '4.1.0'), ('libwebp', '1.1.0'), ('lz4', '1.9.2'), - ('OpenJPEG', '2.4.0'), + ('OpenJPEG', local_openjpeg_maj_min + '.0'), ('snappy', '1.1.8'), ('zlib', '1.2.11'), ('zlib-ng', '2.0.5'), @@ -55,25 +50,22 @@ dependencies = [ ('h5py', '3.1.0'), ] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True -} +use_pip = True +sanity_pip_check = True exts_list = [ ('bitshuffle', '0.3.5', { - 'source_tmpl': '%(version)s.tar.gz', + 'sources': ['%(version)s.tar.gz'], 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'], 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], }), (name, version, { - 'extract_cmd': " tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix ", - 'filename': '%(name)s-%(version)s.tar.gz', - 'source_urls': 'https://pypi.python.org/packages/source/%(nameletter)s/%(name)s', + 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", + 'sources': ['%(name)s-%(version)s.tar.gz'], 'checksums': ['e87994d918ea951a589ec46648c24d9c7e56b7b5c2466d93f3b07883f0ecea19'], + # required for '#include "openjpeg.h"' to work + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-%s/:$CPATH && " % local_openjpeg_maj_min, }), ] -moduleclass = 'tools' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ded422afcf --- /dev/null +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +## + +easyblock = 'CMakeMake' + +name = 'jxrlib' +version = '1.1' + +homepage = 'https://deb.debian.org/debian/pool/main/j/jxrlib/' +description = """Open source implementation of jpegxr""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] +sources = ['%(name)s_%(version)s.orig.tar.gz'] +patches = [ + ('%(name)s-%(version)s-foss-2020b_support_cmake.patch', 1), +] +checksums = [ + 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303', # jxrlib_1.1.orig.tar.gz + 'f1c37976b4acdf393b583afe4126d888b3f79bc519c48d2ba9f93a24821077b5', # jxrlib-1.1-foss-2020b_support_cmake.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +modextrapaths = {'CPATH': 'include/jxrlib'} + +sanity_check_paths = { + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] + +moduleclass = 'lib' From 1c2ab89beb731149fcb3b45ed5e2a4b0512b441e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:24:20 +0100 Subject: [PATCH 1764/2365] use GCCcore toolchain for jxrlib + mention source of jxrlib patch --- .../j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb index ded422afcf..5f5cade0eb 100644 --- a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb @@ -11,24 +11,21 @@ version = '1.1' homepage = 'https://deb.debian.org/debian/pool/main/j/jxrlib/' description = """Open source implementation of jpegxr""" -toolchain = {'name': 'foss', 'version': '2020b'} +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] sources = ['%(name)s_%(version)s.orig.tar.gz'] -patches = [ - ('%(name)s-%(version)s-foss-2020b_support_cmake.patch', 1), -] +patches = [('jxrlib-%(version)s_cmake.patch', 1)] checksums = [ 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303', # jxrlib_1.1.orig.tar.gz - 'f1c37976b4acdf393b583afe4126d888b3f79bc519c48d2ba9f93a24821077b5', # jxrlib-1.1-foss-2020b_support_cmake.patch + 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74', # jxrlib-1.1_cmake.patch ] builddependencies = [ + ('binutils', '2.35'), ('CMake', '3.18.4'), ] -modextrapaths = {'CPATH': 'include/jxrlib'} - sanity_check_paths = { 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], 'dirs': [], @@ -36,4 +33,6 @@ sanity_check_paths = { sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] +modextrapaths = {'CPATH': 'include/jxrlib'} + moduleclass = 'lib' From 820ff60ffafe20c156dc0982d0dfe41085479b70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:37:22 +0100 Subject: [PATCH 1765/2365] stick to GCCcore toolchain for LERC + avoid downloading test program as separate source file --- .../l/LERC/LERC-3.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9331983f7b --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'LERC' +version = '3.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8c0148f5c22d823eff7b2c999b0781f8095e49a7d3195f13c68c5541dd5740a1'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_commands = [ + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp && " + "g++ main.cpp -o lerctest -lLerc && ./lerctest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From 3ee9d50b786ce526587a25595abdadf22c004030 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:40:33 +0100 Subject: [PATCH 1766/2365] copy LERC test program to install directory, so --module-only and --sanity-check-only work --- easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb index 9331983f7b..d46571f3c1 100644 --- a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -21,9 +21,13 @@ builddependencies = [ ('CMake', '3.18.4'), ] +postinstallcmds = [ + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/test.c", +] + sanity_check_commands = [ - "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp && " - "g++ main.cpp -o lerctest -lLerc && ./lerctest", + "mkdir -p %(builddir)s && cd %(builddir)s && g++ %(installdir)s/test.c -o lerctest -lLerc && ./lerctest", ] sanity_check_paths = { From 9b24df48c961c3bf3d5719e8ac227c2acd742f7e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:43:04 +0100 Subject: [PATCH 1767/2365] use lib as moduleclass for LERC --- easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb index d46571f3c1..6e3105ea15 100644 --- a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -35,4 +35,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'lib' From 2812bba27c9175dae5a27ada538c10a402dd37ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:46:42 +0100 Subject: [PATCH 1768/2365] use more informative homepage for jxrlib --- easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb index 5f5cade0eb..6a5a37d6d6 100644 --- a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'jxrlib' version = '1.1' -homepage = 'https://deb.debian.org/debian/pool/main/j/jxrlib/' +homepage = 'https://github.com/4creators/jxrlib' description = """Open source implementation of jpegxr""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From 46c21e48bf11ee0d9eabf6a040932edc21ab7e0e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 21:44:53 +0100 Subject: [PATCH 1769/2365] collapse easyconfigs for batchgenerators, requests, tifffile into nnU-Net easyconfig --- .../n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb | 66 +++++++++---------- 1 file changed, 30 insertions(+), 36 deletions(-) diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb index 64574eb1e4..3feaf09f25 100644 --- a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb @@ -1,23 +1,16 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'nnU-Net' version = '1.7.0' homepage = 'https://github.com/MIC-DKFZ/nnUNet' -description = """ -nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain. -It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset. -""" -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [ - 'https://files.pythonhosted.org/packages/8e/cf/0e5a45faba472c1df80da8d3fcb8d90b31a2258e48fdbc47cd2e30c16233/' -] +description = """nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found + in the domain It condenses and automates the keys decisions for designing a successful segmentation pipeline for + any given dataset.""" -sources = ['nnunet-%(version)s.tar.gz'] -checksums = ['7ad3d5b89af389fa86cea58f409bd2353b511a746587f37d26c00a756849f356'] +toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ ('Bazel', '3.7.2') @@ -25,40 +18,43 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), ('PyTorch', '1.7.1'), ('tqdm', '4.56.2'), ('dicom2nifti', '2.3.0'), ('scikit-image', '0.18.1'), ('TensorFlow', '2.5.0'), - ('SciPy-bundle', '2020.11'), - ('batchgenerators', '0.23'), ('scikit-learn', '0.23.2'), - ('requests', '2.26.0'), ('NiBabel', '3.2.1'), ('SimpleITK', '2.1.0'), - ('tifffile', '2021.8.30'), ('MedPy', '0.4.0'), - ('jax', '0.2.19') + ('jax', '0.2.19'), + ('lxml', '4.6.2'), ] -# sklearn is incorrect package name -preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " - -exts_defaultclass = 'PythonPackage' - -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True +sanity_pip_check = True exts_list = [ + ('linecache2', '1.0.0', { + 'checksums': ['4b26ff4e7110db76eeb6f5a7b64a82623839d595c2038eeda662f2a2db78e97c'], + }), + ('traceback2', '1.4.0', { + 'checksums': ['05acc67a09980c2ecfedd3423f7ae0104839eccb55fc645773e1caa0951c3030'], + }), + ('unittest2', '1.1.0', { + 'checksums': ['22882a0e418c284e1f718a822b3b022944d53d2d908e1690b319a9d3eb2c0579'], + 'preinstallopts': "sed -i 's/.argparse.,//' setup.py && ", + }), + ('batchgenerators', '0.23', { + 'checksums': ['4bc5711ee75678ae97df7b54c50c1cde46f14c94f44d948f6edf4e8c48b2a9e0'], + }), + ('tifffile', '2021.8.30', { + 'checksums': ['8760e61e30106ea0dab9ec42a238d70a3ff55dde9c54456e7b748fe717cb782d'], + }), ('contextlib2', '21.6.0', { 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], }), - ('absl-py', '0.15.0', { - 'modulename': 'absl', - 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], - }), ('dm-haiku', '0.0.4', { 'modulename': 'haiku', 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", @@ -75,14 +71,12 @@ exts_list = [ 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], }), + ('nnunet', version, { + 'preinstallopts': "sed -i 's/sklearn/scikit-learn/g' setup.py && ", + 'checksums': ['7ad3d5b89af389fa86cea58f409bd2353b511a746587f37d26c00a756849f356'], + }), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -options = {'modulename': 'nnunet'} - sanity_check_commands = ['nnUNet_train --help'] moduleclass = 'data' From bf285fd137ca4d99a062d51b4ee7409426e5c7ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 22:30:51 +0100 Subject: [PATCH 1770/2365] clean up SimpleITK easyconfig + fix homepage/description --- .../s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb | 30 +++++++------------ 1 file changed, 11 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb index 956b38dd32..0ad9b52ffd 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb @@ -5,9 +5,9 @@ easyblock = 'CMakeMake' name = 'SimpleITK' version = '2.1.0' -homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' -description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in - datasets showing strong between-class imbalance.""" +homepage = 'http://www.simpleitk.org' +description = """SimpleITK is a simplified programming interface to the algorithms and data structures of + the Insight Toolkit (ITK).""" toolchain = {'name': 'foss', 'version': '2020b'} @@ -26,32 +26,24 @@ dependencies = [ ('ITK', '5.2.1'), ('scikit-build', '0.11.1'), ] -start_dir = 'SimpleITK' - -configopts = '-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF ' -configopts += ' -DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF ' -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -local_pyinstpath = "%(installdir)s/lib/python%(pyshortver)s/site-packages" +start_dir = 'SimpleITK' -local_postinstall_cmds = "mkdir -p %s " % local_pyinstpath -local_postinstall_cmds += " && cd %(builddir)s/easybuild_obj/Wrapping/Python " -local_postinstall_cmds += " && export PYTHONPATH=%s:$PYTHONPATH " % local_pyinstpath -local_postinstall_cmds += " && pip install --prefix=%(installdir)s . " +configopts = "-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF " +configopts += "-DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF " postinstallcmds = [ - local_postinstall_cmds + "cd %(builddir)s/easybuild_obj/Wrapping/Python && " + "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", ] -separate_build_dir = True -# todo make nicer dir path -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/']} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], - 'dirs': ['lib/python%(pyshortver)s/site-packages', 'include/%(name)s-%(version_major_minor)s'], + 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = [('python', "-c 'import %(name)s'")] +sanity_check_commands = ["python -c 'import %(name)s'"] moduleclass = 'tools' From af7a635f6860bec7e75463c2599cfa0bde7b298e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 23:01:49 +0100 Subject: [PATCH 1771/2365] stick to TensorFlow 2.4.1 as dependency in nnU-Net easyconfig using foss/2020b toolchain --- easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb index 3feaf09f25..af8ddb251b 100644 --- a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb @@ -23,7 +23,7 @@ dependencies = [ ('tqdm', '4.56.2'), ('dicom2nifti', '2.3.0'), ('scikit-image', '0.18.1'), - ('TensorFlow', '2.5.0'), + ('TensorFlow', '2.4.1'), ('scikit-learn', '0.23.2'), ('NiBabel', '3.2.1'), ('SimpleITK', '2.1.0'), From 799858cb5d19dd831084cf82d1bd849eb1debfe4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 23:04:08 +0100 Subject: [PATCH 1772/2365] remove unneeded binutils build dependency from dicom2nifti easyconfig --- .../easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb index 4692d2a37e..cadc273847 100644 --- a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb @@ -13,10 +13,6 @@ toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCE_TAR_GZ] checksums = ['808c4ddbcffd492d41ff20a2837b5e2a3cbe2058d43512fe97b99d678a758bfd'] -builddependencies = [ - ('binutils', '2.35'), -] - dependencies = [ ('Python', '3.8.6'), ('pydicom', '2.1.2'), From 13b7764ada96940a2af083542212c09801620043 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 23:06:39 +0100 Subject: [PATCH 1773/2365] add sanity check command for dicom2nifti 2.3.0 --- .../easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb index cadc273847..4d594c3759 100644 --- a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["dicom2nifti --help"] + moduleclass = 'lib' From 6a2a8abc87cfd09e2822c0ce17715bd596313f0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 23:29:29 +0100 Subject: [PATCH 1774/2365] remove double-conversion dependency for ITK 5.2.1, since copy that is included must be used since double-to-string.h is required --- easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb index 69753b7704..4ad17d850e 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb @@ -28,7 +28,6 @@ builddependencies = [ ] dependencies = [ - ('double-conversion', '3.1.5'), ('expat', '2.2.9'), ('HDF5', '1.10.7'), ('libjpeg-turbo', '2.0.5'), @@ -39,7 +38,6 @@ dependencies = [ ] local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] -# local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' From 0d66a0d3eeb921f6b1b80a85c6f91ce0917d5f4f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 10 Nov 2021 11:44:31 +0200 Subject: [PATCH 1775/2365] custom path for packages --- easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb index e6fffcbcc2..b24fcc3c96 100644 --- a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb @@ -27,7 +27,7 @@ postinstallcmds = [ # if package dir doesnt exist yet, initial run of `beauti` creates it 'timeout 10 xvfb-run beauti 2>&1 | grep "Terminated"', # now we can link our installdir to the package dir - 'ln -s %(installdir)s ~/.beast/2.6/STACEY ', + # 'ln -s %(installdir)s ~/.beast/2.6/STACEY ', ] sanity_check_paths = { @@ -35,4 +35,6 @@ sanity_check_paths = { 'dirs': ['lib/', 'templates/', 'examples'], } +modextravars = {'_JAVA_OPTIONS': "-Dbeast.user.package.dir=%(installdir)s"} + moduleclass = 'data' From 5d1837ea193a05ebde216ee1f0cffdaf34651aa1 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 10 Nov 2021 15:24:09 +0100 Subject: [PATCH 1776/2365] Update easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb --- .../h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb index 66d8b4e92b..ad341bc26e 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -34,6 +34,7 @@ exts_list = [ 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), ('horovod', version, { + 'checksums': ['72ab3e5f59df6a000473999937e52e6831ad1a5e4e7bd23885a04bcdd4d8691c'], }), ] From 53168bb8ef41151469f513597da6980bf5878dd2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 10 Nov 2021 16:55:49 +0100 Subject: [PATCH 1777/2365] adding easyconfigs: pmx-2.0-foss-2020b-Python-2.7.18.eb --- .../p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..4361309c23 --- /dev/null +++ b/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pmx' +version = '2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/deGrootLab/pmx' +description = """pmx (formerly pymacs) is a small bunch of classes to +read structure files such as pdb or gro and trajectory data in gromacs +xtc format. Over the years it has been extended towards a versatile +(bio-) molecular structure manipulation package with some additional +functionalities, e.g. gromacs file parsers and scripts for setup and +analysis of free energy calculations.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['323dd5091c62255f1f6cbfc6b4869ef9672a188ce7e3439ed1bb6e9cf2c3804c'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '2.2.5', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['pmx --help'] + +moduleclass = 'tools' From 549baec5b338f631292b9eeb5460a84e7e119557 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 11 Nov 2021 13:10:41 +0100 Subject: [PATCH 1778/2365] pmx: Fix missing versionsuffix on SciPy-bundle version specification. --- easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb index 4361309c23..00f2bd3ae2 100644 --- a/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb @@ -19,7 +19,7 @@ checksums = ['323dd5091c62255f1f6cbfc6b4869ef9672a188ce7e3439ed1bb6e9cf2c3804c'] dependencies = [ ('Python', '2.7.18'), - ('SciPy-bundle', '2020.11'), + ('SciPy-bundle', '2020.11', versionsuffix), ('matplotlib', '2.2.5', versionsuffix), ] From fa3df980f103145ed58044f307525bb9845fa959 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Nov 2021 13:59:36 +0100 Subject: [PATCH 1779/2365] {bio}[foss/2020b] antiSMASH v6.0.1, GlimmerHMM v3.0.4c, HMMER2 v2.3.2 w/ Python 3.8.6 --- .../a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb | 84 +++++++++++++++++++ .../GlimmerHMM-3.0.4c-GCC-10.2.0.eb | 45 ++++++++++ .../h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb | 27 ++++++ 3 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb new file mode 100644 index 0000000000..57cfc9ef19 --- /dev/null +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'antiSMASH' +version = '6.0.1' + +homepage = 'https://github.com/antismash/antismash' +description = """antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary + metabolite biosynthesis gene clusters in bacterial and fungal genomes.""" + +docurls = ['https://docs.antismash.secondarymetabolites.org'] + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('DIAMOND', '2.0.7'), + ('FastTree', '2.1.11'), + ('GlimmerHMM', '3.0.4c'), + ('HMMER2', '2.3.2'), + ('HMMER', '3.3.2'), + ('MUSCLE', '3.8.31'), + ('BLAST+', '2.11.0'), + ('prodigal', '2.6.3'), + ('Biopython', '1.78'), + ('matplotlib', '3.3.3'), + ('scikit-learn', '0.23.2'), +] + +# install MEME as a component in this installation, +# since antiSMASH requires very specific old version +# see https://docs.antismash.secondarymetabolites.org/install/#full-manual-install +components = [ + ('MEME', '5.4.0', { + 'source_urls': ['http://meme-suite.org/meme-software/%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['e446baf78ce8f9b9dc72723bc91c1d60523174a862af19971a92332a7298d56e'], + 'easyblock': 'ConfigureMake', + 'start_dir': 'meme-%(version)s', + }), +] + +use_pip = True + +exts_list = [ + ('helperlibs', '0.2.1', { + 'checksums': ['4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732'], + }), + ('pysvg-py3', '0.2.2.post3', { + 'modulename': 'pysvg', + 'checksums': ['a1183aa5d89871298c11f25d28640edc3798b6ed1e2b2a95c30d35985d6431d0'], + }), + ('bcbio-gff', '0.6.8', { + 'modulename': 'BCBio.GFF', + 'checksums': ['8578d3c917a81e39898fa588e969c934fb942c2f3e11c275fa492c679a5f36a1'], + }), + ('pyScss', '1.3.7', { + 'modulename': 'scss', + 'checksums': ['f1df571569021a23941a538eb154405dde80bed35dc1ea7c5f3e18e0144746bf'], + }), + (name, version, { + 'source_tmpl': '6-0-1.tar.gz', + 'source_urls': ['https://github.com/antismash/antismash/archive/'], + 'checksums': ['3bd162f44e61ed68efb1d5e98968bdf80691b5d8382eecd66257a6f3a2703de7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/antismash', 'bin/meme'], + 'dirs': [], +} + +sanity_check_commands = [ + # 'meme -h' exits with non-zero exit status, so use 'grep' to check for pattern + "meme -h 2>&1 | grep 'Usage:[ \t]*meme'", + "antismash --version", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb new file mode 100644 index 0000000000..947e4cda9a --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + 'trained_dir', 'README', 'train/readme.train', +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = [('%(namelower)s -h')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..496d7c1314 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'HMMER2' +version = '2.3.2' + +homepage = 'http://hmmer.org' +description = """HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://eddylab.org/software/hmmer'] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4'] + +postinstallcmds = ["cd %(installdir)s/bin && for cmd in $(ls); do mv ${cmd} ${cmd}2; done"] + +local_cmd_suffixes = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'index', 'pfam', 'search'] + +sanity_check_paths = { + 'files': ['bin/hmm%s2' % x for x in local_cmd_suffixes], + 'dirs': ['man'], +} + +sanity_check_commands = ["hmm%s2 -h" % x for x in local_cmd_suffixes] + +moduleclass = 'bio' From 9ba4d9278451175e133e8dbbdeaa4442aafec2ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Nov 2021 13:02:08 +0100 Subject: [PATCH 1780/2365] {data}[fosscuda/2020b] nnU-Net v1.7.0 (+ dependencies) w/ Python 3.8.6 --- .../dicom2nifti-2.3.0-fosscuda-2020b.eb | 33 +++++++ .../i/ITK/ITK-5.2.1-fosscuda-2020b.eb | 60 ++++++++++++ .../m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb | 28 ++++++ .../n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb | 82 +++++++++++++++++ .../SimpleITK-2.1.0-fosscuda-2020b.eb | 49 ++++++++++ .../v/VTK/VTK-9.0.1-fosscuda-2020b.eb | 92 +++++++++++++++++++ 6 files changed, 344 insertions(+) create mode 100644 easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..20fcaa7cfc --- /dev/null +++ b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'dicom2nifti' +version = '2.3.0' + +homepage = 'https://github.com/icometrix/dicom2nifti' +description = "Python library for converting dicom files to nifti" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['808c4ddbcffd492d41ff20a2837b5e2a3cbe2058d43512fe97b99d678a758bfd'] + +dependencies = [ + ('Python', '3.8.6'), + ('pydicom', '2.1.2'), + ('NiBabel', '3.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/dicom2nifti'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dicom2nifti --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..0d9fe14e51 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb @@ -0,0 +1,60 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.2.1' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6022b2b64624b8bcec3333fe48d5f74ff6ebceb3bdf98258ba7d7fbbc76b99ab'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Bison', '3.7.1'), + ('Eigen', '3.3.8'), +] + +dependencies = [ + ('expat', '2.2.9'), + ('HDF5', '1.10.7'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('VTK', '9.0.1'), + ('zlib', '1.2.11'), +] + +local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' +configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..e5bb3979d8 --- /dev/null +++ b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb @@ -0,0 +1,28 @@ +# This easyconfig was created by James Carpenter of the BEAR Software team at the University of Birmingham. +# updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'MedPy' +version = '0.4.0' + +homepage = 'https://pypi.org/project/MedPy/' +description = """MedPy is a library and script collection for medical image processing in Python, providing basic + functionalities for reading, writing and manipulating large images of arbitrary dimensionality. Its main + contributions are n-dimensional versions of popular image filters, a collection of image feature extractors, ready + to be used with scikit-learn, and an exhaustive n-dimensional graph-cut package.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f8a94937dbb947ab069e767862dc6b86896b153c41ce8ed9369c7d79c0033a88'] + +dependencies = [ + ('Python', '3.8.6'), + ('SimpleITK', '2.1.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..e00878d774 --- /dev/null +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb @@ -0,0 +1,82 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'nnU-Net' +version = '1.7.0' + +homepage = 'https://github.com/MIC-DKFZ/nnUNet' +description = """nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found + in the domain It condenses and automates the keys decisions for designing a successful segmentation pipeline for + any given dataset.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('Bazel', '3.7.2') +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), + ('dicom2nifti', '2.3.0'), + ('scikit-image', '0.18.1'), + ('TensorFlow', '2.4.1'), + ('scikit-learn', '0.23.2'), + ('NiBabel', '3.2.1'), + ('SimpleITK', '2.1.0'), + ('MedPy', '0.4.0'), + ('jax', '0.2.19'), + ('lxml', '4.6.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('linecache2', '1.0.0', { + 'checksums': ['4b26ff4e7110db76eeb6f5a7b64a82623839d595c2038eeda662f2a2db78e97c'], + }), + ('traceback2', '1.4.0', { + 'checksums': ['05acc67a09980c2ecfedd3423f7ae0104839eccb55fc645773e1caa0951c3030'], + }), + ('unittest2', '1.1.0', { + 'checksums': ['22882a0e418c284e1f718a822b3b022944d53d2d908e1690b319a9d3eb2c0579'], + 'preinstallopts': "sed -i 's/.argparse.,//' setup.py && ", + }), + ('batchgenerators', '0.23', { + 'checksums': ['4bc5711ee75678ae97df7b54c50c1cde46f14c94f44d948f6edf4e8c48b2a9e0'], + }), + ('tifffile', '2021.8.30', { + 'checksums': ['8760e61e30106ea0dab9ec42a238d70a3ff55dde9c54456e7b748fe717cb782d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['5faa387ad6b522516283cbe45adbc4c46bedcf501c82db2f9174945f3ec2ea7d'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), + ('nnunet', version, { + 'preinstallopts': "sed -i 's/sklearn/scikit-learn/g' setup.py && ", + 'checksums': ['7ad3d5b89af389fa86cea58f409bd2353b511a746587f37d26c00a756849f356'], + }), +] + +sanity_check_commands = ['nnUNet_train --help'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..f51b83860c --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'SimpleITK' +version = '2.1.0' + +homepage = 'http://www.simpleitk.org' +description = """SimpleITK is a simplified programming interface to the algorithms and data structures of + the Insight Toolkit (ITK).""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d5d3b805863b9dfcffeebec69a1b79b5709fc814b12cb9ab759ccbd3e4746839'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Lua', '5.3.5'), + ('ITK', '5.2.1'), + ('scikit-build', '0.11.1'), +] + +start_dir = 'SimpleITK' + +configopts = "-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF " +configopts += "-DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF " + +postinstallcmds = [ + "cd %(builddir)s/easybuild_obj/Wrapping/Python && " + "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], + 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import %(name)s'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..3d7c9e1937 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb @@ -0,0 +1,92 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '9.0.1' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + '1b39a5e191c282861e7af4101eaa8585969a2de05f5646c9199a161213a622c7', # VTK-9.0.1.tar.gz + '3f8bfdadd66e0b541bc5580340481abf92bec100b09d787283632ab590b1ce1c', # VTKData-9.0.1.tar.gz + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('XZ', '5.2.5'), + ('libGLU', '9.0.1'), + ('X11', '20201008'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + + +moduleclass = 'vis' From 800d4792ad244bf94e0566f48ab9ade7c687d2ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Nov 2021 16:10:58 +0100 Subject: [PATCH 1781/2365] remove postinstallcmds for STACEY, no longer needed now custom package directory for Beast is specified via $_JAVA_OPTIONS --- .../easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb index b24fcc3c96..3a9050393e 100644 --- a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb @@ -15,21 +15,10 @@ source_urls = ['http://www.indriid.com/2019/'] sources = ['%(name)s.addon.v%(version)s.zip'] checksums = ['a6ce3ce83ddafe3505622961c7d90e696e11b2b51246f7447d820e1b3e717b58'] -builddependencies = [ - ('Xvfb', '1.20.9'), -] dependencies = [ ('Beast', '2.6.4'), ] -# we need to link installdir to hardcoded package directory of Beast (~/.beast/2.6/) -postinstallcmds = [ - # if package dir doesnt exist yet, initial run of `beauti` creates it - 'timeout 10 xvfb-run beauti 2>&1 | grep "Terminated"', - # now we can link our installdir to the package dir - # 'ln -s %(installdir)s ~/.beast/2.6/STACEY ', -] - sanity_check_paths = { 'files': ['stacey.src.jar'], 'dirs': ['lib/', 'templates/', 'examples'], From f5ac3001d0e126245ac2bab26bb3b003184a8076 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Nov 2021 16:11:18 +0100 Subject: [PATCH 1782/2365] add custom sanity check command for STACEY --- easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb index 3a9050393e..f6bec5c108 100644 --- a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb @@ -24,6 +24,9 @@ sanity_check_paths = { 'dirs': ['lib/', 'templates/', 'examples'], } +# takes 5-6min using a single core +sanity_check_commands = ["beast -threads %(parallel)s %(installdir)s/examples/test1/test1.xml"] + modextravars = {'_JAVA_OPTIONS': "-Dbeast.user.package.dir=%(installdir)s"} moduleclass = 'data' From 74f77708026f4b76e0eab5b7fcca8edd25570d3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Nov 2021 17:39:36 +0100 Subject: [PATCH 1783/2365] add missing Python versionsuffix for SSPACE_Basic --- ...CE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..ca5bbccf32 --- /dev/null +++ b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'SSPACE_Basic' +version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nsoranzo/sspace_basic' +description = "SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/nsoranzo/sspace_basic/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a23327a79a18e520544f0ea923b6c92ff2cc869617ade1c75e118b179caa0919'] + +dependencies = [ + ('Perl', '5.32.0'), + ('Python', '2.7.18'), + ('Bowtie', '1.3.0'), +] + +fix_perl_shebang_for = ['*.pl', 'bin/*.pl', 'tools/*.pl'] + +sanity_check_paths = { + 'files': ['dotlib/DotLib.pm', 'README', 'SSPACE_Basic.pl'], + 'dirs': ['bin', 'tools'], +} + +sanity_check_commands = [ + "SSPACE_Basic.pl 2>&1 | grep 'General Parameters'", + "perldoc -lm DotLib", + "qseq2fastq.pl 2>&1 | grep '^Usage:'", + "TQS.py --help", +] + +modextrapaths = { + 'PATH': ['', 'tools'], + 'PERL5LIB': 'dotlib', +} + +moduleclass = 'bio' From e5fc72737750bbe96c4890bbd2fe19cbec820a8c Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 17 Nov 2021 16:59:26 +0000 Subject: [PATCH 1784/2365] adding easyconfigs: torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb --- ...ext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 0000000000..be7e5d73e6 --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.10.0' +local_pytorch_version = '1.9.0' +local_python_suffix = '-Python-%(pyver)s' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['149788775659ceeeaa9ad70a1b12fd5b9825658ac72c2a113cbf0bd0a2e7f5df'] + +builddependencies = [ + ('RE2', '2021-06-01'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SentencePiece', '0.1.96'), + ('tqdm', '4.56.2'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.1.5'), +] + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/BuildExtension/d' setup.py &&" + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 4bba35376cb677c14332b1e4509b339cb626e3d7 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 17 Nov 2021 17:03:29 +0000 Subject: [PATCH 1785/2365] adding easyconfigs: torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb --- ...ion-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 0000000000..4fa09e8900 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,26 @@ +name = 'torchvision' +version = '0.10.0' +local_pytorch_version = '1.9.0' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['82bb2c2b03d8a65f4ea74bb0ee5566b0876a1992aceefb1e11475c7b5d2e857b'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('PyTorch', local_pytorch_version), +] + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'vis' From 6c013e913d99440c7867866841620946c522ebc4 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Nov 2021 18:28:53 +0100 Subject: [PATCH 1786/2365] adding easyconfigs: einops-0.3.2-GCCcore-10.2.0.eb --- .../e/einops/einops-0.3.2-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f9d8338984 --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.3.2' + +homepage = 'https://einops.rocks/' +description = """ +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5200e413539f0377f4177ef00dc019968f4177c49b1db3e836c7883df2a5fe2e'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' From ef7d18ba35eae721be8dd962901cd22918b3d7c4 Mon Sep 17 00:00:00 2001 From: sdavis2 Date: Wed, 17 Nov 2021 12:47:06 -0500 Subject: [PATCH 1787/2365] adding easyconfigs: GTDB-Tk-1.7.0-foss-2020b.eb --- .../g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb new file mode 100644 index 0000000000..d0bc5d3e52 --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'GTDB-Tk' +version = '1.7.0' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/g/gtdbtk'] +sources = ['gtdbtk-%(version)s.tar.gz'] +checksums = ['36b65074845e7edef4d7aeead286c770fb9a03ddbff63946533fa2e1934e8f26'] + +dependencies = [ + ('Python', '3.8.6'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.3.3'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.56.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From acb472420ecf6d853c82d1ff4fd082611bf5feab Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 19 Nov 2021 15:26:59 +0200 Subject: [PATCH 1788/2365] adding easyconfigs: cpu_features-0.6.0-foss-2020b.eb, Shasta-0.8.0-foss-2020b.eb, spoa-3.4.0-GCC-10.2.0.eb and patches: Shasta-0.8.0-foss-2020b-fix_links.patch --- .../s/Shasta/Shasta-0.8.0-foss-2020b.eb | 69 +++++++++++++++++++ .../s/spoa/spoa-3.4.0-GCC-10.2.0.eb | 31 +++++++++ 2 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb new file mode 100644 index 0000000000..6479ec878a --- /dev/null +++ b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb @@ -0,0 +1,69 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMakeCp' + +name = 'Shasta' +version = '0.8.0' + +homepage = 'https://github.com/chanzuckerberg/shasta' +description = """ +The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated +by Oxford Nanopore flow cells as input. Computational methods used by the Shasta assembler include: +Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in +homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. Using in some phases of +the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10). +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/chanzuckerberg/shasta/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + "Shasta-%(version)s-foss-2020b-fix_links.patch" +] +checksums = [ + '8e94767275fc5352ff192afed783b00b720b6214d8779edc44e9ebe636e9833e', # 0.8.0.tar.gz + 'dfda9a6ca33e37236cbbc27a1d65bb54d361f27ecdb2b9855e46ac6dab6e255e', # Shasta-0.8.0-foss-2020b-fix_links.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('cURL', '7.72.0'), + ('Boost', '1.74.0'), + ('libpng', '1.6.37'), + ('SeqAn', '2.4.0'), + ('BLAST', '2.11.0', '-Linux_x86_64', True), + ('gnuplot', '5.4.1'), + ('Graphviz', '2.47.0', '-Java-11'), + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), + ('Cereal', '1.3.0', '', True), + ('spoa', '3.4.0'), + ('ScaLAPACK', '2.1.0'), + ('OpenBLAS', '0.3.12'), + ('cpu_features', '0.6.0'), +] + +prebuildopts = "export CPATH=$EBROOTBOOST/include/boost/:$CPATH && " + +buildopts = " && make install -j %(parallel)s" + +files_to_copy = [ + (['shasta-install/bin/*'], 'bin'), + (['shasta-install/bin/*.a'], 'lib'), + (['shasta-install/bin/*.so'], 'lib') +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['lib/shasta.so', 'lib/shasta.a', 'bin/shasta', 'bin/SaveRun.py', 'bin/Copy.py'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..038094f39e --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '3.4.0' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] +sources = ['spoa-v%(version)s.tar.gz'] +checksums = ['f7411312bd51a0c7e53a702127cc8ba8500247d3f44f01825e591c5b8570f14b'] + +builddependencies = [('CMake', '3.18.4')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a', 'lib/pkgconfig/spoa-1.pc'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +modextrapaths = {'CPATH': 'include/%(namelower)s'} + +moduleclass = 'bio' From 62592626c19bd3599297b4c851ab17869fd59345 Mon Sep 17 00:00:00 2001 From: Laurence Alexander Hurst Date: Mon, 22 Nov 2021 13:58:56 +0000 Subject: [PATCH 1789/2365] BerkeleyGW - 2020b --- .../BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb new file mode 100644 index 0000000000..e40828947d --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb @@ -0,0 +1,34 @@ +name = 'BerkeleyGW' +version = '3.0.1' + +homepage = 'https://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://berkeley.box.com/shared/static/'] +sources = [{'download_filename': 'm1dgnhiemo47lhxczrn6si71bwxoxor8.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'BerkeleyGW-3.0.1_tests.patch', + 'BerkeleyGW-3.0.1_makefile.patch', + 'BerkeleyGW-3.0.1_version.patch', +] +checksums = [ + '7d8c2cc1ee679afb48efbdd676689d4d537226b50e13a049dbcb052aaaf3654f', # BerkeleyGW-3.0.1.tar.gz + 'f66ff15e2b99de5e808f78a552985fda3181f35c25817de4ac7df4d8f7fddf5a', # BerkeleyGW-3.0.1_tests.patch + '56d90dc4e43db379441b6a1802e24f1f1356cd4aca4eb6d8b673f6c7926a7406', # BerkeleyGW-3.0.1_makefile.patch + '414a4f23e430a2c02bab7bad18bcaf9b62129fa9dd1c2f87bd4bbc9fcb3bdded', # BerkeleyGW-3.0.1_version.patch +] + +dependencies = [ + ('ELPA', '2020.11.001'), + ('Python', '3.8.6'), + ('h5py', '3.1.0'), +] + +runtest = True + +moduleclass = 'phys' From f2b8f74b598dbbaea129c2e051bdda7caac3c925 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 22 Nov 2021 17:21:19 +0000 Subject: [PATCH 1790/2365] PhyML-3.3.20200621: missing Automake added --- easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb index 92820f73d6..33168cdcf0 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb @@ -22,6 +22,7 @@ checksums = ['a8243923ee08c74cab609a4b086ade66c6156fc2b24450e2a500108dc644c867'] builddependencies = [ ('Autoconf', '2.69'), ('pkg-config', '0.29.2'), + ('Automake', '1.16.2'), ] preconfigopts = 'sh autogen.sh && ' From 2b9ad751c0b15ad514ee7bff6613f98b47da3dd7 Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Tue, 23 Nov 2021 15:23:27 +0000 Subject: [PATCH 1791/2365] Update easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb index be7e5d73e6..a2d3ea9fb7 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb @@ -3,7 +3,6 @@ easyblock = 'PythonPackage' name = 'torchtext' version = '0.10.0' local_pytorch_version = '1.9.0' -local_python_suffix = '-Python-%(pyver)s' versionsuffix = '-PyTorch-%s' % local_pytorch_version homepage = 'https://github.com/pytorch/text' From a535b688373a0d270bc55696889392b36d0f99d1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 23 Nov 2021 22:20:21 +0100 Subject: [PATCH 1792/2365] adding easyconfigs: photontorch-0.4.1-foss-2020b.eb, photontorch-0.4.1-fosscuda-2020b.eb --- .../photontorch-0.4.1-foss-2020b.eb | 38 +++++++++++++++++++ .../photontorch-0.4.1-fosscuda-2020b.eb | 38 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb new file mode 100644 index 0000000000..0a19fe634e --- /dev/null +++ b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'photontorch' +version = '0.4.1' + +homepage = 'https://docs.photontorch.com/' +description = """ +Photontorch is a photonic simulator for highly parallel simulation and optimization of photonic circuits in time and +frequency domain. Photontorch features CUDA enabled simulation and optimization of photonic circuits. It leverages the +deep learning framework PyTorch to view the photonic circuit as essentially a recurrent neural network. This enables the +use of native PyTorch optimizers to optimize the (physical) parameters of the circuit. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), + ('networkx', '2.5'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('torch-lfilter', '0.0.3', { + 'source_tmpl': 'torch_lfilter-%(version)s.tar.gz', + 'checksums': ['aa613725b73e7b6e7efd63c30580a906d7bb23206b5d045b8452ab770f7a50df'], + }), + (name, version, { + 'checksums': ['50d2e2c8a24c914cc7afee1eea6efb8bccfbc19ff9652a9af46efad28caa6381'], + }), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..75ef1ef367 --- /dev/null +++ b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'photontorch' +version = '0.4.1' + +homepage = 'https://docs.photontorch.com/' +description = """ +Photontorch is a photonic simulator for highly parallel simulation and optimization of photonic circuits in time and +frequency domain. Photontorch features CUDA enabled simulation and optimization of photonic circuits. It leverages the +deep learning framework PyTorch to view the photonic circuit as essentially a recurrent neural network. This enables the +use of native PyTorch optimizers to optimize the (physical) parameters of the circuit. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), + ('networkx', '2.5'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('torch-lfilter', '0.0.3', { + 'source_tmpl': 'torch_lfilter-%(version)s.tar.gz', + 'checksums': ['aa613725b73e7b6e7efd63c30580a906d7bb23206b5d045b8452ab770f7a50df'], + }), + (name, version, { + 'checksums': ['50d2e2c8a24c914cc7afee1eea6efb8bccfbc19ff9652a9af46efad28caa6381'], + }), +] + +moduleclass = 'phys' From 76ddf8416b7732448a1bf222dc3c78de876180ad Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 24 Nov 2021 21:59:54 +0100 Subject: [PATCH 1793/2365] add git as builddependency to Python --- easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 602f3f5c32..4662198909 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -14,6 +14,7 @@ checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21'] builddependencies = [ ('UnZip', '6.0'), + ('git', '2.28.0', '-nodocs'), # required for pbr ] dependencies = [ From a0b12bbf770d0cc271e485091f42e7a28a62e982 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 25 Nov 2021 12:54:04 +0200 Subject: [PATCH 1794/2365] updates after review --- .../cpu_features-0.6.0-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ .../s/Shasta/Shasta-0.8.0-foss-2020b.eb | 20 ++++++------ 2 files changed, 41 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..42da9feba7 --- /dev/null +++ b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'cpu_features' +version = '0.6.0' + +homepage = 'https://github.com/google/cpu_features' +description = """A cross-platform C library to retrieve CPU features (such as available instructions) at runtime.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/cpu_features/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['95a1cf6f24948031df114798a97eea2a71143bd38a4d07d9a758dda3924c1932'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +modextrapaths = {'CPATH': 'include/cpu_features'} + +sanity_check_paths = { + 'files': ['bin/list_cpu_features', 'lib/libcpu_features.a'], + 'dirs': ['include/cpu_features/'] +} + +sanity_check_commands = ['list_cpu_features'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb index 6479ec878a..3781b94855 100644 --- a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb @@ -24,12 +24,12 @@ patches = [ ] checksums = [ '8e94767275fc5352ff192afed783b00b720b6214d8779edc44e9ebe636e9833e', # 0.8.0.tar.gz - 'dfda9a6ca33e37236cbbc27a1d65bb54d361f27ecdb2b9855e46ac6dab6e255e', # Shasta-0.8.0-foss-2020b-fix_links.patch + 'd9696b8a667f6a0db724f779083accb8004398bdfdf5cf15ef5cdaed89f339d0', # Shasta-0.8.0-foss-2020b-fix_links.patch ] builddependencies = [ ('CMake', '3.18.4'), - ('binutils', '2.35'), + ('Cereal', '1.3.0', '', True), ] dependencies = [ @@ -37,33 +37,33 @@ dependencies = [ ('Boost', '1.74.0'), ('libpng', '1.6.37'), ('SeqAn', '2.4.0'), - ('BLAST', '2.11.0', '-Linux_x86_64', True), + ('BLAST+', '2.11.0'), ('gnuplot', '5.4.1'), ('Graphviz', '2.47.0', '-Java-11'), ('Python', '3.8.6'), ('pybind11', '2.6.0'), - ('Cereal', '1.3.0', '', True), - ('spoa', '3.4.0'), - ('ScaLAPACK', '2.1.0'), - ('OpenBLAS', '0.3.12'), + ('spoa', '3.4.0'), # older spoa is needed, since new is truly incompatible ('cpu_features', '0.6.0'), ] prebuildopts = "export CPATH=$EBROOTBOOST/include/boost/:$CPATH && " +# we need this because CMakeLists here is hard to configure, so we stick to default install path (inside sub-folder) +# and copy installed files afterwards buildopts = " && make install -j %(parallel)s" files_to_copy = [ (['shasta-install/bin/*'], 'bin'), - (['shasta-install/bin/*.a'], 'lib'), - (['shasta-install/bin/*.so'], 'lib') + (['shasta-install/bin/*.a', 'shasta-install/bin/*.%s' % SHLIB_EXT], 'lib') ] fix_python_shebang_for = ['bin/*.py'] sanity_check_paths = { - 'files': ['lib/shasta.so', 'lib/shasta.a', 'bin/shasta', 'bin/SaveRun.py', 'bin/Copy.py'], + 'files': ['bin/Copy.py', 'bin/SaveRun.py', 'bin/shasta', 'lib/shasta.a', 'lib/shasta.%s' % SHLIB_EXT], 'dirs': [] } +sanity_check_commands = ['shasta --help'] + moduleclass = 'bio' From 08862311617a762688852ac2de07715ee1d61361 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 15:01:16 +0100 Subject: [PATCH 1795/2365] add missing XZ dependency to recent PROJ easyconfigs --- easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb index cb19aeb08e..4d8bb71381 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb @@ -31,6 +31,7 @@ dependencies = [ ('SQLite', '3.33.0'), ('LibTIFF', '4.1.0'), ('cURL', '7.72.0'), + ('XZ', '5.2.5'), ] sanity_check_paths = { From 624acd8df0dec0f9ce6ee0b88183655aa19fca09 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 25 Nov 2021 15:40:45 +0000 Subject: [PATCH 1796/2365] adding easyconfigs: PAL2NAL-14-GCCcore-10.2.0.eb, PAL2NAL-14-GCCcore-10.3.0.eb --- .../p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1a78c40f46 --- /dev/null +++ b/easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Tarball' + +name = 'PAL2NAL' +version = '14' + +homepage = 'http://www.bork.embl.de/pal2nal/' +description = """PAL2NAL is a program that converts a multiple sequence alignment of proteins and + the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically + assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the + input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the + input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment + can further be subjected to the calculation of synonymous (d_S) and non-synonymous (d_N) subs- + titution rates. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://www.bork.embl.de/pal2nal/distribution/'] +sources = ['%(namelower)s.v%(version)s.tar.gz'] +checksums = ['0e458d38571ab6d61078047a9e80d843bb2e733414eeff8b1144d1c6bc13848f'] + +dependencies = [('Perl', '5.32.0')] + +fix_perl_shebang_for = ['%(namelower)s.pl'] + +sanity_check_paths = { + 'files': ['%(namelower)s.pl', 'README', 'test.aln', 'test.nuc'], + 'dirs': [], +} + +sanity_check_commands = [ + 'pal2nal.pl -h', + 'pal2nal.pl test.aln test.nuc -output paml -nogap', +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From f318467299345959b43147b5c29f7ec026e9d8b6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 25 Nov 2021 15:41:31 +0000 Subject: [PATCH 1797/2365] adding easyconfigs: PAML-4.9j-GCCcore-10.2.0.eb, PAML-4.9j-GCCcore-10.3.0.eb --- .../p/PAML/PAML-4.9j-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f201448d6c --- /dev/null +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'PAML' +version = '4.9j' + +homepage = 'http://abacus.gene.ucl.ac.uk/software/paml.html' +description = """PAML is a package of programs for phylogenetic + analyses of DNA or protein sequences using maximum likelihood.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://abacus.gene.ucl.ac.uk/software'] +sources = ['%(namelower)s%(version)s.tgz'] +checksums = ['9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d'] + +# Avoid multiple definition linking errors +prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +builddependencies = [('binutils', '2.35')] + +start_dir = 'src' + +files_to_copy = [ + (['GeneticCode.txt', '%(builddir)s/%(namelower)s%(version)s/README.txt'], ''), + (['*.trees', '*.ctl', '*.nuc', '*.dat', 'paup*', 'stewart.aa'], ''), + (['src/baseml', 'src/basemlg', 'src/chi2', 'src/codeml', 'src/evolver'], 'bin'), + (['src/infinitesites', 'src/mcmctree', 'src/pamp', 'src/yn00'], 'bin'), + (['dat/*'], 'dat'), + (['doc/*'], 'doc'), + (['examples/*'], 'examples'), + (['Technical/*'], 'Technical'), +] + +sanity_check_paths = { + 'files': ['bin/baseml'], + 'dirs': ['bin'] +} + +moduleclass = 'bio' From 6fad01069f4b7d5c4dee80830a82f9b46674ae6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 21:42:36 +0100 Subject: [PATCH 1798/2365] move down (pre)buildops below start_dir in PAML 4.9j easyconfigs --- easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb index f201448d6c..32b19dcda7 100644 --- a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb @@ -13,14 +13,14 @@ source_urls = ['http://abacus.gene.ucl.ac.uk/software'] sources = ['%(namelower)s%(version)s.tgz'] checksums = ['9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d'] -# Avoid multiple definition linking errors -prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' - builddependencies = [('binutils', '2.35')] start_dir = 'src' +# Avoid multiple definition linking errors +prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + files_to_copy = [ (['GeneticCode.txt', '%(builddir)s/%(namelower)s%(version)s/README.txt'], ''), (['*.trees', '*.ctl', '*.nuc', '*.dat', 'paup*', 'stewart.aa'], ''), From bec768957f86bfa4619c02a816cfe35e970a2bb5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 22:03:01 +0100 Subject: [PATCH 1799/2365] enhance sanity check for PAML 4.9j --- easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb index 32b19dcda7..8055bdba34 100644 --- a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb @@ -33,8 +33,13 @@ files_to_copy = [ ] sanity_check_paths = { - 'files': ['bin/baseml'], - 'dirs': ['bin'] + 'files': ['baseml.ctl', 'codeml.ctl', 'bin/baseml', 'bin/codeml'], + 'dirs': ['dat', 'doc', 'examples'], } +sanity_check_commands = [ + "mkdir -p %(builddir)s && cp -a %(installdir)s/examples/HIVNSsites %(builddir)s && " + "cd %(builddir)s/HIVNSsites && codeml", +] + moduleclass = 'bio' From 75e7d790e96d78df130e66603a717eb9794f8f5a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 22:31:31 +0100 Subject: [PATCH 1800/2365] use %(parallel)s template rather than using hardcoded value in PySide2 easyconfig --- .../p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb index 4d1fe0c1f1..b2ad02c66b 100644 --- a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'PySide2' version = '5.14.2.3' -homepage = "https://pypi.python.org/pypi/%(name)s/" +homepage = 'https://pypi.python.org/pypi/PySide2' description = """PySide2 is the official Python module from the Qt for Python project, which provides access to the complete Qt 5.12+ framework.""" @@ -31,10 +31,10 @@ download_dep_fail = True preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' -buildcmd = 'build --parallel=16' +buildcmd = 'build --parallel=%(parallel)s' preinstallopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' -install_target = 'install --parallel=16' +install_target = 'install --parallel=%(parallel)s' options = {'modulename': 'PySide2'} From 8721638d82b1393f52046a72edaba20806e387b9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 26 Nov 2021 12:24:06 +0000 Subject: [PATCH 1801/2365] adding easyconfigs: Relate-20211123-foss-2020b-R-4.0.3.eb and patches: Relate-20211123_add-cmake-install-targets.patch --- .../Relate-20211123-foss-2020b-R-4.0.3.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..71a26a09f3 --- /dev/null +++ b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb @@ -0,0 +1,68 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CMakeMake' + +name = 'Relate' +version = '20211123' +local_commit = '78964f4' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://myersgroup.github.io/relate/' +description = "Software for estimating genome-wide genealogies for thousands of samples" +citing = """ +[1] Leo Speidel, Marie Forest, Sinan Shi, Simon Myers. A method for estimating genome-wide + genealogies for thousands of samples. Nature Genetics 51: 1321-1329, 2019. +[2] Leo Speidel, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, Simon Myers. + Inferring population histories for ancient genomes using genome-wide genealogies. + bioRxiv:2021.02.17.431573. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'MyersGroup' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20211123_add-cmake-install-targets.patch'] +checksums = [ + 'cc19a50036f78ede9f4d52cc0cbb81d90d1bdb51f8b70a1f001a4f32dd26dbd0', # 78964f4.tar.gz + # Relate-20211123_add-cmake-install-targets.patch + 'd4565aeef0036013b82b37e00909965a6447ab14b154caa3e304307d6f7818e4', +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('zlib', '1.2.11'), + ('R', '4.0.3'), # required for some analysis scripts +] + +runtest = 'test' + +# script directories to add to path: +local_scripts = ['DetectSelection', 'EstimatePopulationSize', 'PrepareInputFiles', 'RelateParallel', + 'SampleBranchLengths', 'TreeView'] +# un/comment as appropriate: +# local_scripts += ['RelateLSF'] +# local_scripts += ['EstimatePopulationSizeSGE', 'RelateSGE'] +# local_scripts += ['RelateSlurm'] + +local_bins = ['bin/%s%s' % (name, x) for x in ['', 'CoalescentRate', 'Extract', 'FileFormats', + 'MutationRate', 'Selection', 'TreeView']] +local_libs = ['lib/libtskitStatic.a'] + [ + 'lib/lib%s%s' % (x, y) for x in ['gzstream', 'kastore', 'relate'] for y in ['Shared.so', 'Static.a'] +] + +sanity_check_paths = { + 'files': local_bins + local_libs, + 'dirs': ['bin', 'lib', 'example'] + ['scripts/%s' % x for x in local_scripts], +} + +sanity_check_commands = [ + "%(name)s --help", + "cd %(builddir)s/relate-*/example && gunzip data/*.gz && Relate --mode All -m 1.25e-8 -N 30000 \ + --haps data/example.haps --sample data/example.sample --map data/genetic_map_*.txt \ + --annot data/example.annot --seed 1 -o example", +] + +modextrapaths = {'PATH': ['scripts/%s' % x for x in local_scripts]} + +moduleclass = 'bio' From 508ef7d926be7c095659162f59957326500b6cf6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Nov 2021 13:59:24 +0100 Subject: [PATCH 1802/2365] add patch for GCCcore 10.1-11.1 to fix compatibility with recent kernel headers --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 4ce3d1f4b9..98d75b65b5 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -37,6 +37,7 @@ patches = [ 'GCCcore-10.2.0_fix-ice-on-arm.patch', 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCC-10.x_fix-libsanitizer-cyclades.patch', ] checksums = [ '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz @@ -54,6 +55,7 @@ checksums = [ # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch ] builddependencies = [ From 496cafe1684f3ea5c3e529c5955e5630646d6d71 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 29 Nov 2021 17:32:40 +0000 Subject: [PATCH 1803/2365] Autoconf and Automake replaced with Autotools --- easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb index 33168cdcf0..02ccca5454 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb @@ -20,9 +20,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['a8243923ee08c74cab609a4b086ade66c6156fc2b24450e2a500108dc644c867'] builddependencies = [ - ('Autoconf', '2.69'), + ('Autotools', '20200321'), ('pkg-config', '0.29.2'), - ('Automake', '1.16.2'), ] preconfigopts = 'sh autogen.sh && ' From 1fb32e079791a1d38eb04607700618cda86d6bc4 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 30 Nov 2021 10:04:24 +0000 Subject: [PATCH 1804/2365] use `SHLIB_EXT` instead of `.so` Co-authored-by: Miguel Dias Costa --- .../easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb index 71a26a09f3..18a8467356 100644 --- a/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb @@ -48,7 +48,7 @@ local_scripts = ['DetectSelection', 'EstimatePopulationSize', 'PrepareInputFiles local_bins = ['bin/%s%s' % (name, x) for x in ['', 'CoalescentRate', 'Extract', 'FileFormats', 'MutationRate', 'Selection', 'TreeView']] local_libs = ['lib/libtskitStatic.a'] + [ - 'lib/lib%s%s' % (x, y) for x in ['gzstream', 'kastore', 'relate'] for y in ['Shared.so', 'Static.a'] + 'lib/lib%s%s' % (x, y) for x in ['gzstream', 'kastore', 'relate'] for y in ['Shared.%s' % SHLIB_EXT, 'Static.a'] ] sanity_check_paths = { From 54554480702d7bad1128c95418c1e0dd78e949cb Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 30 Nov 2021 14:11:47 +0000 Subject: [PATCH 1805/2365] Add a modloadmsg, and a missing numpy (scipy-bundle) dep --- .../Relate-20211123-foss-2020b-R-4.0.3.eb | 29 ++++++++++++++----- 1 file changed, 21 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb index 18a8467356..22e5374dd0 100644 --- a/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb @@ -32,18 +32,21 @@ builddependencies = [('CMake', '3.18.4')] dependencies = [ ('zlib', '1.2.11'), - ('R', '4.0.3'), # required for some analysis scripts + # Python (numpy), and R required for some scripts + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('R', '4.0.3'), ] runtest = 'test' # script directories to add to path: -local_scripts = ['DetectSelection', 'EstimatePopulationSize', 'PrepareInputFiles', 'RelateParallel', - 'SampleBranchLengths', 'TreeView'] +local_script_dirs = ['DetectSelection', 'EstimatePopulationSize', 'PrepareInputFiles', 'RelateParallel', + 'SampleBranchLengths', 'TreeView'] # un/comment as appropriate: -# local_scripts += ['RelateLSF'] -# local_scripts += ['EstimatePopulationSizeSGE', 'RelateSGE'] -# local_scripts += ['RelateSlurm'] +# local_script_dirs += ['RelateLSF'] +# local_script_dirs += ['EstimatePopulationSizeSGE', 'RelateSGE'] +# local_script_dirs += ['RelateSlurm'] local_bins = ['bin/%s%s' % (name, x) for x in ['', 'CoalescentRate', 'Extract', 'FileFormats', 'MutationRate', 'Selection', 'TreeView']] @@ -53,7 +56,7 @@ local_libs = ['lib/libtskitStatic.a'] + [ sanity_check_paths = { 'files': local_bins + local_libs, - 'dirs': ['bin', 'lib', 'example'] + ['scripts/%s' % x for x in local_scripts], + 'dirs': ['bin', 'lib', 'example'] + ['scripts/%s' % x for x in local_script_dirs], } sanity_check_commands = [ @@ -63,6 +66,16 @@ sanity_check_commands = [ --annot data/example.annot --seed 1 -o example", ] -modextrapaths = {'PATH': ['scripts/%s' % x for x in local_scripts]} +modextrapaths = {'PATH': ['scripts/%s' % x for x in local_script_dirs]} + +modloadmsg = """ +Relate provides various scripts for parallel execution, supporting a variety of schedulers (LSF, + SGE, Slurm), located in `$EBROOTRELATE/scripts`. If the suitable script directory is not already + in `$PATH`, you can add this with: + [*] LSF : export PATH=$EBROOTRELATE/scrips/RelateLSF:$PATH + [*] SGE : export PATH=$EBROOTRELATE/scrips/RelateSGE:$EBROOTRELATE/scripts/EstimatePopulationSizeSGE:$PATH + [*] Slurm : export PATH=$EBROOTRELATE/scrips/RelateSlurm:$PATH + This should not be necessary for the other data preparation, output and analysis scripts included. +""" moduleclass = 'bio' From 56a0eb48b5e432b12c4a403b181a4d475fe292d7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Dec 2021 13:41:01 +0000 Subject: [PATCH 1806/2365] add patch to fix CVE-2021-43527 in NSS --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 0635704817..6d30fd97e4 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -13,10 +13,12 @@ source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_ sources = [SOURCELOWER_TAR_GZ] patches = [ 'NSS-3.39_pkgconfig.patch', + 'NSS-3.42.1_CVE-2021-43527.patch', ] checksums = [ '55a86c01be860381d64bb4e5b94eb198df9b0f098a8af0e58c014df398bdc382', # nss-3.57.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + 'cc17945edcc8f6d951e8710a4e99604439a1758e38539d1b7b8c0cd95ac59355', # NSS-3.42.1_CVE-2021-43527.patch ] builddependencies = [('binutils', '2.35')] From 67bb3e1936a89ebae87b6814c5848572ca02217b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Dec 2021 15:52:42 +0000 Subject: [PATCH 1807/2365] enhance sanity check --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 6d30fd97e4..39ccefdf99 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -42,10 +42,15 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] sanity_check_paths = { - 'files': ['lib/libnss.a'], - 'dirs': ['bin', 'include/dbm', 'include/nss'], + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], } +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + modextrapaths = {'CPATH': 'include/nss'} moduleclass = 'lib' From 341aeeb68a08e516777585069f353f779583cc07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Dec 2021 19:33:17 +0100 Subject: [PATCH 1808/2365] remove versionsuffix for idemux (no longer used with Python 3.x) + use proper dependency for tqdm --- .../i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d156b3c22f --- /dev/null +++ b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'idemux' +version = '0.1.6' + +homepage = 'https://github.com/Lexogen-Tools/idemux' +description = """idemux - inline barcode demultiplexing +Idemux is a command line tool designed to demultiplex paired-end FASTQ files from QuantSeq-Pool.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('coverage', '5.5'), + ('tqdm', '4.60.0'), +] + +use_pip = True + +exts_list = [ + ('pytest-runner', '5.3.0', { + 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], + 'modulename': 'ptr', + }), + (name, version, { + 'checksums': ['590980baaf810c8a02705efd50eb4ace644c360470fc3dc4491d077bbb6b26fc'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/idemux'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["idemux -h"] + +moduleclass = 'bio' From f0e21b787556c43b9913528ff138f3e2efb928c0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Dec 2021 12:11:32 +0000 Subject: [PATCH 1809/2365] pass tests on A* GPUs by setting 'NVIDIA_TF32_OVERRIDE=0' in jax 0.2.19 --- easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index 1da5dfa47a..d14b441c64 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -115,7 +115,8 @@ exts_list = [ # see https://github.com/google/jax/issues/7323 and # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; - 'runtest': 'CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests', + # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests", }), ] From b8c5338533e4d6f6ea1566fa276e9044a68e58e3 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 6 Dec 2021 12:24:04 +0100 Subject: [PATCH 1810/2365] easyconfigs for dune-core and dune-fem in foss/2020b --- .../dune-core-2.8.0.post1-foss-2020b.eb | 56 +++++++++++++++ .../d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 71 +++++++++++++++++++ 2 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb new file mode 100644 index 0000000000..3c4f56daeb --- /dev/null +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'dune-core' +version = '2.8.0.post1' + +homepage = "https://www.dune-project.org/groups/core/" +description = """The Dune core modules build the stable basis of Dune. +They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. +These modules build the foundation for higher-level components. + +User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('CMake', '3.18.4'), +] + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + +exts_list = [ + ('portalocker', '2.3.2', { + 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], + }), + ('dune-common', version, { + 'modulename': 'dune.common', + 'checksums': ['b6736c69d5213688405bc1d953ac907c1440ecda1174c0cf08bf6cf69ee585a1'], + }), + ('dune-geometry', version, { + 'modulename': 'dune.geometry', + 'checksums': ['7fc655c42fde485bc563d362d9309db332acd08229df2ad215fa0fd292e18a54'], + }), + ('dune-grid', version, { + 'modulename': 'dune.grid', + 'checksums': ['1faf909dba2a590086aa0a2e5926905fcbbe3521e9d920359c984ab496a3c5fb'], + }), + ('dune-localfunctions', version, { + 'modulename': 'dune.localfunctions', + 'checksums': ['d19cb354cbce72654220228613f53ed1be3b960718d8738523b987da6d108406'], + }), + ('dune-istl', version, { + 'modulename': 'dune.istl', + 'checksums': ['0227acaf6b93700036403c3fe8312c00b33edc9dc09d89b295768cbe84eff507'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb new file mode 100644 index 0000000000..20d66b9fdd --- /dev/null +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'dune-fem' +version = '2.8.0.6' + +homepage = "https://www.dune-project.org/modules/dune-fem/" +description = """DUNE-FEM is a discretization module based on DUNE containing all +the building blocks required to implement efficient solvers for a wide range +of (systems of non linear) partial differential equations. DUNE-FEM can also +be used through an extensive Python interface which brings all +components of DUNE-FEM and the DUNE core modules to Python. + +User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PETSc', '3.14.4'), + ('CMake', '3.18.4'), + ('dune-core', '2.8.0.post1'), + ('matplotlib', '3.3.4'), +] + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + +exts_list = [ + ('fenics-ufl', '2019.1.0', { + 'modulename': 'ufl', + 'checksums': ['f778cb914f0fe57be76ad288a9209c1f4034a65692e13907171d994a4747bf81'], + }), + ('dune-alugrid', '2.8.0.post1', { + 'modulename': 'dune.alugrid', + 'checksums': ['3ee0ecdc19add77535c211c60058bf28162f9ad3c54b8b3b2bfcafc4d6269c55'], + }), + ('dune-spgrid', '2.8.0.post1', { + 'modulename': 'dune.spgrid', + 'checksums': ['9c6047d5672aabef1b39e9604f03611a1097070935e3c2b1224f69f8758fa336'], + }), + ('dune-polygongrid', '2.8.0.post1', { + 'modulename': 'dune.polygongrid', + 'checksums': ['a1b3dd301a403db6ea0b0a2d9e267b292dd6c5b3d12801f5154890bd4b6d63a8'], + }), + (name, version, { + 'modulename': 'dune.fem', + 'checksums': ['85151aa6fe54d14ae7cee12feff90afc580e0e41f5636bf51a6fbb2b9921bf10'], + }), + ('dune-fem-dg', version, { + 'modulename': 'dune.femdg', + 'checksums': ['bb81fdaf0ba0f59915dca8080d82f2c6b1d2ad98cd51cf8548b0c96d88adebb0'], + }), + ('triangle', '20200424', { + 'checksums': ['fc207641f8f39986f7d2bee1b91688a588cd235d2e67777422f94e61fece27e9'], + }), + ('dune-vem', version, { + 'modulename': 'dune.vem', + 'checksums': ['452145b85f2755cda24aa683efd4cc6c90fd49af395333dd766fb6cf479f969b'], + }), +] + + + +moduleclass = 'math' From f4fc1262e8e3674cf84b198dc31f303bf959fb35 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 7 Dec 2021 14:37:38 +0100 Subject: [PATCH 1811/2365] Updated matplotlib version in dune-fem --- easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index 20d66b9fdd..fa6041e980 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -21,7 +21,7 @@ dependencies = [ ('PETSc', '3.14.4'), ('CMake', '3.18.4'), ('dune-core', '2.8.0.post1'), - ('matplotlib', '3.3.4'), + ('matplotlib', '3.3.3'), ] use_pip = True From 79773248fc89db65b8c3c9d9e72f619d9dd4caf1 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 7 Dec 2021 15:14:19 +0100 Subject: [PATCH 1812/2365] removed unwanted whitespace in dune-fem configuration --- easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index fa6041e980..6d875c7c14 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -66,6 +66,4 @@ exts_list = [ }), ] - - moduleclass = 'math' From 9a84a6e5b6f9f16bb5aa1fa5ceb279ff907054bc Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 8 Dec 2021 22:20:43 +0100 Subject: [PATCH 1813/2365] Adding PyOpenCL for fosscuda/2020b --- .../PyOpenCL-2021.1.2-fosscuda-2020b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..0f033662e7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2021.1.2' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.1', { + 'checksums': ['073ae22a0ae946e2db97164f2eb24a599cd3a51430384aa40859dffd73056c40'], + }), + ('pyopencl', version, { + 'checksums': ['18871bc80c5a94869521189cf2c04d72c88367a441a9a033f72f66792ac33d29'], + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + }), +] + +moduleclass = 'vis' From 100b25456f74ba700a0fb12e0e298415e6c489b5 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 9 Dec 2021 13:45:08 +0100 Subject: [PATCH 1814/2365] {chem}[foss/2020b] yaff 1.6.0 --- .../m/molmod/molmod-1.4.8-foss-2020b.eb | 34 +++++++++++++++ .../y/yaff/yaff-1.6.0-foss-2020b.eb | 43 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb new file mode 100644 index 0000000000..55945818bb --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = [ + '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8', # molmod-1.4.8.tar.gz +] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb new file mode 100644 index 0000000000..e86af8d99d --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# Building this in interactive Slurm session will result in freeze during either +# runtest phase or sanity_check_commands phase (python -c 'import yaff') +# +# If you submit this as non-interactive Slurm job, it will build just fine. +# Possibly root cause: https://github.com/h5py/h5py/issues/917 +# +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.6.0' + +homepage = 'https://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + # Needs h5py version 2 + ('h5py', '2.10.0'), + ('molmod', '1.4.8'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +moduleclass = 'chem' From 4d6e12d61d72afe1a840c0e99d3fe372328ee632 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Dec 2021 11:44:34 +0100 Subject: [PATCH 1815/2365] bundle h5py to yaff v2 --- .../y/yaff/yaff-1.6.0-foss-2020b.eb | 32 +++++++++++++------ 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb index e86af8d99d..e7103d4a5c 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -8,7 +8,7 @@ # If you submit this as non-interactive Slurm job, it will build just fine. # Possibly root cause: https://github.com/h5py/h5py/issues/917 # -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'yaff' version = '1.6.0' @@ -18,15 +18,12 @@ description = """Yaff stands for 'Yet another force field'. It is a pythonic for toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] +builddependencies = [('pkgconfig', '1.5.1', '-python')] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - # Needs h5py version 2 - ('h5py', '2.10.0'), + ('HDF5', '1.10.7'), ('molmod', '1.4.8'), ] @@ -34,10 +31,25 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True +local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +local_runtest += "python setup.py build_ext -i; nosetests -v" + +exts_list = [ + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + 'source_urls': ['https://pypi.python.org/packages/source/h/h5py'], + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch + ], + }), + (name, version, { + 'source_urls': ['https://github.com/molmod/yaff/releases/download/%(version)s'], + 'runtest': local_runtest, + 'checksums': ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'], + }), +] -runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -runtest += "python setup.py build_ext -i; nosetests -v" moduleclass = 'chem' From 21730ea1ebab885f63931207e81c2dc58a76b7b9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Dec 2021 12:21:21 +0100 Subject: [PATCH 1816/2365] remove download_dep_fail --- easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb index e7103d4a5c..229465a24e 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -28,7 +28,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " From 7256e3914cd23f7d30cb772f836434dd68a312c7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 10 Dec 2021 20:01:21 +0100 Subject: [PATCH 1817/2365] adding easyconfigs: Eigen-3.4.0-GCCcore-10.2.0.eb --- .../e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..97fabdb318 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.4.0' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.35'), # to make CMake compiler health check pass on old systems + ('CMake', '3.18.4'), +] + +moduleclass = 'math' From 6673e42345e9c43cf819286489a6e6732b4850b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Dec 2021 10:25:09 +0100 Subject: [PATCH 1818/2365] add missing Perl build dependency for Longshot --- .../easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb index 07d70a35c9..f3c93e26ad 100644 --- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb @@ -25,6 +25,7 @@ builddependencies = [ ('Clang', '11.0.1'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('Perl', '5.32.0'), ] extract_sources = True From 6b10463da7e78ad7227191ad50ce9240f34c8a65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Dec 2021 10:35:08 +0100 Subject: [PATCH 1819/2365] add googletest build dependency for Highway --- .../easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb index 5111d10fd4..0f1af103e8 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb @@ -19,8 +19,11 @@ checksums = ['e1d47ce510429fdcf31f41697ca74fb0dcd59d933196e531a86d51751a56f4cc'] builddependencies = [ ('binutils', '2.35'), ('CMake', '3.18.4'), + ('googletest', '1.10.0'), ] +configopts = "-DHWY_SYSTEM_GTEST=ON" + runtest = "test" sanity_check_paths = { From 8a6dfa0505f86a135987b33a3123f21e0185c5b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Dec 2021 20:42:56 +0100 Subject: [PATCH 1820/2365] seed in PCRE2 sources to fix broken MariaDB 10.5.8 + 10.6.4 easyconfigs --- .../m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb index 83ee345b1d..db3b9cf4a4 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb @@ -9,11 +9,19 @@ Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] -sources = [SOURCELOWER_TAR_GZ] +local_pcre2_ver = '10.34' +source_urls = [ + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', + 'https://downloads.sourceforge.net/project/pcre/pcre2/%s/' % local_pcre2_ver, +] +sources = [ + SOURCELOWER_TAR_GZ, + {'filename': 'pcre2-%s.zip' % local_pcre2_ver, 'extract_cmd': "cp %s %(builddir)s/"}, +] patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] checksums = [ 'eb4824f6f2c532cd3fc6a6bce7bf78ea7c6b949f8bdd07656b2c84344e757be8', # mariadb-10.5.8.tar.gz + '75a19013a10ab543fe923bbc9b7c2750559d2cca3b4c3611ab91392e5f62041c', # pcre2-10.34.zip '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch ] @@ -35,7 +43,9 @@ dependencies = [ ('Judy', '1.0.5'), # needed by OQGraph ] -separate_build_dir = True +# replace download URL for PCRE2 with path to pre-downloaded PRCE2 source file +local_pcre2_path = '%%(builddir)s/pcre2-%s.zip' % local_pcre2_ver +preconfigopts = "sed -i 's@http://.*.zip@file://%s@g' ../mariadb-%%(version)s/cmake/pcre.cmake && " % local_pcre2_path configopts = "-DCMAKE_BUILD_TYPE=Release " configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker From 7021dce4f2cd8ed38cf3b986b9514eaaa2b16b94 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 14 Dec 2021 19:08:56 +0100 Subject: [PATCH 1821/2365] adding easyconfigs: CHERAB-1.3.0-intel-2020b.eb, Raysect-0.7.1-intel-2020b.eb --- .../c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 30 +++++++++++++++++++ .../r/Raysect/Raysect-0.7.1-intel-2020b.eb | 24 +++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb new file mode 100644 index 0000000000..a1ad1f6bc9 --- /dev/null +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'CHERAB' +version = '1.3.0' + +homepage = 'https://cherab.github.io/documentation/index.html' + +description = """CHERAB is a python library for forward modelling diagnostics + based on spectroscopic plasma emission.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = False + +sanity_check_commands = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && python -c "import cherab"'] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb new file mode 100644 index 0000000000..d506edd8c8 --- /dev/null +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Raysect' +version = '0.7.1' + +homepage = 'https://raysect.org' + +description = """Raysect is an OOP ray-tracing framework for Python""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c91f7dc406fd64dfaa4096b259c31250ac50881a301a46b2a1d607a2746f968'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True + +moduleclass = 'vis' From 0e850a3fc01f7417fa864c999fb96211eb1d405f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 14 Dec 2021 20:52:03 +0100 Subject: [PATCH 1822/2365] adding easyconfigs: STRUMPACK-6.1.0-foss-2020b.eb, STRUMPACK-6.1.0-intel-2020b.eb --- .../s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 52 ++++++++++++++++++ .../STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 53 +++++++++++++++++++ 2 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb new file mode 100644 index 0000000000..26e9142f8f --- /dev/null +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '6.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['219ec7360594172464aafa6ecac1fd161097db6fb9ee35af5c1ca61531f4f5c4'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.1.0'), +] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpifort ' +configopts += '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DNO_MODULES=ON ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb new file mode 100644 index 0000000000..4938fb4262 --- /dev/null +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '6.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['219ec7360594172464aafa6ecac1fd161097db6fb9ee35af5c1ca61531f4f5c4'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.1.0'), +] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' +configopts += '-DCMAKE_C_COMPILER=mpiicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpiifort ' +configopts += '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DNO_MODULES=ON ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' +configopts += '-DTPL_SCALAPACK_LIBRARIES="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl" ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], +} + +moduleclass = 'numlib' From e875488ae7c7cf23084a9e35db7b58f8cde81d67 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 14 Dec 2021 21:02:20 +0100 Subject: [PATCH 1823/2365] CHERAB/1.3.0 style corrections --- easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb index a1ad1f6bc9..7d3d731a92 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -10,7 +10,6 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] @@ -25,6 +24,9 @@ download_dep_fail = True use_pip = True sanity_pip_check = False -sanity_check_commands = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && python -c "import cherab"'] +sanity_check_commands = [ + 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && ' + 'python -c "import cherab"' +] moduleclass = 'phys' From 8046012e23a0ceb86ef8f7f1d7f9b162a4e0210e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 15 Dec 2021 14:57:38 +0100 Subject: [PATCH 1824/2365] Update style of Raysect v0.7.1 EB files --- .../r/Raysect/Raysect-0.7.1-foss-2020b.eb | 25 +++++++++++++++++++ .../r/Raysect/Raysect-0.7.1-intel-2020b.eb | 3 ++- 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb new file mode 100644 index 0000000000..53e51415d5 --- /dev/null +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Raysect' +version = '0.7.1' + +homepage = 'https://raysect.org' + +description = """Raysect is an OOP ray-tracing framework for Python""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c91f7dc406fd64dfaa4096b259c31250ac50881a301a46b2a1d607a2746f968'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb index d506edd8c8..0d104c5782 100644 --- a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb @@ -9,7 +9,6 @@ description = """Raysect is an OOP ray-tracing framework for Python""" toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['5c91f7dc406fd64dfaa4096b259c31250ac50881a301a46b2a1d607a2746f968'] @@ -20,5 +19,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True +sanity_pip_check = True moduleclass = 'vis' From 8a6b6613a1863c84e360fd391284e0c9b9afb6aa Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 15 Dec 2021 15:05:43 +0100 Subject: [PATCH 1825/2365] ParMETIS v4.0.3 for iimpi/2020b --- .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb new file mode 100644 index 0000000000..8cc997b562 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb @@ -0,0 +1,25 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.18.4')] + +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' From efa9cd436cd8e9fe91d9bb082999a916284612d8 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 15 Dec 2021 15:55:48 +0100 Subject: [PATCH 1826/2365] adding easyconfigs: phonopy-2.12.0-foss-2020b.eb --- .../p/phonopy/phonopy-2.12.0-foss-2020b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb new file mode 100644 index 0000000000..3a1f3d0bc3 --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '2.12.0' + +homepage = 'https://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ff65065f418ccbff9fbc1186b9a65581e83b42789aa4a656f45badfff9bd3f61'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('matplotlib', '3.3.3'), + ('PyYAML', '5.3.1'), + ('h5py', '3.1.0'), + ('spglib-python', '1.16.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["phonopy --help"] + +sanity_pip_check = True + +moduleclass = 'lib' From 2c1d96700216718f4aef4153dcf715e75299df6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 12:54:13 +0100 Subject: [PATCH 1827/2365] add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot --- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index 2e64f84446..1de0bc6126 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -checksums = ['3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98'] +patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] +checksums = [ + '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz + '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch +] builddependencies = [ ('binutils', '2.35'), From 8cb67787082d1464173acd3d833c38247816f5ed Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 17 Dec 2021 14:43:22 +0200 Subject: [PATCH 1828/2365] adding easyconfigs: PyTorch-1.10.0-fosscuda-2020b.eb, CMake-3.20.1-GCCcore-10.2.0.eb, expecttest-0.1.3-GCCcore-10.2.0.eb --- .../c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb | 32 +++++ .../expecttest-0.1.3-GCCcore-10.2.0.eb | 25 ++++ .../PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 120 ++++++++++++++++++ 3 files changed, 177 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..16e8766c69 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +name = 'CMake' +version = '3.20.1' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3f1808b9b00281df06c91dd7a021d7f52f724101000da7985a401678dfe035b0'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.72.0'), + ('libarchive', '3.4.3'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1e133b2aea --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.1.3' + +homepage = "https://github.com/ezyang/expecttest" +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['83057695811d94128aed13ed094a070db90e0a92ea40071f8ee073cbab57149a'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..af85117afc --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -0,0 +1,120 @@ +name = 'PyTorch' +version = '1.10.0' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_skip_failing_ops_tests.patch', + 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch + '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', + # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch + '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-test-cond-cpu.patch + '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-vnni-detection.patch + '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch + 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_skip_failing_ops_tests.patch + '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', + # PyTorch-1.10.0_skip_nan_tests_openblas.patch + '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), # Needs 3.20 or newer. + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('expecttest', '0.1.3'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + # 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + # 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From 5287aec3a42f0fadaa08ec3d020f7c8e42a72251 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 15:20:54 +0100 Subject: [PATCH 1829/2365] use 'readelf -l' to determine path to interpreter in patch file for Rust --- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index 1de0bc6126..d9802f22e0 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ sources = ['rustc-%(version)s-src.tar.gz'] patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] checksums = [ '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz - '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch + 'e3db7005585eb807ecb69929818740f00417cac247b1065a9d43a7f16cf05e0b', # Rust-1.52.1_sysroot-fix-interpreter.patch ] builddependencies = [ From 71fa9e7d60df9ad172d82210ede1668c17352bce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 17:19:38 +0100 Subject: [PATCH 1830/2365] enhance sanity check for PyTorch 1.10.0 with fosscuda/2020b --- .../p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index af85117afc..a7ff2a282f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -114,7 +114,13 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' -sanity_check_commands = ["python -c 'import caffe2.python'"] +# The readelf sanity check can be taken out once the TestRPATH test from https://github.com/pytorch/pytorch/pull/68912 +# is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "python -c 'import caffe2.python'", + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'devel' From c7e42968b861e9b0a9b2d137f05e726d0c56eb63 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Dec 2021 01:44:06 +0100 Subject: [PATCH 1831/2365] explain why h5py v2.10.0 is bundled in yaff-1.6.0-foss-2020b.eb --- easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb index 229465a24e..03214bbd47 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -34,6 +34,7 @@ local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/m local_runtest += "python setup.py build_ext -i; nosetests -v" exts_list = [ + # yaff v1.6.0 does not work with h5py>=3.0, the default version in foss/2020b ('h5py', '2.10.0', { 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', From 61b545e8739382b15facd41a32ccf506912b6dd3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Dec 2021 01:45:20 +0100 Subject: [PATCH 1832/2365] remove default sanity checks from molmod v1.4.8 --- easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb index 55945818bb..1aa8772b2a 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -26,9 +26,4 @@ sanity_pip_check = True runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" runtest += "python setup.py build_ext -i; pytest -ra" -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' From d52efb7c35317d1b57d2de9b0e07c4e530f332c5 Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 14:28:32 +0200 Subject: [PATCH 1833/2365] adding easyconfigs: MultiQC-1.10.1-foss-2020b.eb --- .../m/MultiQC/MultiQC-1.10.1-foss-2020b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb new file mode 100644 index 0000000000..c89209dad0 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.10.1' + +homepage = 'https://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('PyYAML', '5.3.1'), + ('networkx', '2.5'), +] + +use_pip = True + +exts_list = [ + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('Markdown', '3.2.1', { + 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], + }), + ('lzstring', '1.0.4', { + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('rich', '10.16.0', { + 'checksums': ['06a1355131feda5eba4511dd749e9187ac0fb42209e189845d81e94505fc268e'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('multiqc', version, { + 'checksums': ['a4be38dd72da6b3b042d5dffbdcafd3e368189fbc4e767c79ce0aea1987c3a79'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 5e908627fda53b16c93e4fb0acf37c0564670ea2 Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 15:56:46 +0100 Subject: [PATCH 1834/2365] Update easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit added info comments Co-authored-by: Bob Dröge --- .../easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb index c89209dad0..ef76f02541 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb @@ -1,3 +1,13 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + easyblock = 'PythonBundle' name = 'MultiQC' From fa5ace79eccf4fa6eb7285420c40b86adad81161 Mon Sep 17 00:00:00 2001 From: Max Voit Date: Tue, 21 Dec 2021 12:03:15 +0100 Subject: [PATCH 1835/2365] adding easyconfigs: CAFE5-5.0.0-GCC-10.2.0.eb --- .../c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..e1a52c7d44 --- /dev/null +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'CAFE5' +version = '5.0.0' + +homepage = 'https://github.com/hahnlab/CAFE5' + +description = """Software for Computational Analysis of gene Family Evolution + +The purpose of CAFE is to analyze changes in gene family size in a way that +accounts for phylogenetic history and provides a statistical foundation for +evolutionary inferences. The program uses a birth and death process to model +gene gain and loss across a user-specified phylogenetic tree. The distribution +of family sizes generated under this model can provide a basis for assessing the +significance of the observed family size differences among taxa. +""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +#toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] + +builddependencies = [] + +dependencies = [] + +install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' + +sanity_check_paths = { + 'files': ['bin/cafe5', + ], + 'dirs': ['bin', 'examples'], +} + +moduleclass = 'bio' From 1c76287971fe22d40129bff18b0e5cb2bee18e83 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 12:06:28 +0100 Subject: [PATCH 1836/2365] Update CAFE5-5.0.0-GCC-10.2.0.eb --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index e1a52c7d44..8b45dda0bc 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -1,7 +1,5 @@ # EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# Author: Max Voit easyblock = 'ConfigureMake' From ce1202d4caef3d914019899dd4a1ac2cd77080cf Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:50:54 +0100 Subject: [PATCH 1837/2365] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 8b45dda0bc..63828151ad 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -15,8 +15,7 @@ accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the -significance of the observed family size differences among taxa. -""" +significance of the observed family size differences among taxa.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} #toolchainopts = {'openmp': True} From 04c4fd03bb4c8b2f00bad0d21550ec8de993d690 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:06 +0100 Subject: [PATCH 1838/2365] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 63828151ad..3c49fe6508 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} #toolchainopts = {'openmp': True} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] -sources = ['%(name)s-%(version)s.tar.gz'] +sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] builddependencies = [] From 18d7c3d583cd66642ba3b8265edb8ee1f16574da Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:14 +0100 Subject: [PATCH 1839/2365] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 3c49fe6508..1e837f985a 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -23,11 +23,6 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] - -builddependencies = [] - -dependencies = [] - install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' sanity_check_paths = { From 70835058b66e22bb8939453d96f8c8795ffc0899 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:19 +0100 Subject: [PATCH 1840/2365] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 1e837f985a..a631bd275a 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -26,8 +26,7 @@ checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' sanity_check_paths = { - 'files': ['bin/cafe5', - ], + 'files': ['bin/cafe5'], 'dirs': ['bin', 'examples'], } From f112aef42f2edeb569ac97d9fdb81326c4461bf8 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:27 +0100 Subject: [PATCH 1841/2365] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index a631bd275a..efbb78a668 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -30,4 +30,6 @@ sanity_check_paths = { 'dirs': ['bin', 'examples'], } +sanity_check_commands = ['cafe5 --help'] + moduleclass = 'bio' From a202f95f9b4ffbb72eaf3bca8de155920c3e505b Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 14:48:59 +0100 Subject: [PATCH 1842/2365] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index efbb78a668..01a1de1614 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -27,7 +27,7 @@ install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 sanity_check_paths = { 'files': ['bin/cafe5'], - 'dirs': ['bin', 'examples'], + 'dirs': ['examples'], } sanity_check_commands = ['cafe5 --help'] From 848a126895ab001f51ae74a565e8add96ffeeb09 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 14:49:05 +0100 Subject: [PATCH 1843/2365] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 01a1de1614..9b18ee2115 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -23,6 +23,8 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] + +buildopts = 'CFLAGS="$CXXFLAGS -I. -include config.h" LINKER="$CXX $CXXFLAGS -o" ' install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' sanity_check_paths = { From c1b5facd7fa3e18693f87f6a273f6f8248e7f807 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 14:49:12 +0100 Subject: [PATCH 1844/2365] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 9b18ee2115..9706d2a722 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -18,7 +18,7 @@ of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -#toolchainopts = {'openmp': True} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] sources = [SOURCE_TAR_GZ] From 3207db81247bcdeccb7ae9b829203e3f2b953cc2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 22 Dec 2021 09:19:23 +0000 Subject: [PATCH 1845/2365] adding easyconfigs: numdiff-5.9.0-GCCcore-10.2.0.eb --- .../n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9c49693bbc --- /dev/null +++ b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'numdiff' +version = '5.9.0' + +homepage = 'https://savannah.nongnu.org/projects/numdiff' +description = """Numdiff (which I will also write numdiff) is a little program that can be used to compare putatively + similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats. + Equivalently, Numdiff is a program with the capability to appropriately compare files containing numerical fields + (and not only).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['87284a117944723eebbf077f857a0a114d818f8b5b54d289d59e73581194f5ef'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/ndselect', 'bin/numdiff'], + 'dirs': ['share'], +} + +sanity_check_commands = ["numdiff --help"] + +moduleclass = 'tools' From 16c2993b74130e6f852644566a3471aa00fa4862 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 22 Dec 2021 09:36:16 +0000 Subject: [PATCH 1846/2365] switch homepage MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb index 9c49693bbc..b8f9bfcd13 100644 --- a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'numdiff' version = '5.9.0' -homepage = 'https://savannah.nongnu.org/projects/numdiff' +homepage = 'https://www.nongnu.org/numdiff/' description = """Numdiff (which I will also write numdiff) is a little program that can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats. Equivalently, Numdiff is a program with the capability to appropriately compare files containing numerical fields From 0347354a019a207bc793a769587eb637c18af652 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 09:13:12 +0100 Subject: [PATCH 1847/2365] add patch to fix build of Arrow 0.17.1 on aarch64 systems + fix configure options --- .../a/Arrow/Arrow-0.17.1-foss-2020b.eb | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb index e4c0d64a27..e348b0044c 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -9,15 +9,12 @@ description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [ - 'http://apache.belnet.be/arrow/arrow-%(version)s/', - 'https://www-eu.apache.org/dist/arrow/arrow-%(version)s/', -] +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -patches = ['Arrow-0.16.0_fix-intel.patch'] +patches = ['Arrow-0.17.1_fix-arm.patch'] checksums = [ 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz - '7c1569087f93959a0dfc163d80e5f542edb4d7ed0b9d71a2a05b4081211ad2b9', # Arrow-0.16.0_fix-intel.patch + 'd1076d35966056c39e0c88b8fadaaa7660ee4d8c07fc2c5bdf1d5d6e683ff44a', # Arrow-0.17.1_fix-arm.patch ] builddependencies = [ @@ -35,18 +32,18 @@ dependencies = [ ('Boost', '1.74.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] From 11f1722eeaab286909353d7a3afb39ee747fe3f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 09:13:28 +0100 Subject: [PATCH 1848/2365] add archive source URL for Spark 3.1.1 --- easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb index ba34f767b6..5cb1ec3c5e 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -11,6 +11,7 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' ] sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] @@ -25,13 +26,13 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ ('py4j', '0.10.9.2', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], }), ] From 815d6eb33b5b12f16d689a495eac37724f710a14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 13:55:18 +0100 Subject: [PATCH 1849/2365] fix broken patch file for recent GPAW versions --- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb index 1dd3ad51a4..1b32207461 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb @@ -19,7 +19,7 @@ patches = [ checksums = [ '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb index 8264ef0a7f..861a80e2fd 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -19,7 +19,7 @@ patches = [ checksums = [ '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb index 77370423b3..7a2e4989e8 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb @@ -20,7 +20,7 @@ patches = [ checksums = [ '96843b68e04bd1c12606036c9f99b0ddfa5e6ee08ce46835e6bb347a6bd560a3', # gpaw-21.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb index f8f2758be1..1f22f89cc8 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb @@ -20,7 +20,7 @@ patches = [ checksums = [ '96843b68e04bd1c12606036c9f99b0ddfa5e6ee08ce46835e6bb347a6bd560a3', # gpaw-21.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb index f2b603dd33..582e90ea73 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb index bedc11e904..bba61ad120 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] # The intel version is not built with libvdwxc support, as that library is incompatible with MKL. From 13bc9e4babc0f2fa9d29fd0d650494dde66915c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 24 Dec 2021 10:51:38 +0100 Subject: [PATCH 1850/2365] add simple sanity check command --- easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb index 75cf15432a..0572262410 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb @@ -27,4 +27,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['muscle -version'] + moduleclass = 'bio' From 06caa72a386353acb63e616cf10c041c32512b7f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 24 Dec 2021 11:09:44 +0100 Subject: [PATCH 1851/2365] use toolchain's default muscle version --- easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb index a0c8a90bc5..db39bb21b3 100644 --- a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('GlimmerHMM', '3.0.4c'), ('HMMER2', '2.3.2'), ('HMMER', '3.3.2'), - ('MUSCLE', '3.8.1551'), + ('MUSCLE', '3.8.31'), ('BLAST+', '2.11.0'), ('prodigal', '2.6.3'), ('Biopython', '1.78'), From d18127d322991615d360e10ff6ae59e3ca54eca3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Dec 2021 11:18:51 +0100 Subject: [PATCH 1852/2365] remove unused MUSCLE easyconfig --- .../m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb deleted file mode 100644 index 0572262410..0000000000 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'MakeCp' - -name = 'MUSCLE' -version = "3.8.1551" - -homepage = 'https://drive5.com/muscle/' -description = """MUSCLE is one of the best-performing multiple alignment programs - according to published benchmark tests, with accuracy and speed that are consistently - better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users - learn everything they need to know about MUSCLE in a few minutes-only a handful of - command-line options are needed to perform common alignment tasks.""" - -toolchain = {'name': 'GCC', 'version': '10.2.0'} - -source_urls = ['https://www.drive5.com/muscle/'] -sources = ['%(namelower)s_src_%(version)s.tar.gz'] -checksums = ['c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e'] - -# use correct compiler flags + -# don't use -static when linking, since that implies requiring glibc-static to be installed -buildopts = 'CFLAGS="$CXXFLAGS" LDLIBS="-lm"' - -files_to_copy = [(["muscle"], 'bin')] - -sanity_check_paths = { - 'files': ["bin/%(namelower)s"], - 'dirs': [], -} - -sanity_check_commands = ['muscle -version'] - -moduleclass = 'bio' From f2a1885773a37a1c3b9262b5a99ed949f0b6bac8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 29 Dec 2021 19:57:00 +0200 Subject: [PATCH 1853/2365] adding easyconfigs: FTGL-2.1.3-rc5-GCCcore-10.2.0.eb --- .../f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6f17150fb6 --- /dev/null +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FTGL' +version = '2.1.3-rc5' + +homepage = 'http://ftgl.sourceforge.net/docs/html/' +description = """ FTGL is a free open source library to enable developers to use arbitrary +fonts in their OpenGL (www.opengl.org) applications. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5458d62122454869572d39f8aa85745fc05d5518001bcefa63bd6cbb8d26565b'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('freetype', '2.10.3'), + ('libGLU', '9.0.1'), + ('Mesa', '20.2.1'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/ftgl.pc', 'lib/libftgl.a', 'lib/libftgl.la', 'lib/libftgl.%s' % SHLIB_EXT], + 'dirs': ['include/FTGL', 'share'] +} + +moduleclass = 'lib' From b7d896f0ec3e1038813681fac5e06eed9e3557e1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 3 Jan 2022 17:54:52 +0100 Subject: [PATCH 1854/2365] Update STRUMPACK-6.1.0-foss-2020b.eb and STRUMPACK-6.1.0-intel-2020b.eb Co-authored-by: Alex Domingo --- .../s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 16 +++++----------- .../s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 16 +++++----------- 2 files changed, 10 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb index 26e9142f8f..a47c361c4c 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -8,7 +8,7 @@ description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pghysels/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] @@ -24,14 +24,7 @@ dependencies = [ ('SCOTCH', '6.1.0'), ] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpifort ' -configopts += '-DSTRUMPACK_USE_OPENMP=ON ' -configopts += '-DNO_MODULES=ON ' +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' configopts += '-DTPL_ENABLE_BPACK=OFF ' @@ -42,11 +35,12 @@ configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' -configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], - 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + +[ 'lib'], } moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb index 4938fb4262..47b5368522 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -8,7 +8,7 @@ description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" toolchain = {'name': 'intel', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pghysels/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] @@ -24,14 +24,7 @@ dependencies = [ ('SCOTCH', '6.1.0'), ] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' -configopts += '-DCMAKE_C_COMPILER=mpiicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpiifort ' -configopts += '-DSTRUMPACK_USE_OPENMP=ON ' -configopts += '-DNO_MODULES=ON ' +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' configopts += '-DTPL_SCALAPACK_LIBRARIES="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl" ' @@ -43,11 +36,12 @@ configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' -configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], - 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + +[ 'lib'], } moduleclass = 'numlib' From c68451640dccc93d9d2e1b8e7fc192a7077c1da5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 3 Jan 2022 18:51:09 +0000 Subject: [PATCH 1855/2365] stick to torchvision 0.8.2 as dependency in 2020b --- ...ch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb diff --git a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..28c09209b9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,51 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'PyTorch3D' +version = '0.4.0' +local_pytorch_version = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = "https://pytorch3d.org/" +description = """PyTorch3D is FAIR's library of reusable components for deep learning with 3D data.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('tqdm', '4.56.2'), + ('PyTorch', local_pytorch_version), + ('imageio', '2.9.0'), + ('IPython', '7.18.1'), + ('torchvision', '0.8.2', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('portalocker', '2.3.0', { + 'checksums': ['4e913d807aa6598c320e8a50c50e2ee0602bc45240b485e3f8bc06f13060084c'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('yacs', '0.1.8', { + 'checksums': ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'], + }), + ('iopath', '0.1.8', { + 'source_tmpl': '%(namelower)s-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['e11029c30ee77616b3efd82888aa80941d12afcc5940c2ef57e04a8e93a10f9f'], + }), + ('fvcore', '0.1.5.post20210617', { + 'checksums': ['1f1fb91b82166f85ed0f7da8906e87688de9e1b4879b478dc3969d93d24f0379'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/facebookresearch/%(namelower)s/archive'], + 'checksums': ['6f33c45c8b698b068ff267287ad490dc2f8f48ad2f486175438b0426575e391a'], + }), +] + +moduleclass = 'tools' From 3f6546a3c43b3756c8ca734972506372ca41baa0 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 4 Jan 2022 15:15:03 +0100 Subject: [PATCH 1856/2365] Patch CHERAB/1.3.0 for intel/2020b and foss/2020b --- .../c/CHERAB/CHERAB-1.3.0-foss-2020b.eb | 31 +++++++++++++++++++ .../c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 13 ++++---- 2 files changed, 37 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb new file mode 100644 index 0000000000..bb77bca770 --- /dev/null +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'CHERAB' +version = '1.3.0' + +homepage = 'https://cherab.github.io/documentation/index.html' + +description = """CHERAB is a python library for forward modelling diagnostics + based on spectroscopic plasma emission.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(namelower)s-%(version)s_no-namespace.patch'] +checksums = [ + '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz + '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb index 7d3d731a92..c0847561d7 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -11,7 +11,11 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'intel', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] -checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] +patches = ['%(namelower)s-%(version)s_no-namespace.patch'] +checksums = [ + '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz + '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +] dependencies = [ ('Python', '3.8.6'), @@ -22,11 +26,6 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_pip_check = False - -sanity_check_commands = [ - 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && ' - 'python -c "import cherab"' -] +sanity_pip_check = True moduleclass = 'phys' From 6a166bdcabd3f950617a0f1513abe20ace35bbd1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 19:56:53 +0100 Subject: [PATCH 1857/2365] use %(arch)s template to avoid hardcoding x86_64 in recent XML-LibXML easyconfigs --- .../x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb index ee314c18f7..62cc7c77d1 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb @@ -50,7 +50,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' From 18136cbf14892a7a8857dacf053b29306933865c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 5 Jan 2022 10:45:21 +0100 Subject: [PATCH 1858/2365] Add Cython/3.0a5 build dependency for CHERAB/1.3.0 --- .../c/CHERAB/CHERAB-1.3.0-foss-2020b.eb | 8 +-- .../c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 8 +-- .../c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb | 54 +++++++++++++++++++ 3 files changed, 62 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb index bb77bca770..9a080037a6 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb @@ -11,10 +11,10 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] -patches = ['%(namelower)s-%(version)s_no-namespace.patch'] -checksums = [ - '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz - '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +builddependencies = [ + ('Cython', '3.0a5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb index c0847561d7..f80768c259 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -11,10 +11,10 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'intel', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] -patches = ['%(namelower)s-%(version)s_no-namespace.patch'] -checksums = [ - '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz - '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +builddependencies = [ + ('Cython', '3.0a5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..08933e6092 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb @@ -0,0 +1,54 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , +# Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +# Updated: Pavel Grochal (INUITS) +## +# Thomas Hoffmann, EMBL Heidelberg: Adapted to v0.29.22, GCCcore 10.2.0 +# 2021/03 +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0a5' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['22060abe55a55a59096982f3e81de2dc8f28c29917d20fa5182f49c4530e27ec'] + +builddependencies = [('binutils', '2.35')] + +# Can't use multi_dep because EBPYTHONPREFIXES are not loaded in order. +# This results in not beeing able to choose Cython version in multi_dep. +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True + +use_pip = True + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cython --version', +] + +moduleclass = 'lang' From e7cbebdaf38e0fdfa72c7443b77803bc05d3ea64 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 11:19:08 +0100 Subject: [PATCH 1859/2365] fix formatting of STRUMPACK-6.1.0-foss-2020b.eb --- .../s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb index a47c361c4c..d6c33b40db 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -26,21 +26,21 @@ dependencies = [ configopts = '-DSTRUMPACK_USE_OPENMP=ON ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' -configopts += '-DTPL_ENABLE_BPACK=OFF ' -configopts += '-DTPL_ENABLE_ZFP=OFF ' -configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_PARMETIS=ON ' configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + -[ 'lib'], + [ 'lib'], } moduleclass = 'numlib' From 03f8ba7c9b917e3e4e17447f67cc9087dd6a1eab Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 15:25:08 +0100 Subject: [PATCH 1860/2365] fix formatting of STRUMPACK-6.1.0-intel-2020b.eb --- .../s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb index 47b5368522..f5abbb782b 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -25,23 +25,23 @@ dependencies = [ ] configopts = '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DTPL_SCALAPACK_LIBRARIES="${LIBSCALAPACK_MT}" ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' -configopts += '-DTPL_SCALAPACK_LIBRARIES="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl" ' -configopts += '-DTPL_ENABLE_BPACK=OFF ' -configopts += '-DTPL_ENABLE_ZFP=OFF ' -configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_PARMETIS=ON ' configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + -[ 'lib'], + [ 'lib'], } moduleclass = 'numlib' From 7a25ea0e6fdf346da07bd4537fb0c6c29b5d3bf4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 15:41:12 +0100 Subject: [PATCH 1861/2365] remove whitespace in STRUMPACK-6.1.0-foss-2020b.eb --- easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb index d6c33b40db..7dd06980ec 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -40,7 +40,7 @@ configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + - [ 'lib'], + ['lib'], } moduleclass = 'numlib' From e7410769fd306888fc6a58f78b0dad33b7e13c0e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 15:41:37 +0100 Subject: [PATCH 1862/2365] remove whitespace in STRUMPACK-6.1.0-intel-2020b.eb --- .../easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb index f5abbb782b..4f358cbc2f 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -41,7 +41,7 @@ configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + - [ 'lib'], + ['lib'], } moduleclass = 'numlib' From 3591b15e61887dca7a2855e845aac7ae48b3d489 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 11 Jan 2022 16:21:16 +0100 Subject: [PATCH 1863/2365] Removed reference to DUNE_PY_DIR environment variable --- .../easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb | 2 -- easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb index 3c4f56daeb..966f23ed47 100644 --- a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -7,8 +7,6 @@ homepage = "https://www.dune-project.org/groups/core/" description = """The Dune core modules build the stable basis of Dune. They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. These modules build the foundation for higher-level components. - -User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. """ toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index 6d875c7c14..e838e7272a 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -9,8 +9,6 @@ the building blocks required to implement efficient solvers for a wide range of (systems of non linear) partial differential equations. DUNE-FEM can also be used through an extensive Python interface which brings all components of DUNE-FEM and the DUNE core modules to Python. - -User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. """ toolchain = {'name': 'foss', 'version': '2020b'} From 8bbf219efa56074bd8f168fb31b5fea65f7b30a2 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 12 Jan 2022 09:21:42 +0100 Subject: [PATCH 1864/2365] Moved builddependencies before dependencies as requested by code review in pull request (both configs) --- .../d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb | 10 +++++----- .../d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb index 966f23ed47..b6aae99f16 100644 --- a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -11,6 +11,11 @@ These modules build the foundation for higher-level components. toolchain = {'name': 'foss', 'version': '2020b'} +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -20,11 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -builddependencies = [ - ('scikit-build', '0.11.1'), - ('Ninja', '1.10.1'), -] - exts_list = [ ('portalocker', '2.3.2', { 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index e838e7272a..52e3809d42 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -13,6 +13,11 @@ components of DUNE-FEM and the DUNE core modules to Python. toolchain = {'name': 'foss', 'version': '2020b'} +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -25,11 +30,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -builddependencies = [ - ('scikit-build', '0.11.1'), - ('Ninja', '1.10.1'), -] - exts_list = [ ('fenics-ufl', '2019.1.0', { 'modulename': 'ufl', From b5ea144b2526d5a9cb8a3c84281762637cc11a5c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 14 Jan 2022 20:21:30 +0100 Subject: [PATCH 1865/2365] Fix OpenMPI memleak that heavily affects CP2K, SIESTA, QUantumESPRESSO, VASP --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 3 +++ .../o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 3 +++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb | 3 +++ .../easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb | 3 +++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 3 +++ 5 files changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb index 110d6438af..1536146190 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb index 503f955baf..383370dd6f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -13,12 +13,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb index 12093c5a84..3746daadf8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb index d33ec82375..de0f5b3d2e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index 084adbc63f..b82c542c42 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a', # openmpi-4.1.0.tar.gz @@ -20,6 +21,8 @@ checksums = [ # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', ] builddependencies = [ From a7c1b3ce50056b6741d34f894315ab13b7a6e22e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 13:31:37 +0100 Subject: [PATCH 1866/2365] set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension included with TensorFlow 2.5.0+ --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index a394921436..b7a9a39b86 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -86,6 +86,7 @@ exts_list = [ ('grpcio', '1.34.1', { 'modulename': 'grpc', 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 9794ccd903..c1662ad3a3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -88,6 +88,7 @@ exts_list = [ ('grpcio', '1.34.1', { 'modulename': 'grpc', 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', From 37c4fb6cfff12113b8a92624240843012a3d7306 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 13:36:47 +0100 Subject: [PATCH 1867/2365] set for installing grcpio extension included with TensorFlow 2.2.3-2.4.1 with 2020* toolchain --- .../easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index 9678677ff3..a41e687495 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -95,6 +95,7 @@ exts_list = [ ('grpcio', '1.39.0', { 'modulename': 'grpc', 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index 2c463ccdf3..2342aee9b6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -98,6 +98,7 @@ exts_list = [ ('grpcio', '1.32.0', { 'modulename': 'grpc', 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 34a3a4c37f..ea58071275 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -99,6 +99,7 @@ exts_list = [ ('grpcio', '1.32.0', { 'modulename': 'grpc', 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', From 8f80dd2eda0278ddf69295d3af39dce21cf0a52d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 17 Jan 2022 13:13:34 +0100 Subject: [PATCH 1868/2365] Newer CMake versions uses the cmake-config files from OS installed boost. Make sure it is not used when looking for the internally built boost. --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb index 8e067a6bd0..edbae709f1 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -51,6 +51,8 @@ preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmak configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +# Make sure CMake doesn't use any system install Boost versions cmake-config files. +configopts += '-DBoost_NO_BOOST_CMAKE=ON ' sanity_check_paths = { 'files': ['bin/bcl2fastq'], From 4cc8729f7ce5ddb395467b979d2e2c62110e0034 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Jan 2022 17:25:40 +0200 Subject: [PATCH 1869/2365] add libaio.so.1 to libaio v0.3.112 --- .../l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb index 699303eba6..1be5c814b9 100644 --- a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'libaio' version = '0.3.112' -local_libversion = '1.0.1' +_libversion = '1.0.1' homepage = 'https://pagure.io/libaio' description = "Asynchronous input/output library that uses the kernels native interface." @@ -16,15 +16,23 @@ checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] builddependencies = [('binutils', '2.35')] +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + files_to_copy = [ - (["src/libaio.a", "src/libaio.%s.%s" % (SHLIB_EXT, local_libversion)], "lib"), + (["src/libaio.a", "src/%s" % _soname], "lib"), (["src/libaio.h"], "include"), ] -postinstallcmds = ["cd %%(installdir)s/lib; ln -s libaio.%s.%s libaio.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT)] +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] sanity_check_paths = { - 'files': ['lib/libaio.a', 'lib/libaio.%s.%s' % (SHLIB_EXT, local_libversion), 'include/libaio.h'], + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], 'dirs': [], } From b47036b9f30b3730021ad7e6c5ef229a2d9534c9 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 18 Jan 2022 08:35:39 +0100 Subject: [PATCH 1870/2365] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 9706d2a722..61b807a25d 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -1,7 +1,7 @@ # EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Max Voit -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'CAFE5' version = '5.0.0' From 789a5b038c6282355cd4801fed83250a8e8bc4b3 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 18 Jan 2022 08:36:09 +0100 Subject: [PATCH 1871/2365] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 61b807a25d..2f7bc2e4c9 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -25,7 +25,9 @@ sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] buildopts = 'CFLAGS="$CXXFLAGS -I. -include config.h" LINKER="$CXX $CXXFLAGS -o" ' -install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' +with_configure = True +files_to_copy = ['bin', 'examples'] +postinstallcmds = ['chmod -x %(installdir)s/examples/*.txt'] sanity_check_paths = { 'files': ['bin/cafe5'], From 818a958f0904e58f4c37914376690ae98f971ef8 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 18 Jan 2022 11:37:07 +0100 Subject: [PATCH 1872/2365] update build dependencies for binutils 2.34, 2.35, 2.36.1 and GCCcore 9.3.0, 10.1.0, 10.2.0, 10.3.0 and 11.1.0 with system toolchain --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 98d75b65b5..d4408b29aa 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -59,7 +59,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.35'), ] From 0742de8aabcba771b94ca1139d18a0f4ba7982fa Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 18 Jan 2022 12:24:41 +0100 Subject: [PATCH 1873/2365] make sure libxslt does not pick up OS installed libgcrypt or Python --- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb index 764ee9417e..d17aa440dc 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.10'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], From 94ec9ac53287b19ca776d4c0e1b704476908b5b4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Jan 2022 19:00:03 +0200 Subject: [PATCH 1874/2365] fix CVE-2021-23437 in Pillow v7 and v8 --- .../easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 9304f308f9..bff212b445 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -10,7 +10,11 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '10.2.0'} sources = [SOURCE_TAR_GZ] -checksums = ['11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + '11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e', # Pillow-8.0.1.tar.gz + 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.35')] From 9b95d825b5eddc4f2ddba99a6961e406d46a0888 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Jan 2022 20:26:28 +0200 Subject: [PATCH 1875/2365] fix checksum of Pillow-8_CVE-2021-23437.patch --- easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index bff212b445..7bdf247647 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] checksums = [ '11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e', # Pillow-8.0.1.tar.gz - 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch ] builddependencies = [('binutils', '2.35')] From 544613fbba0ac84c27869ee8d982a24bd22a23ee Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 19 Jan 2022 17:15:45 +0000 Subject: [PATCH 1876/2365] the Pillow v8 patch also works for Pillow-SIMD v7 --- .../p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb index 712cf054a0..9c4aa141b7 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa'] +patches = ['Pillow-8_CVE-2021-23437.patch'] +checksums = [ + '72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa', # 7.1.2.tar.gz + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.35')] From 4621898724637e25680d23471b6a7d8d3e614b87 Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 20 Jan 2022 08:33:07 +0000 Subject: [PATCH 1877/2365] Update easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb index 7fd2267fc9..c4abf6d5d2 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb @@ -17,6 +17,10 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] +builddependencies = [ + ('tcsh', '6.22.03'), +] + dependencies = [ ('Tcl', '8.6.10'), ] From 7f09339652000ddbcafb5290861d4aea43143189 Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 20 Jan 2022 08:33:15 +0000 Subject: [PATCH 1878/2365] Update easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb index c4abf6d5d2..b7b2e5f300 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb @@ -25,9 +25,6 @@ dependencies = [ ('Tcl', '8.6.10'), ] -# /bin/csh is required by 'config' script -osdependencies = ['tcsh'] - # Hard to make charm build the mpi version with gcc on POWER, so we don't currently try. charm_arch = 'mpi-linux-x86_64' charm_extra_cxxflags = '-fpermissive' From 780eef979bc3e1153140cdd421242a16992f9e50 Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 20 Jan 2022 08:35:55 +0000 Subject: [PATCH 1879/2365] Update easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb index 98aeeb12b8..7c4a94a649 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb @@ -20,6 +20,10 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] +builddependencies = [ + ('tcsh', '6.22.03'), +] + # support for GCC 8+ on POWER dependencies = [ ('Tcl', '8.6.10'), From dcefd71cbca3ed38683fb6c5fa9c96e0100b85aa Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 20 Jan 2022 08:36:03 +0000 Subject: [PATCH 1880/2365] Update easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb index 7c4a94a649..b938c172e6 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb @@ -29,9 +29,6 @@ dependencies = [ ('Tcl', '8.6.10'), ] -# /bin/csh is required by 'config' script -osdependencies = ['tcsh'] - charm_arch = "multicore-linux-%(arch)s" charm_extra_cxxflags = '-fpermissive' From 4fbdc71259aaf7b877d34c406b623ab39965b363 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Jan 2022 15:01:27 +0000 Subject: [PATCH 1881/2365] add libXfont2 patch to fix build when libbsd is present --- easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb index 041c9f6a6a..d1a9f51ec0 100644 --- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -126,7 +126,12 @@ components = [ 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], }), ('libXfont2', '2.0.4', { # 2019-09-14 - 'checksums': ['74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a'], + 'patches': ['libXfont2-2.0.4_libbsd.patch'], + 'checksums': [ + '74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a', # libXfont2-2.0.4.tar.gz + '5c8d51f9e65d4e9f49c0fb5f82cfbf87b3cf02f67c1dacf6521a56d8ffb1ae91', # libXfont2-2.0.4_libbsd.patch + ], + 'preconfigopts': "autoreconf -i && ", }), ('libXft', '2.3.3', { # 2019-03-16 'checksums': ['3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701'], From 14c3bc15b06d197f0d87b81b3a467cf136a3480a Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 26 Jan 2022 12:56:18 +0000 Subject: [PATCH 1882/2365] xxd builddependencies added (see PR 14846) --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb | 4 ++++ easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb index 3fb97d9ba7..da1d6cc277 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -20,6 +20,10 @@ source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s sources = [SOURCE_TGZ] checksums = ['1ab3153db2010406852b30201ed94112e25eca4c4c8c4b41a29c22a7a3303f96'] +builddependencies = [ + ('xxd', '8.2.4220'), +] + dependencies = [ ('zlib', '1.2.11'), ('GSL', '2.6'), diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb index 05666961bc..efbec7485f 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -18,6 +18,10 @@ source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s sources = [SOURCE_TGZ] checksums = ['b23399a3300ce3ae080e81263274ab8551e00217c3f37cb33cb7e37954fe8572'] +builddependencies = [ + ('xxd', '8.2.4220'), +] + dependencies = [ ('zlib', '1.2.11'), ('GSL', '2.6'), From 532a558a244c78749afa8fb446fe4f3088a4b876 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 26 Jan 2022 13:02:18 +0000 Subject: [PATCH 1883/2365] Changed to GCCcore --- .../x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1248cb3faf --- /dev/null +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +# Last contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'xxd' +version = '8.2.4220' + +homepage = 'https://www.vim.org' +description = """xxd is part of the VIM package and this will only install xxd, not vim! +xxd converts to/from hexdumps of binary files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/vim/vim/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz +] + +start_dir = 'src/xxd' + +files_to_copy = [ + (['xxd'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/xxd'], + 'dirs': [], +} + +moduleclass = 'tools' From 4617fc671173d7bf22981f290de55f74b55fbd2c Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 26 Jan 2022 14:06:11 +0000 Subject: [PATCH 1884/2365] Missing binutils build dependeny added --- easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb index 1248cb3faf..d731b2429f 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb @@ -19,6 +19,10 @@ checksums = [ '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz ] +builddependencies = [ + ('binutils', '2.35'), +] + start_dir = 'src/xxd' files_to_copy = [ From a3eced34fbf518be9136bf1b4d52d90ecb59d210 Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Thu, 27 Jan 2022 18:34:52 +0100 Subject: [PATCH 1885/2365] librsb: add v1.2.0.10/v1.2.0.11/v1.3.0.0 (#14860) --- .../l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb | 29 +++++++++++++++++++ .../l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb | 29 +++++++++++++++++++ .../l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb | 29 +++++++++++++++++++ 3 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb new file mode 100644 index 0000000000..e61290dd63 --- /dev/null +++ b/easybuild/easyconfigs/l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +## +# Author: Michele Martone +## +easyblock = 'ConfigureMake' + +name = 'librsb' +version = '1.2.0.10' + +homepage = 'https://sourceforge.net/projects/librsb/' +description = """A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ec49f3f78a7c43fc9e10976593d100aa49b1863309ed8fa3ccbb7aad52d2f7b8'] + +dependencies = [ + ('zlib', '1.2.11') +] + +configopts = '--enable-openmp --enable-fortran-module-install' + +sanity_check_paths = { + 'files': ['bin/rsbench', 'lib/librsb.a', 'lib/librsb.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb new file mode 100644 index 0000000000..fac25cf212 --- /dev/null +++ b/easybuild/easyconfigs/l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +## +# Author: Michele Martone +## +easyblock = 'ConfigureMake' + +name = 'librsb' +version = '1.2.0.11' + +homepage = 'https://sourceforge.net/projects/librsb/' +description = """A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['0686be29bbe277e227c6021de6bd0564e4fc83f996b787886437d28048057bc8'] + +dependencies = [ + ('zlib', '1.2.11') +] + +configopts = '--enable-openmp --enable-fortran-module-install' + +sanity_check_paths = { + 'files': ['bin/rsbench', 'lib/librsb.a', 'lib/librsb.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..3bdfc0ca85 --- /dev/null +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +## +# Author: Michele Martone +## +easyblock = 'ConfigureMake' + +name = 'librsb' +version = '1.3.0.0' + +homepage = 'https://sourceforge.net/projects/librsb/' +description = """A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2ac8725d1f988f57df9383ae6b0bb2ed221ec935187d31ebb62ea95ee868a790'] + +dependencies = [ + ('zlib', '1.2.11') +] + +configopts = '--enable-openmp --enable-fortran-module-install' + +sanity_check_paths = { + 'files': ['bin/rsbench', 'lib/librsb.a', 'lib/librsb.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 6296a203b603e80b889ced12bf1ee3ceecfa4c6a Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 28 Jan 2022 16:47:46 +0100 Subject: [PATCH 1886/2365] Delete PyOpenCL-2021.1.2-fosscuda-2020b.eb --- .../PyOpenCL-2021.1.2-fosscuda-2020b.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb deleted file mode 100644 index cec1342f8e..0000000000 --- a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PyOpenCL' -version = '2021.1.2' - -homepage = "https://mathema.tician.de/software/pyopencl/" -description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" - -toolchain = {'name': 'fosscuda', 'version': '2020b'} - -dependencies = [ - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('pocl', '1.6'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('appdirs', '1.4.4', { - 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], - }), - ('pytools', '2021.1', { - 'checksums': ['073ae22a0ae946e2db97164f2eb24a599cd3a51430384aa40859dffd73056c40'], - }), - ('pyopencl', version, { - 'checksums': ['18871bc80c5a94869521189cf2c04d72c88367a441a9a033f72f66792ac33d29'], - 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", - }), -] - -moduleclass = 'vis' From 4570d29269cb0869365f1f9ae99f4bb42f850dd1 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 1 Feb 2022 14:39:32 +0100 Subject: [PATCH 1887/2365] ftp/https patch in rsync_from_ncbi.pl is needed --- .../easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb index f24d9c3b21..7069cfa02d 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb @@ -19,11 +19,15 @@ toolchainopts = {'openmp': True, 'cstd': 'c++11'} github_account = 'DerrickWood' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['Kraken2-2.1.1_fix_installation_for_easybuild.patch'] +patches = [ + 'Kraken2-2.1.1_fix_installation_for_easybuild.patch', + 'Kraken2-2.1.2_fix_ncbi_https_server.patch', +] checksums = [ '8f3e928cdb32b9e8e6f55b44703d1557b2a5fc3f30f63e8d16e465e19a81dee4', # v2.1.1.tar.gz # Kraken2-2.1.1_fix_installation_for_easybuild.patch '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11', + '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116', # Kraken2-2.1.2_fix_ncbi_https_server.patch ] dependencies = [ From 804725ad393f8a34eb4e928e85fe94cd36396e7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Feb 2022 08:59:01 +0100 Subject: [PATCH 1888/2365] improve description for xxd Co-authored-by: Alex Domingo --- easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb index d731b2429f..6544bfe789 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb @@ -8,8 +8,7 @@ name = 'xxd' version = '8.2.4220' homepage = 'https://www.vim.org' -description = """xxd is part of the VIM package and this will only install xxd, not vim! -xxd converts to/from hexdumps of binary files.""" +description = "xxd is part of the VIM package and serves to convert to/from hexdumps of binary files." toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From f795a5fc29ce416c928b00d3c1f6e84a66843a42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Feb 2022 09:12:00 +0100 Subject: [PATCH 1889/2365] add custom sanity check command for xxd --- easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb index 6544bfe789..5f89705193 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb @@ -33,4 +33,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"] + moduleclass = 'tools' From 93d563598f90cc226a803c194fa6011762ec6f6b Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Thu, 3 Feb 2022 21:46:42 +0100 Subject: [PATCH 1890/2365] fix: patch configure: it breaks --rebuild librsb-1.3.0.0's librsbpp/configure ended up using librsb's ./librsb-config, which would point to the installation (--prefix) directories, and that is wrong for several reasons; one of them being `eb --rebuild` removing those directories just before `make install`. --- easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb index 3bdfc0ca85..3f3d962933 100644 --- a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -19,6 +19,8 @@ dependencies = [ ('zlib', '1.2.11') ] +preconfigopts = "sed -i 's/export LIBRSB_CONFIG=.*$/export LIBRSB_CONFIG=no;export LIBRSB_CONFIG_VERSION=1.3.0;/g' configure*; sed -i 's/^ true/CPPFLAGS+=\" -I.. -DRSBPP_HAS_RSB_H=1\"/g' librsbpp/configure*;" + configopts = '--enable-openmp --enable-fortran-module-install' sanity_check_paths = { From c9fce3b7f4db94a69be76fab3f585d8d91327ada Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Feb 2022 22:49:39 +0100 Subject: [PATCH 1891/2365] disable building of tests/benchmarks for snappy 1.1.8 to avoid failing build --- easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb index 4397a7c987..3627cd3967 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb @@ -19,7 +19,9 @@ builddependencies = [ ('CMake', '3.18.4'), ] -configopts = ['', '-DBUILD_SHARED_LIBS=ON'] +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] sanity_check_paths = { 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], From d389bbac530c2ef221ec987ea306f42f76b6b281 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Feb 2022 23:06:38 +0100 Subject: [PATCH 1892/2365] disable use of -Werror for recent NSS versions --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 39ccefdf99..8e2acaccc7 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -31,7 +31,7 @@ dependencies = [ parallel = 1 # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" NSS_ENABLE_WERROR=0 ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) From bef95471d490ebb2b3b579392d7235395ded30ad Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Feb 2022 12:33:02 +0100 Subject: [PATCH 1893/2365] add TensorFlow versionsuffix to AlphaFold-2.1.2-foss-2020b.eb --- ...aFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb | 183 ++++++++++++++++++ 1 file changed, 183 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..8b9e592efd --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,183 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.2' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-{}'.format(local_tf_version) + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4', ), + ('Doxygen', '1.8.20', ), + # required for installing dm-tree + ('Bazel', '3.7.2', ), + ('SWIG', '4.0.2', ), +] + +dependencies = [ + ('Python', '3.8.6', ), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1', ), + ('TensorFlow', local_tf_version), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0',), + ('HMMER', '3.3.2',), + ('Kalign', '3.3.1', ), + ('jax', '0.2.19'), # also provides absl-py +] +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.1.2_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '6af91706b2a001494ddc0947f89f8b3d3adfcc26177c373824fe8ea1a58c0b48', # AlphaFold-2.1.2_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +modextravars = { + 'ALPHAFOLD_DATA_DIR': '/scratch/AlphaFold_DBs', # adapt +} + +moduleclass = 'bio' From a7a3f3eca6a194840dd942d776bb064913acfcd6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Feb 2022 12:34:22 +0100 Subject: [PATCH 1894/2365] add TensorFlow versionsuffix to AlphaFold-2.1.2-fosscuda-2020b.eb --- ...d-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb | 183 ++++++++++++++++++ 1 file changed, 183 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..26ae15f4f3 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,183 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.2' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-{}'.format(local_tf_version) + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4', ), + ('Doxygen', '1.8.20', ), + # required for installing dm-tree + ('Bazel', '3.7.2', ), + ('SWIG', '4.0.2', ), +] + +dependencies = [ + ('Python', '3.8.6', ), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1', ), + ('TensorFlow', local_tf_version), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0',), + ('HMMER', '3.3.2',), + ('Kalign', '3.3.1', ), + ('jax', '0.2.19'), # also provides absl-py +] +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.1.2_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '6af91706b2a001494ddc0947f89f8b3d3adfcc26177c373824fe8ea1a58c0b48', # AlphaFold-2.1.2_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +modextravars = { + 'ALPHAFOLD_DATA_DIR': '/scratch/AlphaFold_DBs', # adapt +} + +moduleclass = 'bio' From be05bceabc05c1df99a685f87e49bdeb858f5510 Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Fri, 4 Feb 2022 17:34:04 +0100 Subject: [PATCH 1895/2365] keep preconfigopts setting line within 120 chars --- easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb index 3f3d962933..3596f82d24 100644 --- a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -19,7 +19,8 @@ dependencies = [ ('zlib', '1.2.11') ] -preconfigopts = "sed -i 's/export LIBRSB_CONFIG=.*$/export LIBRSB_CONFIG=no;export LIBRSB_CONFIG_VERSION=1.3.0;/g' configure*; sed -i 's/^ true/CPPFLAGS+=\" -I.. -DRSBPP_HAS_RSB_H=1\"/g' librsbpp/configure*;" +preconfigopts = "sed -i 's/export LIBRSB_CONFIG=.*$/export LIBRSB_CONFIG=no LIBRSB_CONFIG_VERSION=1.3.0;/g' configure*;" +preconfigopts += " sed -i 's/^ true/CPPFLAGS+=\" -I.. -DRSBPP_HAS_RSB_H=1\"/g' librsbpp/configure*;" configopts = '--enable-openmp --enable-fortran-module-install' From fcc183d6ce99f125004fc0bb0967382dc895632a Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Sat, 5 Feb 2022 11:08:20 +0100 Subject: [PATCH 1896/2365] clearer way to force right rsb.h usage Workaround around ./configure and ./librsbpp/configure defects. Thanks to Alex Domingo for mentoring on the specifics of easybuild. --- .../easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb index 3596f82d24..cf1234b9e3 100644 --- a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -19,8 +19,13 @@ dependencies = [ ('zlib', '1.2.11') ] +# workaround to a configure defect manifesting during --rebuild: avoid mistaken detection of already existing librsb installation preconfigopts = "sed -i 's/export LIBRSB_CONFIG=.*$/export LIBRSB_CONFIG=no LIBRSB_CONFIG_VERSION=1.3.0;/g' configure*;" -preconfigopts += " sed -i 's/^ true/CPPFLAGS+=\" -I.. -DRSBPP_HAS_RSB_H=1\"/g' librsbpp/configure*;" + +# workaround to a configure defect manifesting during --rebuild: ensure librsbpp/configure sees and uses root dir rsb.h +local_cppflags = 'CPPFLAGS="${CPPFLAGS} -I%(builddir)s"' +prebuildopts = local_cppflags +preinstallopts = local_cppflags configopts = '--enable-openmp --enable-fortran-module-install' From 702a9d0f9f2b2d379b61f6eeb1dd9d17c4ce4a90 Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Sat, 5 Feb 2022 17:00:38 +0100 Subject: [PATCH 1897/2365] Update easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb Do not rely on `librsb-config --I_opts`, it will inject paths in install dir (suggested by Alex Domingo) Co-authored-by: Alex Domingo --- .../l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb index cf1234b9e3..41f09407b0 100644 --- a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -15,17 +15,17 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2ac8725d1f988f57df9383ae6b0bb2ed221ec935187d31ebb62ea95ee868a790'] +builddependencies = [ + ('Autotools', '20200321'), +] + dependencies = [ ('zlib', '1.2.11') ] -# workaround to a configure defect manifesting during --rebuild: avoid mistaken detection of already existing librsb installation -preconfigopts = "sed -i 's/export LIBRSB_CONFIG=.*$/export LIBRSB_CONFIG=no LIBRSB_CONFIG_VERSION=1.3.0;/g' configure*;" - -# workaround to a configure defect manifesting during --rebuild: ensure librsbpp/configure sees and uses root dir rsb.h -local_cppflags = 'CPPFLAGS="${CPPFLAGS} -I%(builddir)s"' -prebuildopts = local_cppflags -preinstallopts = local_cppflags +# do not rely on `librsb-config --I_opts`, it will inject paths in install dir +preconfigopts = "sed -i '21,22d' librsbpp/configure.ac && " +preconfigopts += "autoreconf -fi &&" configopts = '--enable-openmp --enable-fortran-module-install' From e9d1369d8373dbeb85a38242b523f527406fa272 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 6 Feb 2022 16:11:42 +0000 Subject: [PATCH 1898/2365] adding easyconfigs: nvtop-1.2.2-GCCcore-10.2.0.eb, nvtop-1.2.2-GCCcore-10.3.0.eb --- .../n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c047696132 --- /dev/null +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'nvtop' +version = '1.2.2' + +homepage = 'https://github.com/Syllo/nvtop' +description = 'htop-like GPU usage monitor' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/Syllo/nvtop/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d6ca7f467cc1048ebd1ebf7add753650c5d7c8868752c0c57ed2c85df62f5810'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +# Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency. +dependencies = [ + ('ncurses', '6.2'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/nvtop'], + 'dirs': [], +} + +sanity_check_commands = ["nvtop --help"] + +moduleclass = 'tools' From eed21df1f823b059211d5a902b04f3e825d7cddf Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Mon, 7 Feb 2022 17:36:44 +0000 Subject: [PATCH 1899/2365] Remove CUDA dependency --- easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb index d8de7f1805..5d464d98c1 100644 --- a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb @@ -17,15 +17,13 @@ builddependencies = [ ('CMake', '3.18.4'), ] +# Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency. dependencies = [ - ('CUDAcore', '11.1.1', '', True), ('ncurses', '6.2'), ] separate_build_dir = True -configopts = '-DNVML_INCLUDE_DIRS=$EBROOTCUDA/include -DNVML_LIBRARIES=$EBROOTCUDA/lib64/stubs/libnvidia-ml.so' - sanity_check_paths = { 'files': ['bin/nvtop'], 'dirs': [], From c652a04b7d2e68df2b4ead26a2d69aa6aa887529 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Feb 2022 11:51:32 +0100 Subject: [PATCH 1900/2365] consistently apply patch for mapDamage 2.2.1 to use external seqtk --- .../m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb index a949307ab3..e59fa99490 100644 --- a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb @@ -15,7 +15,11 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c'] +patches = ['%(name)s-2.2.1_use-external-seqtk.patch'] +checksums = [ + 'f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c', # 2.2.1.tar.gz + 'f01a90c29123460f8cb6ba2fe0f42e9ec66b0febff430d4ec4f0ab1197c552e7', # mapDamage-2.2.1_use-external-seqtk.patch +] dependencies = [ ('Python', '3.8.6'), From d0e19015c45bd83baf66c1ea7d8480229efbf217 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 8 Feb 2022 11:14:32 +0000 Subject: [PATCH 1901/2365] Fix name templating in source urls --- .../easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb index 1d6a13798f..0dda15cefb 100644 --- a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ 'https://cran.r-project.org/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', ] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'] From a00e582f00a2e0d7dc3c383e986a8313bb37ed56 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 13 Feb 2022 12:18:42 +0000 Subject: [PATCH 1902/2365] avoid pollution in the tmp directory when running the AlphaFold tests --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index d7f3a32793..bd80f4af1c 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -78,7 +78,8 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', - 'AlphaFold-2.0.1_relax_gpu.patch' + 'AlphaFold-2.0.1_relax_gpu.patch', + 'AlphaFold-2.1_fix-alphafold-tests.patch', ], 'checksums': [ '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz @@ -89,6 +90,7 @@ components = [ '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch + '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', # AlphaFold-2.1_fix-alphafold-tests.patch ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From 78a8676d46d3fdf9b1338104734a70b1f89d9dd5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 13 Feb 2022 12:32:00 +0000 Subject: [PATCH 1903/2365] line length --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index bd80f4af1c..458badb2a7 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -90,7 +90,8 @@ components = [ '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch - '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', # AlphaFold-2.1_fix-alphafold-tests.patch + # AlphaFold-2.1_fix-alphafold-tests.patch + '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From 0b9a12166cb1fe292f0b01ec8882c0c955375316 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 15 Feb 2022 11:00:58 +0000 Subject: [PATCH 1904/2365] reference upstream issue in patch --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index 458badb2a7..1cff76362a 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -91,7 +91,7 @@ components = [ '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch # AlphaFold-2.1_fix-alphafold-tests.patch - '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From b8130935fb59f5ea4265ba458282b6296cfc6de1 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 16 Feb 2022 10:22:09 +0100 Subject: [PATCH 1905/2365] Update easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb index 26ae15f4f3..7400f8d4a0 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -80,6 +80,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.1_fix-alphafold-tests.patch', ], 'checksums': [ 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz From 6228e58619523e355c0a823f187368e18a977a37 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 16 Feb 2022 10:22:32 +0100 Subject: [PATCH 1906/2365] Update easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb index 7400f8d4a0..15061d7ae7 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -90,6 +90,8 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + # AlphaFold-2.1_fix-alphafold-tests.patch + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From 552d543935f0ea188d7b89d0f4f12ee6913fd1b8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 16 Feb 2022 10:22:56 +0100 Subject: [PATCH 1907/2365] Update easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb index 8b9e592efd..2f7e104ba0 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb @@ -89,6 +89,8 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + # AlphaFold-2.1_fix-alphafold-tests.patch + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From 7f23c55b675e4e31f686eccdb56ba1b352b2412f Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 16 Feb 2022 10:23:19 +0100 Subject: [PATCH 1908/2365] Update easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb index 2f7e104ba0..8a7378e0a4 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb @@ -80,6 +80,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.1_fix-alphafold-tests.patch', ], 'checksums': [ 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz From d8ebb1087ea964236fb1ebc87e03c810f7f955aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Feb 2022 13:36:19 +0100 Subject: [PATCH 1909/2365] minor style tweaks + set missing environment variables for AlphaFold 2.1.2 easyconfigs using foss(cuda)/2020b toolchain --- ...aFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb | 19 +++++++------- ...d-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb | 25 ++++++++++++------- 2 files changed, 26 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb index 8a7378e0a4..c9603b16d6 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'AlphaFold' version = '2.1.2' local_tf_version = '2.5.0' -versionsuffix = '-TensorFlow-{}'.format(local_tf_version) +versionsuffix = '-TensorFlow-%s' % local_tf_version homepage = 'https://deepmind.com/research/case-studies/alphafold' description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" @@ -12,24 +12,25 @@ toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.18.4', ), - ('Doxygen', '1.8.20', ), + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), # required for installing dm-tree - ('Bazel', '3.7.2', ), - ('SWIG', '4.0.2', ), + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), ] dependencies = [ - ('Python', '3.8.6', ), + ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('PyYAML', '5.3.1', ), + ('PyYAML', '5.3.1'), ('TensorFlow', local_tf_version), ('Biopython', '1.78'), ('HH-suite', '3.3.0',), ('HMMER', '3.3.2',), - ('Kalign', '3.3.1', ), + ('Kalign', '3.3.1'), ('jax', '0.2.19'), # also provides absl-py ] + local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " @@ -180,7 +181,7 @@ modextrapaths = { } modextravars = { - 'ALPHAFOLD_DATA_DIR': '/scratch/AlphaFold_DBs', # adapt + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb index 15061d7ae7..2dcc49bc3a 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'AlphaFold' version = '2.1.2' local_tf_version = '2.5.0' -versionsuffix = '-TensorFlow-{}'.format(local_tf_version) +versionsuffix = '-TensorFlow-%s' % local_tf_version homepage = 'https://deepmind.com/research/case-studies/alphafold' description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" @@ -12,24 +12,25 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.18.4', ), - ('Doxygen', '1.8.20', ), + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), # required for installing dm-tree - ('Bazel', '3.7.2', ), - ('SWIG', '4.0.2', ), + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), ] dependencies = [ - ('Python', '3.8.6', ), + ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('PyYAML', '5.3.1', ), + ('PyYAML', '5.3.1'), ('TensorFlow', local_tf_version), ('Biopython', '1.78'), ('HH-suite', '3.3.0',), ('HMMER', '3.3.2',), - ('Kalign', '3.3.1', ), + ('Kalign', '3.3.1'), ('jax', '0.2.19'), # also provides absl-py ] + local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " @@ -180,7 +181,13 @@ modextrapaths = { } modextravars = { - 'ALPHAFOLD_DATA_DIR': '/scratch/AlphaFold_DBs', # adapt + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt + # these allow to make predictions on proteins that would typically be too long to fit into GPU memory; + # see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', + # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 + 'OPENMM_RELAX': 'CUDA', } moduleclass = 'bio' From eaeedf09f642f9c964e5e35a978084556efdf268 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 17 Feb 2022 17:04:08 +0000 Subject: [PATCH 1910/2365] disable building of documentation for DBus 1.13.18 --- easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb index 83b477ea36..b049fce156 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb @@ -29,7 +29,9 @@ dependencies = [ ('expat', '2.2.9'), ] -configopts = '--without-systemdsystemunitdir' +configopts = '--with-systemdsystemunitdir=no ' +# disable documentation +configopts += '--disable-xml-docs --disable-doxygen-docs --disable-ducktype-docs' sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in From 3b6209c4ad5814eee563e87142be9af4c154a299 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 14:59:59 +0100 Subject: [PATCH 1911/2365] Update OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb --- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb index 739dde4021..d97ead0d86 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb @@ -7,13 +7,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From 18523e3de58bc37cecfa899c643987e296e2487a Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:02:21 +0100 Subject: [PATCH 1912/2365] Update OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb --- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb index 94f086b13d..270c18b7eb 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb @@ -7,13 +7,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From 106c837d2c66eb4c75beade3ee7dba4d9de7d24c Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:03:14 +0100 Subject: [PATCH 1913/2365] Update OSU-Micro-Benchmarks-5.7-gompi-2020b.eb --- .../OSU-Micro-Benchmarks-5.7-gompi-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb index 7df7a5b835..8d4a54aa05 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb @@ -10,13 +10,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From 8dd9029c4a040ae7dca99ba16d5c3859ca3abbf8 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:03:35 +0100 Subject: [PATCH 1914/2365] Update OSU-Micro-Benchmarks-5.7-gompic-2020b.eb --- .../OSU-Micro-Benchmarks-5.7-gompic-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb index 1dd7a5a6e6..90d4b73806 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb @@ -10,13 +10,13 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompic', 'version': '2020b'} +toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] -configopts = 'CC="$MPICC" CXX="$MPICC"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA' local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] From 11c8864fe214ac9a947db553f1dd83f09e02fe66 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:03:50 +0100 Subject: [PATCH 1915/2365] Update OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb --- .../OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb index a1e5881a08..fed8129584 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb @@ -10,13 +10,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From 7e70eac15b3b5477240eccb1ee8abe570493e9df Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 24 Feb 2022 19:27:10 +0100 Subject: [PATCH 1916/2365] Update LAPACK-3.9.1-GCC-10.2.0.eb The original URL was failing --- easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb index 3990b2cebe..14d4bb284c 100644 --- a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb @@ -9,7 +9,7 @@ description = """LAPACK is written in Fortran90 and provides routines for solvin toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/Reference-LAPACK/lapack/archive/'] +source_urls = ['https://github.com/Reference-LAPACK/lapack/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] checksums = ['d0085d2caf997ff39299c05d4bacb6f3d27001d25a4cc613d48c1f352b73e7e0'] From fc56b85d62e4f48be3e0228352f45e33630e3809 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Feb 2022 21:33:47 +0100 Subject: [PATCH 1917/2365] add patch to fix linking error for imread extension in scikit-image easyconfigs using intel toolchain --- .../s/scikit-image/scikit-image-0.18.1-intel-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb index d92ee21ee4..e72dbff85f 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb @@ -28,7 +28,11 @@ exts_list = [ 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], }), ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + 'patches': ['imread-0.7.1_fix-library-order.patch'], + 'checksums': [ + '0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f', # imread-0.7.4.tar.gz + '0702321112ddcc1e6b98dc0a20eed8f93e5ee271304e2a6dc26d64ea83bddedf', # imread-0.7.1_fix-library-order.patch + ], }), ('pooch', '1.3.0', { 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], From 37444e79f479c7586215b7853beb08b08d68a3c8 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Sat, 5 Mar 2022 17:32:45 +0100 Subject: [PATCH 1918/2365] Adding matplotlib-inline-0.1.3-GCCcore-10.2.0.eb --- .../matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..87dc05503d --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'matplotlib-inline' +version = '0.1.3' + +homepage = 'https://github.com/ipython/matplotlib-inline' +description = """Matplotlib Inline Back-end for IPython and Jupyter.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a04bfba22e0d1395479f866853ec1ee28eea1485c1d69a6faf00dc3e24ff34ee'] + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), # has traitlets +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use matplotlib-inline backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'module://matplotlib_inline.backend_inline'} + +moduleclass = 'vis' From 112d56952734fa3cd03212fb2044a98b9e0eb19f Mon Sep 17 00:00:00 2001 From: Zdenek Date: Sat, 5 Mar 2022 18:07:35 +0100 Subject: [PATCH 1919/2365] Removing comment --- .../matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb index 87dc05503d..31aab81115 100644 --- a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ checksums = ['a04bfba22e0d1395479f866853ec1ee28eea1485c1d69a6faf00dc3e24ff34ee'] dependencies = [ ('Python', '3.8.6'), - ('IPython', '7.18.1'), # has traitlets + ('IPython', '7.18.1'), ] use_pip = True From e71f73d401db926ad0f79e26f4a4071f05b3d421 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Sat, 5 Mar 2022 18:32:03 +0100 Subject: [PATCH 1920/2365] Trying with binutils in builddeps --- .../matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb index 31aab81115..bc21d00bf0 100644 --- a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -11,9 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} sources = [SOURCELOWER_TAR_GZ] checksums = ['a04bfba22e0d1395479f866853ec1ee28eea1485c1d69a6faf00dc3e24ff34ee'] +builddependencies = [('binutils', '2.35')] + dependencies = [ ('Python', '3.8.6'), - ('IPython', '7.18.1'), + ('IPython', '7.18.1'), # has traitlets ] use_pip = True From 3a9ecc99c6582886e53e5b7fb10d0c289c6dc4aa Mon Sep 17 00:00:00 2001 From: Zdenek Date: Sat, 5 Mar 2022 19:29:49 +0100 Subject: [PATCH 1921/2365] Spaces before inline comment --- .../matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb index bc21d00bf0..5d1e53c412 100644 --- a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -15,7 +15,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '3.8.6'), - ('IPython', '7.18.1'), # has traitlets + ('IPython', '7.18.1'), # has traitlets ] use_pip = True From b5fb86d022e8daa0747b584bd66036a3687ced05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Mar 2022 16:38:02 +0100 Subject: [PATCH 1922/2365] adding easyconfigs: BUSCO-4.0.6-foss-2020b.eb --- .../b/BUSCO/BUSCO-4.0.6-foss-2020b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb new file mode 100644 index 0000000000..48d0a53aeb --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb @@ -0,0 +1,54 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'BUSCO' +version = '4.0.6' + +homepage = 'https://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['bad1c1cb52950d991eb771eb9f3a78cf0bebb861e3b806320ee8cbe4cfbd75ea'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for pandas + ('R', '4.0.3'), + ('Biopython', '1.78'), + ('BLAST+', '2.11.0'), + ('HMMER', '3.3.2'), + ('prodigal', '2.6.3'), + ('AUGUSTUS', '3.4.0'), + ('SEPP', '4.4.0'), + ('MetaEuk', '4'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/test_data %(installdir)s', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s', +] + +sanity_check_paths = { + 'files': ['bin/busco', 'bin/generate_plot.py'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages/busco'] +} + +sanity_check_commands = [ + "busco --help", + "busco -i %(installdir)s/test_data/bacteria/genome.fna --mode geno --out test_bacteria.out", + "busco -i %(installdir)s/test_data/eukaryota/genome.fna --mode geno --out test_eukaryota.out", +] + +moduleclass = 'bio' From ecb0d02cd1fe1619b2e53023bb1fdac731efbf3c Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Tue, 8 Mar 2022 21:52:19 +0100 Subject: [PATCH 1923/2365] adding easyconfigs: matplotlib-3.5.1-foss-2020b.eb, matplotlib-3.5.1-intel-2020b.eb --- .../matplotlib/matplotlib-3.5.1-foss-2020b.eb | 65 +++++++++++++++++++ .../matplotlib-3.5.1-intel-2020b.eb | 65 +++++++++++++++++++ 2 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb new file mode 100644 index 0000000000..2d5f0cfade --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.1' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template > mplsetup.cfg && " + + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + ('fontTools', '4.29.1', { + 'modulename' : 'fontTools', + 'source_tmpl': 'fonttools-%(version)s.zip', + 'checksums': ['2b18a172120e32128a80efee04cff487d5d140fe7d817deb648b2eee023a40e4'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'checksums': ['b2e9810e09c3a47b73ce9cab5a72243a1258f61e7900969097a817232246ce1c'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb new file mode 100644 index 0000000000..832416adda --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.1' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template > mplsetup.cfg && " + + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + ('fontTools', '4.29.1', { + 'modulename' : 'fontTools', + 'source_tmpl': 'fonttools-%(version)s.zip', + 'checksums': ['2b18a172120e32128a80efee04cff487d5d140fe7d817deb648b2eee023a40e4'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'checksums': ['b2e9810e09c3a47b73ce9cab5a72243a1258f61e7900969097a817232246ce1c'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From e70a76df583088ecaacc571656f5649e6b3f6395 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 9 Mar 2022 08:33:48 +0000 Subject: [PATCH 1924/2365] set XLA_PYTHON_CLIENT_ALLOCATOR=platform in jax CUDA easyconfigs --- easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index d14b441c64..f138187813 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -110,13 +110,13 @@ exts_list = [ 'a431ce1b6588b5098872f36575dc2c5023b1010760bf6aaa889125c9a09227b0', ], # deliberately not testing in parallel, as that results in (additional) failing tests; - # use XLA_PYTHON_CLIENT_ALLOCATOR=platform when running GPU tests in parallel, - # to avoid each test fully allocating the GPU memory..., + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, # see https://github.com/google/jax/issues/7323 and # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; - 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests", + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + "JAX_ENABLE_X64=true pytest tests", }), ] From 63b92be0512f4dbc5b9212863c787c96098483a2 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 9 Mar 2022 11:18:51 +0100 Subject: [PATCH 1925/2365] Removing MPLBACKEND=module://matplotlib_inline.backend_inline --- .../matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb index 5d1e53c412..0cbbd4ffc6 100644 --- a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -22,8 +22,4 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -# use matplotlib-inline backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'module://matplotlib_inline.backend_inline'} - moduleclass = 'vis' From b100b49ef2b3a4177355c5cbc0a96e6f31108669 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Thu, 10 Mar 2022 09:53:36 +0100 Subject: [PATCH 1926/2365] Fix whitespace style --- .../easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb | 2 +- .../easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb index 2d5f0cfade..b369894467 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb @@ -43,7 +43,7 @@ exts_list = [ 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), ('fontTools', '4.29.1', { - 'modulename' : 'fontTools', + 'modulename': 'fontTools', 'source_tmpl': 'fonttools-%(version)s.zip', 'checksums': ['2b18a172120e32128a80efee04cff487d5d140fe7d817deb648b2eee023a40e4'], }), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb index 832416adda..0d03bf7e8c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb @@ -43,7 +43,7 @@ exts_list = [ 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), ('fontTools', '4.29.1', { - 'modulename' : 'fontTools', + 'modulename': 'fontTools', 'source_tmpl': 'fonttools-%(version)s.zip', 'checksums': ['2b18a172120e32128a80efee04cff487d5d140fe7d817deb648b2eee023a40e4'], }), From f4067e4c954fa69718519470032a8c0faaf61b11 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 10 Mar 2022 14:03:50 -0800 Subject: [PATCH 1927/2365] add rMATS_P cli tools --- .../easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb index c4ab2d228d..41bc0020a7 100644 --- a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb @@ -33,7 +33,7 @@ components = [ 'easyblock': 'MakeCp', 'start_dir': 'rmats-turbo-%(version)s/rMATS_C', 'buildopts': "%s" % local_buildopts, - 'files_to_copy': [(['rMATSexe', '../rmats.py'], 'bin')], + 'files_to_copy': [(['rMATSexe', '../rmats.py', '../rMATS_C', '../rMATS_R', '../rMATS_P'], 'bin')] }), ('rmats-turbo-python', version, { 'easyblock': 'PythonPackage', From 6518309282ffb3aa64b9874ce52caa2c5172e19a Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Fri, 11 Mar 2022 21:00:40 +0100 Subject: [PATCH 1928/2365] Add Qhull dependency although it will link system Qhull if available --- .../easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb | 1 + .../easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb index b369894467..7069e0d149 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb @@ -21,6 +21,7 @@ dependencies = [ ('freetype', '2.10.3'), ('Tkinter', '%(pyver)s'), ('Pillow', '8.0.1'), + ('Qhull', '2020.2') ] use_pip = True diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb index 0d03bf7e8c..0c81a702dd 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb @@ -21,6 +21,7 @@ dependencies = [ ('freetype', '2.10.3'), ('Tkinter', '%(pyver)s'), ('Pillow', '8.0.1'), + ('Qhull', '2020.2') ] use_pip = True From 23f42814ba2a2adc4646dc0943d0ba585731dbc8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Mar 2022 10:30:25 +0100 Subject: [PATCH 1929/2365] set $HTSLIB_DIR when configuring build of Bio-DB-HTS to ensure that HTSlib dependency is picked up --- .../easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb index 147bdf54a2..124fad4ecb 100644 --- a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb @@ -20,6 +20,8 @@ dependencies = [ ('HTSlib', '1.11'), ] +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + options = {'modulename': 'Bio::DB::HTS'} sanity_check_paths = { From f539df50d14913febbe76e187cc4cc427e634947 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 21 Mar 2022 17:02:27 +0100 Subject: [PATCH 1930/2365] Cleanup PSolver and futile easyconfigs and add dynamic libs. --- .../f/futile/futile-1.8.3-foss-2020b.eb | 27 ++++++++++++------ .../f/futile/futile-1.8.3-intel-2020b.eb | 25 +++++++++++------ .../p/PSolver/PSolver-1.8.3-foss-2020b.eb | 28 +++++++++++-------- .../p/PSolver/PSolver-1.8.3-intel-2020b.eb | 27 ++++++++++-------- 4 files changed, 67 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb index 6648c32dd2..3b00140697 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb @@ -10,27 +10,36 @@ description = """ """ toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] -checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] +patches = ['futile_index_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '5ef5f8ad7644259da0d2d2bcb64c44b923cb64b1eedf03898d0da18228ea392f', # futile_index_bug.patch +] unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" start_dir = "futile-%(version)s" -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCLAGS -fallow-argument-mismatch" ' -configopts += '--enable-mpi ' -configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' -configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' -configopts += '--with-yaml-path=$EBROOTLIBYAML ' +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libyaml', '0.2.5'), +] + +preconfigopts = 'export FCFLAGS="$FCLAGS -fallow-argument-mismatch" && ' -dependencies = [('libyaml', '0.2.5')] +configopts = '--enable-dynamic-libraries ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' sanity_check_paths = { 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + - [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + ['lib/libfutile-1.a', 'lib/libfutile-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb index 318f3bb9b9..a06c36e332 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb @@ -10,13 +10,17 @@ description = """ """ toolchain = {'name': 'intel', 'version': '2020b'} -toolchainopts = {'usempi': True} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] -patches = ['futile_intel_bug.patch'] +patches = [ + 'futile_index_bug.patch', + 'futile_intel_bug.patch', +] checksums = [ '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '5ef5f8ad7644259da0d2d2bcb64c44b923cb64b1eedf03898d0da18228ea392f', # futile_index_bug.patch 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch ] @@ -24,17 +28,20 @@ unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 & unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" start_dir = "futile-%(version)s" -configopts = 'CC=$MPICC FC=$MPIFC ' -configopts += '--enable-mpi ' -configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' -configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' -configopts += '--with-yaml-path=$EBROOTLIBYAML ' +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libyaml', '0.2.5'), +] -dependencies = [('libyaml', '0.2.5')] +configopts = '--enable-dynamic-libraries ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' sanity_check_paths = { 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + - [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + ['lib/libfutile-1.a', 'lib/libfutile-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb index 34640f7529..f0a3a90c1f 100644 --- a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb @@ -9,29 +9,35 @@ description = """ """ toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True, 'opt': True} +toolchainopts = {'pic': True, 'usempi': True, 'opt': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] -local_cddir = ' cd psolver-%(version_major_minor)s && ' -preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I$EBROOTFUTILE/include" ' -configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ - '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' -configopts += ' --with-mpi3 ' -prebuildopts = local_cddir -preinstallopts = local_cddir +builddependencies = [ + ('pkg-config', '0.29.2'), +] dependencies = [ ('libyaml', '0.2.5'), - ('futile', '1.8.3') + ('futile', '1.8.3'), ] +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +preconfigopts += 'export FCFLAGS="$FCFLAGS -fallow-argument-mismatch" && ' + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-futile-incs=-I$EBROOTFUTILE/include ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' + +prebuildopts = local_cddir +preinstallopts = local_cddir + sanity_check_paths = { 'files': ['include/poisson_solver.mod'] + - [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + ['lib/libPSolver-1.a', 'lib/libPSolver-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb index df8ca360b5..beb8698e91 100644 --- a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb @@ -9,29 +9,34 @@ description = """ """ toolchain = {'name': 'intel', 'version': '2020b'} -toolchainopts = {'usempi': True, 'opt': True} +toolchainopts = {'pic': True, 'usempi': True, 'opt': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] -local_cddir = ' cd psolver-%(version_major_minor)s && ' -preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -I$EBROOTFUTILE/include" ' -configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ - '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' -configopts += ' --with-mpi3 ' -prebuildopts = local_cddir -preinstallopts = local_cddir +builddependencies = [ + ('pkg-config', '0.29.2'), +] dependencies = [ ('libyaml', '0.2.5'), - ('futile', '1.8.3') + ('futile', '1.8.3'), ] +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-futile-incs=-I$EBROOTFUTILE/include ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' + +prebuildopts = local_cddir +preinstallopts = local_cddir + sanity_check_paths = { 'files': ['include/poisson_solver.mod'] + - [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + ['lib/libPSolver-1.a', 'lib/libPSolver-1.%s' % SHLIB_EXT], 'dirs': [] } From 16ff75971cd718ba5e26572cce7eff254d306556 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 22 Mar 2022 13:07:49 +0100 Subject: [PATCH 1931/2365] raise likwid to GCC/intel-compiler level due to Fortran modules usage. --- .../l/likwid/likwid-5.2.0-GCC-10.2.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..7e6a0d4e6b --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_EB_hwloc.patch', +] +checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] + +builddependencies = [ + ('Perl', '5.32.0'), +] + +dependencies = [ + ('hwloc', '2.2.0'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' From be81da0554baab3d20c8e27108a3b53abcc775c5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 22 Mar 2022 13:41:46 +0100 Subject: [PATCH 1932/2365] add likwid for intel-compilers/iccifort, and fix typo in others --- .../l/likwid/likwid-5.2.0-GCC-10.2.0.eb | 3 +- .../likwid-5.2.0-iccifort-2020.4.304.eb | 51 +++++++++++++++++++ 2 files changed, 53 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb index 7e6a0d4e6b..a6b230f13e 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb @@ -39,7 +39,8 @@ prebuildopts += """ make/include_GCC.mk && """ buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' buildopts += 'FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' maxparallel = 1 diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..9fbbc61c89 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_EB_hwloc.patch', +] +checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] + +builddependencies = [ + ('Perl', '5.32.0'), +] + +dependencies = [ + ('hwloc', '2.2.0'), +] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'COMPILER=ICC FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' From 523613b7b7c81db85a22b0b1b63605c6d7dcf390 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 22 Mar 2022 16:41:58 +0100 Subject: [PATCH 1933/2365] add missing checksums. --- easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb | 5 ++++- .../easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb index a6b230f13e..c723d1fccb 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb @@ -19,7 +19,10 @@ sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_use_EB_hwloc.patch', ] -checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] +checksums = [ + 'aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0', # v5.2.0.tar.gz + '76ef41001efcdd107e34e2833325ffa876b8ac526740301ae9bace91150cfb8f', # likwid-5.2.0_use_EB_hwloc.patch +] builddependencies = [ ('Perl', '5.32.0'), diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb index 9fbbc61c89..e2774c4ac8 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb @@ -19,7 +19,10 @@ sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_use_EB_hwloc.patch', ] -checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] +checksums = [ + 'aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0', # v5.2.0.tar.gz + '76ef41001efcdd107e34e2833325ffa876b8ac526740301ae9bace91150cfb8f', # likwid-5.2.0_use_EB_hwloc.patch +] builddependencies = [ ('Perl', '5.32.0'), From fc42130fc9cfa3818c83c9011e37406d947682fb Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 23 Mar 2022 14:33:33 +0000 Subject: [PATCH 1934/2365] xxd added to these PLUMED versions as well --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb index 16200c8e59..86b9edfe39 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb @@ -20,6 +20,10 @@ source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s sources = [SOURCE_TGZ] checksums = ['1ab3153db2010406852b30201ed94112e25eca4c4c8c4b41a29c22a7a3303f96'] +builddependencies = [ + ('xxd', '8.2.4220'), +] + dependencies = [ ('zlib', '1.2.11'), ('GSL', '2.6'), From 419587fdb13606b45d7b2896d5d5ea6d5a5deb58 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 24 Mar 2022 14:41:59 +0000 Subject: [PATCH 1935/2365] Add postinstallcmds to copy scripts directory to installdir --- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 734f106ab1..2c9468819f 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -49,9 +49,13 @@ preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|fileve preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = {'PATH': ['scripts']} + sanity_check_paths = { 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': [], + 'dirs': ['bin', 'lib', 'scripts'], } sanity_check_commands = ["vcfremap"] From 8a0ad15a41c420a5010b6c6f9e8224cea0104a92 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 24 Mar 2022 22:10:42 +0200 Subject: [PATCH 1936/2365] adding easyconfigs: PyFrag-2019-20220216-intel-2020b-ASA.eb and patches: PyFrag-2019_fix_flaky_input_fetch.patch --- .../PyFrag-2019-20220216-intel-2020b-ASA.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb diff --git a/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb b/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb new file mode 100644 index 0000000000..0a8957eac4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb @@ -0,0 +1,52 @@ +easyblock = 'Tarball' + +name = 'PyFrag' +version = '2019-20220216' +versionsuffix = '-ASA' +_commit = '5618d5518a8f4a1fc22805feac57b6e6717a08dc' + +homepage = 'https://pyfragdocument.readthedocs.io/en/latest/includeme.html' +description = """ +PyFrag 2019 resolves three main challenges associated with the automatized computational exploration of reaction +mechanisms: 1) the management of multiple parallel calculations to automatically find a reaction path; 2) the monitoring +of the entire computational process along with the extraction and plotting of relevant information from large amounts of +data; and 3) the analysis and presentation of these data in a clear and informative way. + +This module provides the Activation Strain Analysis (ASA) Module of PyFrag 2019 +""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +github_account = 'sunxb05' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%s.tar.gz' % _commit] +patches = ['PyFrag-2019_fix_flaky_input_fetch.patch'] +checksums = [ + # 5618d5518a8f4a1fc22805feac57b6e6717a08dc.tar.gz + 'b987a94c21ddc828167209be3439f13d4f284c56aeb672f8f0bf4c8ae8b25e67', + 'f93f5496caa75fe8886f03605f82b8520842c6b99abbaf4ad830f78b616bfe48', # PyFrag-2019_fix_flaky_input_fetch.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('dill', '0.3.3'), +] + +start_dir = 'host' + +# for PBS based schedulers: +# postinstallcmds = ["sed -i 's/sbatch/qsub/' %(installdir)s/bin/adf.sh"] + +sanity_check_paths = { + 'files': ['bin/pyfrag'], + 'dirs': ['argueparce', 'result', 'standalone'], +} + +sanity_check_commands = ['pyfrag -h | grep "^Usage:"'] + +modextrapaths = { + 'HOSTPYFRAG': '', +} + +moduleclass = 'chem' From 1a42bd1f0864eeb44e7ecfb8b897e20ce800b858 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 25 Mar 2022 00:35:49 +0200 Subject: [PATCH 1937/2365] fix checksum of PyFrag-2019_fix_flaky_input_fetch.patch --- .../p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb b/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb index 0a8957eac4..a9df7f318e 100644 --- a/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb +++ b/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb @@ -24,7 +24,7 @@ patches = ['PyFrag-2019_fix_flaky_input_fetch.patch'] checksums = [ # 5618d5518a8f4a1fc22805feac57b6e6717a08dc.tar.gz 'b987a94c21ddc828167209be3439f13d4f284c56aeb672f8f0bf4c8ae8b25e67', - 'f93f5496caa75fe8886f03605f82b8520842c6b99abbaf4ad830f78b616bfe48', # PyFrag-2019_fix_flaky_input_fetch.patch + 'bb47a31f14329f5ccb7b58e03ce4bde133739acccc76e65ca0e1d69a8ac3694e', # PyFrag-2019_fix_flaky_input_fetch.patch ] dependencies = [ From 9e177178e20b75eff97f6ac7153c2035f3267714 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 29 Mar 2022 11:59:40 +0100 Subject: [PATCH 1938/2365] Remove extraneous bin, lib directory sanity checks --- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 2c9468819f..80eb772517 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -55,7 +55,7 @@ modextrapaths = {'PATH': ['scripts']} sanity_check_paths = { 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': ['bin', 'lib', 'scripts'], + 'dirs': ['scripts'], } sanity_check_commands = ["vcfremap"] From 14eed3d5d57479a7b486caf428fa11f2107b18c7 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 29 Mar 2022 15:42:40 +0100 Subject: [PATCH 1939/2365] Fix linking of vcflib shared library --- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 734f106ab1..2692dd43c0 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -14,7 +14,10 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['vcflib-1.0.2_use-external-deps.patch'] +patches = [ + 'vcflib-1.0.2_use-external-deps.patch', + 'vcflib-1.0.2_fix-shared-linking.patch', +] checksums = [ 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch From 226b08c7a20276b9e0242e06642faeec798d1a30 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 29 Mar 2022 15:44:28 +0100 Subject: [PATCH 1940/2365] Checksums --- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 2692dd43c0..2047f76e3d 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -21,6 +21,7 @@ patches = [ checksums = [ 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch + '3904fb7ad5d144bf1b6500c985c84c15a5e4ba5299763628de7965cb4efa97f7', # vcflib-1.0.2_fix-shared-linking.patch ] builddependencies = [ From e701980a105c48ebe441a6524433f9a32f7205e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2022 09:45:39 +0200 Subject: [PATCH 1941/2365] fix failing sanity check for PRINSEQ --- .../p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb index c2fccb2c6a..d0822cc92c 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb @@ -24,6 +24,9 @@ dependencies = [ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") +# prevent that sanity check requires PRINSEQ itself to be available as a Perl module +options = {'modulename': False} + exts_list = [ ('ExtUtils::Depends', '0.8001', { 'source_tmpl': 'ExtUtils-Depends-%(version)s.tar.gz', From 3fe9d1f547b900cafd695695eb7bbf0fff7dcb1c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 1 Apr 2022 12:13:14 +0100 Subject: [PATCH 1942/2365] also use x.py to build/install other recent Rust easyconfigs --- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index d9802f22e0..eaec7699da 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -34,6 +34,12 @@ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " # since Rust is a build dependency for cryptography that is included with Python configopts += "--set=llvm.ninja=false " +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + # avoid failure when home directory is an NFS mount, # see https://github.com/rust-lang/cargo/issues/6652 prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " From 9b07f3f995211f89de546de7789652f9924f06c3 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 4 Apr 2022 10:19:48 +0900 Subject: [PATCH 1943/2365] adding easyconfigs: EigenExa-2.11-intel-2020b.eb --- .../e/EigenExa/EigenExa-2.11-intel-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb b/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb new file mode 100644 index 0000000000..9f69333421 --- /dev/null +++ b/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'EigenExa' +version = '2.11' + +homepage = 'https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/' +description = """EigenExa, a part of KMATHLIB, is a high performance eigen-solver.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['87dee8ac13f410a007e82df2688fa7f143883229dac729fd20836f4a28fac43d'] + +preconfigopts = './cleanup && ./bootstrap && ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libEigenExa.a'], + 'dirs': [] +} + +moduleclass = 'math' From 5473fa56618a90c4f96c90eb11efbf8b02700bc9 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 4 Apr 2022 10:21:34 +0900 Subject: [PATCH 1944/2365] adding easyconfigs: ELPA-2021.05.002-intel-2020b.eb and patches: ELPA-2021.05.002_fix_hardcoded_perl_path.patch --- .../e/ELPA/ELPA-2021.05.002-intel-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb new file mode 100644 index 0000000000..bd153664f9 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.05.002' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s_bugfix/'] +sources = ['elpa-%(version)s_bugfix.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'deabc48de5b9e4b2f073d749d335c8f354a7ce4245b643a23b7951cd6c90224b', # elpa-2021.05.002_bugfix.tar.gz + # ELPA-2021.05.002_fix_hardcoded_perl_path.patch + '69d2a7dcb61a7a699dd469a134a693e74c72b157dc72b3eba7a5dc12eb29893d', +] + +builddependencies = [ + ('Autotools', '20200321'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' From 154ea70124591f576f11c41405540a5e73fc7392 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 4 Apr 2022 10:53:23 +0900 Subject: [PATCH 1945/2365] adding easyconfigs: NTPoly-2.7.1-intel-2020b.eb --- .../n/NTPoly/NTPoly-2.7.1-intel-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb new file mode 100644 index 0000000000..218a4c9aa7 --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.7.1' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': False, 'usempi': True} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c15d9f51ac054b4ef0565ce5c4c8589c10bdbab4dc3442ebd109691e2bbfc7e2'] + +builddependencies = [('CMake', '3.18.4')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' \ No newline at end of file From c85900941a3123465683aa5cefd6d08ea85b2d3f Mon Sep 17 00:00:00 2001 From: Daniel Hedman Date: Mon, 4 Apr 2022 21:06:23 +0900 Subject: [PATCH 1946/2365] Update NTPoly-2.7.1-intel-2020b.eb Add newline to end of file --- easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb index 218a4c9aa7..09ce90d741 100644 --- a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb @@ -25,4 +25,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' From f04c68d82d23697f477b404a10dbccec391e0696 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 13 Apr 2022 14:28:46 +0200 Subject: [PATCH 1947/2365] adding easyconfigs: MIRA-5.0rc2-foss-2020b.eb --- .../m/MIRA/MIRA-5.0rc2-foss-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb new file mode 100644 index 0000000000..eacfc93d08 --- /dev/null +++ b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'MIRA' +version = '5.0rc2' + +homepage = 'https://sourceforge.net/p/mira-assembler/wiki/Home/' +description = """MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), + IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads).""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = ['mira-V5rc2.tar.bz2'] +source_urls = ['https://github.com/bachev/mira/releases/download/V5rc2/'] +checksums = ['4255aa9c4f09ec686b1c717bffe2dd124d3ef9b87f00e74d1bcd51b8599b8e44'] + +preconfigopts = 'export CFLAGS="$CFLAGS -fpermissive" && ' +preconfigopts += 'export CXXFLAGS="$CXXFLAGS -fpermissive" && ' + +configopts = '--with-boost=$EBROOTBOOST --with-expat=$EBROOTEXPAT --with-zlib=$EBROOTZLIB ' +configopts += '--with-tcmalloc-dir=$EBROOTGPERFTOOLS/lib ' + +builddependencies = [ + ('flex', '2.6.4'), +] +dependencies = [ + ('Boost', '1.74.0'), + ('zlib', '1.2.11'), + ('expat', '2.2.9'), +] + +sanity_check_paths = { + 'files': ["bin/mira"], + 'dirs': ["bin"], +} + +moduleclass = 'bio' From f34e0a63e428fcc13317092935c2e919c0bbb5e4 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 14 Apr 2022 08:13:15 +0200 Subject: [PATCH 1948/2365] Update easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb works for us Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb index eacfc93d08..ec820ab8c2 100644 --- a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb @@ -26,6 +26,7 @@ dependencies = [ ('Boost', '1.74.0'), ('zlib', '1.2.11'), ('expat', '2.2.9'), + ('gperftools', '2.9.1'), ] sanity_check_paths = { From e33b5b9fc382ae8daee99b8fd24b4fe4b25c7399 Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Thu, 14 Apr 2022 16:34:19 +0800 Subject: [PATCH 1949/2365] make configure step at the installdir --- .../RepeatMasker-4.1.2-p1-foss-2020b.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb index 9d3c0d8724..7b7bd2f8ef 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb @@ -36,9 +36,16 @@ dependencies = [ local_default_search_engine = 'RMBlast' -preinstall_cmd = './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' -preinstall_cmd += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' -preinstall_cmd += '-default_search_engine %s' % local_default_search_engine.lower() +#preinstall_cmd = './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +#preinstall_cmd += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +#preinstall_cmd += '-default_search_engine %s' % local_default_search_engine.lower() + +local_config_command = 'cd %(installdir)s &&' +local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() + +postinstallcmds = [ local_config_command, ] fix_perl_shebang_for = ['RepeatMasker'] From bdc241878d9b64c31bbb86ebc5a23630560e3960 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 14 Apr 2022 12:04:36 +0200 Subject: [PATCH 1950/2365] remove trailing whitespace --- easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb index ec820ab8c2..69c6533045 100644 --- a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb @@ -20,7 +20,7 @@ configopts = '--with-boost=$EBROOTBOOST --with-expat=$EBROOTEXPAT --with-zlib=$E configopts += '--with-tcmalloc-dir=$EBROOTGPERFTOOLS/lib ' builddependencies = [ - ('flex', '2.6.4'), + ('flex', '2.6.4'), ] dependencies = [ ('Boost', '1.74.0'), From 4720b19a300b1d380506a4d3b9c58917cf113602 Mon Sep 17 00:00:00 2001 From: easybuild Date: Sat, 16 Apr 2022 14:59:08 +0900 Subject: [PATCH 1951/2365] Updated based on jfgrimm comments --- .../b/Bader/Bader-1.04-iccifort-2020.4.304.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..ef4cb6bb24 --- /dev/null +++ b/easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'Bader' +version = '1.04' + +homepage = 'http://theory.cm.utexas.edu/henkelman/code/bader/' +description = "A fast algorithm for doing Bader's analysis on a charge density grid." + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] +sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f20a0a021157d911bea06666911763b737c4ff38b39e793b8560f940fe391b8e'] + +buildopts = '-f makefile.lnx_ifort FFLAGS="$FFLAGS" LINK="-static-intel"' +parallel = 1 + +files_to_copy = [(['bader'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bader'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s -h"] + +moduleclass = 'chem' From 5f8b32a1a6347fa05dd8b40bd4ade1a9e5cc8cdb Mon Sep 17 00:00:00 2001 From: easybuild Date: Sat, 16 Apr 2022 15:09:59 +0900 Subject: [PATCH 1952/2365] Updated based on jfgrimm comments --- .../easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb b/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb index 9f69333421..c9a3c391ab 100644 --- a/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb +++ b/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb @@ -13,12 +13,16 @@ source_urls = ['https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/'] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['87dee8ac13f410a007e82df2688fa7f143883229dac729fd20836f4a28fac43d'] +builddependencies = [ + ('Autotools', '20200321') +] + preconfigopts = './cleanup && ./bootstrap && ' parallel = 1 sanity_check_paths = { - 'files': ['lib/libEigenExa.a'], + 'files': ['lib/libEigenExa.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': [] } From fa6cf58b74fbcdfe889366c7cd19d8abdf86083d Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 20 Apr 2022 15:50:00 +0000 Subject: [PATCH 1953/2365] Remove pkg-config use from SeqLib configure patch There was a syntax error in the autoconf macro, which causes an error if pkg-config is available, and if not available simply causes configure to issue a warning and ignore it. Since the result is not used anyway, we can remove it. --- easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb index 507c2fec11..83b25b6648 100644 --- a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb @@ -21,7 +21,7 @@ checksums = [ '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', - '8a90edf72f95a52c61e4aed62a9a951bbd56f7c668dec326f2d3836f76b0f71d', # SeqLib-1.2.0_use-external-deps.patch + '413f0ad8e0963d8922205d31e0c361cfa98a10f93e7d3e0506e0bed539ec70eb', # SeqLib-1.2.0_use-external-deps.patch ] builddependencies = [('Autotools', '20200321')] From b2e667f0945eb13f6637bc36676dfb8b72128d9c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 21 Apr 2022 21:25:00 +0200 Subject: [PATCH 1954/2365] update source URL for isl in GCCcore --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index d4408b29aa..d6d21047a9 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools From d4ff611a3105858e76cb6295d7ff58f2927e4d32 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 22 Apr 2022 13:42:43 +0200 Subject: [PATCH 1955/2365] perl scripts in HH-suite need HHLIB set to the installation dir. --- .../easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 4 ++++ .../easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index 231c60d49b..3eae6fe8e4 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -63,4 +63,8 @@ modextrapaths = { 'PERL5LIB': 'scripts', } +modextravars = { + 'HHLIB': '%(installdir)s', +} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb index e3d70a3e26..5e469b0e3d 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb @@ -63,4 +63,8 @@ modextrapaths = { 'PERL5LIB': 'scripts', } +modextravars = { + 'HHLIB': '%(installdir)s', +} + moduleclass = 'bio' From d5aa3aa03feba5909d863ad94ed9c80f57b86351 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 22 Apr 2022 12:49:54 +0100 Subject: [PATCH 1956/2365] URL updated to fallback as original URL for source code is broken right now --- easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb index 9d9730518a..4b96a924b4 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb @@ -9,7 +9,10 @@ description = "Yet Another eXchange Tool" toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = ['https://www.dkrz.de/redmine/attachments/download/498/'] +source_urls = [ + ('https://swprojects.dkrz.de/redmine/attachments/download/498/'), + ('https://www.dkrz.de/redmine/attachments/download/498/'), +] sources = [SOURCELOWER_TAR_GZ] checksums = ['d3673e88c1cba3b77e0821393b94b5952d8ed7dc494305c8cf93e7ebec19483c'] From ac674384aa46f09d9c244348bff5c5fb8ee314ea Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Sat, 23 Apr 2022 18:55:01 +0200 Subject: [PATCH 1957/2365] Add missing makedepend --- .../makedepend-1.0.6-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3295f02cc8 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.6' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['845f6708fc850bf53f5b1d0fb4352c4feab3949f140b26f71b22faba354c3365'] + +builddependencies = [ + ('binutils', '2.35'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' From 348561cb5d7bc6ec05e11fd50ab355d0bb3a1a6f Mon Sep 17 00:00:00 2001 From: kosl Date: Sat, 23 Apr 2022 19:11:01 +0200 Subject: [PATCH 1958/2365] Update and rename ToFu-1.5.0-foss-2020b-Python-3.8.6.eb to ToFu-1.5.0-foss-2020b.eb --- .../t/ToFu/ToFu-1.5.0-foss-2020b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb new file mode 100644 index 0000000000..fdcf696edd --- /dev/null +++ b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'ToFu' +version = '1.5.0' + +homepage = 'https://github.com/ToFuProject/tofu' +description = """Tomography for Fusion.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +exts_list = [ + ('docutils', '0.18', { + 'checksums': ['c1d5dab2b11d16397406a282e53953fe495a46d69ae329f55aa98a5c4e3c5fbb'], + }), + ('Polygon3', '3.0.9.1', { + 'modulename': 'Polygon', + 'checksums': ['2ddf8d06975f728d5b40786136c82e5b9d38a846bce236b7e6587bbd6a5e9b49'], + }), + ('zope.interface', '5.4.0', { + 'checksums': ['5dba5f530fec3f0988d83b78cc591b58c0b6eb8431a85edd1569a0539a8a5a0e'], + }), + ('DateTime', '4.3', { + 'modulename': 'DateTime', + 'checksums': ['5cef605bab8259ff61281762cdf3290e459fbf0b4719951d5fab967d5f2ea0ea'], + }), + ('tofu', version, { + 'checksums': ['3ef4df7750b3e2d445f73f6e58cc3e3cbaeeda064246c86348b020c7f151f790'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import tofu.geom'"] + +moduleclass = 'tools' From 3de4497ca8ac4a2d78248864db2450405919fc2c Mon Sep 17 00:00:00 2001 From: kosl Date: Sat, 23 Apr 2022 19:11:57 +0200 Subject: [PATCH 1959/2365] Update and rename ToFu-1.5.0-intel-2020b-Python-3.8.6.eb to ToFu-1.5.0-intel-2020b.eb --- .../t/ToFu/ToFu-1.5.0-intel-2020b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb new file mode 100644 index 0000000000..1f32acaf35 --- /dev/null +++ b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'ToFu' +version = '1.5.0' + +homepage = 'https://github.com/ToFuProject/tofu' +description = """Tomography for Fusion.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +exts_list = [ + ('docutils', '0.18', { + 'checksums': ['c1d5dab2b11d16397406a282e53953fe495a46d69ae329f55aa98a5c4e3c5fbb'], + }), + ('Polygon3', '3.0.9.1', { + 'modulename': 'Polygon', + 'checksums': ['2ddf8d06975f728d5b40786136c82e5b9d38a846bce236b7e6587bbd6a5e9b49'], + }), + ('zope.interface', '5.4.0', { + 'checksums': ['5dba5f530fec3f0988d83b78cc591b58c0b6eb8431a85edd1569a0539a8a5a0e'], + }), + ('DateTime', '4.3', { + 'modulename': 'DateTime', + 'checksums': ['5cef605bab8259ff61281762cdf3290e459fbf0b4719951d5fab967d5f2ea0ea'], + }), + ('tofu', version, { + 'checksums': ['3ef4df7750b3e2d445f73f6e58cc3e3cbaeeda064246c86348b020c7f151f790'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import tofu.geom'"] + +moduleclass = 'tools' From 00f9fdfdbfabb3a54937775774dc0d3979d9a92e Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Sat, 23 Apr 2022 19:30:53 +0200 Subject: [PATCH 1960/2365] Add missing g2clib and g2lib --- .../g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..eeb1ed2cd3 --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +name = 'g2lib' +version = '3.2.0' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = [ + '%(name)s-%(version)s_compilation.patch', + # '%(name)s-%(version)s_makefile.patch', + # '%(name)s-%(version)s-kind.patch', + # '%(name)s-1.4.0-with-JasPer-2.x.patch', +] +checksums = [ + '9d3866de32e13e80798bfb08dbbea9223f32cec3fce3c57b6838e76f27d5a1d3', # g2lib-3.2.0.tar + 'f85286a1c0dec16e4a9f0abb4517218e4c652080775e34a1806e3687e1277dbb', # g2lib-3.2.0_compilation.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('JasPer', '2.0.24'), + ('libpng', '1.6.37'), +] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 ' +buildopts += '-D__64BIT__" FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -I." FC=$FC CC=$CC' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' From 68f8d76b6ba81614daf38195b5290e848331e58a Mon Sep 17 00:00:00 2001 From: kosl Date: Sun, 24 Apr 2022 01:11:04 +0200 Subject: [PATCH 1961/2365] Delete makedepend-1.0.6-GCCcore-10.2.0.eb --- .../makedepend-1.0.6-GCCcore-10.2.0.eb | 26 ------------------- 1 file changed, 26 deletions(-) delete mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb deleted file mode 100644 index 3295f02cc8..0000000000 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'makedepend' -version = '1.0.6' - -homepage = 'https://linux.die.net/man/1/makedepend' -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = [XORG_UTIL_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['845f6708fc850bf53f5b1d0fb4352c4feab3949f140b26f71b22faba354c3365'] - -builddependencies = [ - ('binutils', '2.35'), - ('xproto', '7.0.31'), - ('xorg-macros', '1.19.2'), -] - -sanity_check_paths = { - 'files': ['bin/makedepend'], - 'dirs': [], -} - -moduleclass = 'devel' From 865da3148c7d4230cbad014c9a0bb38e70cf1472 Mon Sep 17 00:00:00 2001 From: kosl Date: Sun, 24 Apr 2022 01:12:45 +0200 Subject: [PATCH 1962/2365] Delete g2lib-3.2.0-GCCcore-10.2.0.eb --- .../g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb deleted file mode 100644 index eeb1ed2cd3..0000000000 --- a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -name = 'g2lib' -version = '3.2.0' - -homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = [homepage] -sources = ['%(name)s-%(version)s.tar'] -patches = [ - '%(name)s-%(version)s_compilation.patch', - # '%(name)s-%(version)s_makefile.patch', - # '%(name)s-%(version)s-kind.patch', - # '%(name)s-1.4.0-with-JasPer-2.x.patch', -] -checksums = [ - '9d3866de32e13e80798bfb08dbbea9223f32cec3fce3c57b6838e76f27d5a1d3', # g2lib-3.2.0.tar - 'f85286a1c0dec16e4a9f0abb4517218e4c652080775e34a1806e3687e1277dbb', # g2lib-3.2.0_compilation.patch -] - -builddependencies = [('binutils', '2.35')] - -dependencies = [ - ('JasPer', '2.0.24'), - ('libpng', '1.6.37'), -] - -buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 ' -buildopts += '-D__64BIT__" FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -I." FC=$FC CC=$CC' - -# parallel build tends to fail -parallel = 1 - -moduleclass = 'data' From 544fb90face3d1936ab8efa159a671ac4eb91fdd Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Sun, 24 Apr 2022 02:06:44 +0200 Subject: [PATCH 1963/2365] adding easyconfigs: OpenMPI-4.1.2-GCC-10.2.0.eb --- .../o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..b9c33a4d32 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb @@ -0,0 +1,37 @@ +name = 'OpenMPI' +version = '4.1.2' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9b78c7cf7fc32131c5cf43dd2ab9740149d9d87cadb2e2189f02685749a6b527'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('libevent', '2.1.12'), + ('UCX', '1.9.0'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), +] + +# replace -march=skylake-avx512 option with equivalent -m* flags, +# to avoid problems when building on systems which don't support AVX-512; +# cfr. https://github.com/open-mpi/ompi/issues/8306 +preconfigopts = "sed -i 's/-march=skylake-avx512/-mavx512f -mavx512bw -mavx512vl -mavx512dq/g' configure && " + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts = '--with-slurm --with-pmi=/usr --with-pmi-libdir=/usr/lib64' + +moduleclass = 'mpi' From ef275954facc3061fa1eb3b51168c1ee03c3e2eb Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 25 Apr 2022 10:29:35 +0200 Subject: [PATCH 1964/2365] remove unneeded parentheses --- easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb index 4b96a924b4..7febddd76e 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb @@ -10,8 +10,8 @@ toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'usempi': True} source_urls = [ - ('https://swprojects.dkrz.de/redmine/attachments/download/498/'), - ('https://www.dkrz.de/redmine/attachments/download/498/'), + 'https://swprojects.dkrz.de/redmine/attachments/download/498/', + 'https://www.dkrz.de/redmine/attachments/download/498/', ] sources = [SOURCELOWER_TAR_GZ] checksums = ['d3673e88c1cba3b77e0821393b94b5952d8ed7dc494305c8cf93e7ebec19483c'] From bad40ccbaf757d38ba506e351cdc83447d62737d Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Thu, 28 Apr 2022 06:57:29 +0200 Subject: [PATCH 1965/2365] Remove unneeded preconfig opts --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb index b9c33a4d32..5148de10aa 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb @@ -23,15 +23,11 @@ dependencies = [ ('PMIx', '3.1.5'), ] -# replace -march=skylake-avx512 option with equivalent -m* flags, -# to avoid problems when building on systems which don't support AVX-512; -# cfr. https://github.com/open-mpi/ompi/issues/8306 -preconfigopts = "sed -i 's/-march=skylake-avx512/-mavx512f -mavx512bw -mavx512vl -mavx512dq/g' configure && " # disable MPI1 compatibility for now, see what breaks... # configopts = '--enable-mpi1-compatibility ' -# to enable SLURM integration (site-specific) +# to enable SLURM integration use e.g. --try-amend="configopts=--with-slurm" # configopts = '--with-slurm --with-pmi=/usr --with-pmi-libdir=/usr/lib64' moduleclass = 'mpi' From 4a9d1f5b51c77e9a1f6534e3ff7a44243889ebf9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 28 Apr 2022 10:02:54 +0200 Subject: [PATCH 1966/2365] Prokka needs parallel --- easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb index 0ba029a4f1..6b0f94eac8 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -24,6 +24,7 @@ dependencies = [ ('BLAST+', '2.11.0'), ('Java', '11', '', True), ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20210322'), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', From bcc67fbb4c8b027d0dd6800909fe3035d8e191fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2022 17:09:30 +0200 Subject: [PATCH 1967/2365] adding easyconfigs: parallel-fastq-dump-0.6.7-gompi-2020b.eb --- .../parallel-fastq-dump-0.6.7-gompi-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb new file mode 100644 index 0000000000..c74bb75c50 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'parallel-fastq-dump' +version = '0.6.7' + +homepage = 'https://github.com/rvalieris/parallel-fastq-dump' +description = "parallel fastq-dump wrapper" +docurls = ["https://github.com/rvalieris/parallel-fastq-dump"] + +toolchain = {'name': 'gompi', 'version': '2020b'} + +# https://github.com/rvalieris/parallel-fastq-dump/archive/ +github_account = 'rvalieris' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['cb33ea0ed0b1123c100aee7b9ea60a3fc3fc81a3a46be5237c85ba56380617de'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('SRA-Toolkit', '2.10.9'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + "files": ["bin/parallel-fastq-dump"], + "dirs": ["lib/python%(pyshortver)s/site-packages"], +} + +# This package doesn't produce importable module, only executable script. +options = {'modulename': False} + +sanity_check_commands = ["parallel-fastq-dump --version"] + +sanity_pip_check = True + +moduleclass = "bio" From 4b29ebc2b98b0ca869657264161948b0a8331cc2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 29 Apr 2022 11:02:44 +0200 Subject: [PATCH 1968/2365] add missing tbl2asn dependency for prokka 1.14.5 --- easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb index 6b0f94eac8..8f30af1ba5 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -25,6 +25,7 @@ dependencies = [ ('Java', '11', '', True), ('Bio-SearchIO-hmmer', '1.7.3'), ('parallel', '20210322'), + ('tbl2asn', '20220427', '-linux64', True), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', From 9300c0d03f0f155dac58f5a7beba0d5466f62d00 Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Sun, 1 May 2022 17:41:21 +0200 Subject: [PATCH 1969/2365] librsb: add v1.3.0.1 (#15401) --- .../l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..52dbf8d89f --- /dev/null +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb @@ -0,0 +1,33 @@ +## +# Author: Michele Martone +## +easyblock = 'ConfigureMake' + +name = 'librsb' +version = '1.3.0.1' + +homepage = 'https://sourceforge.net/projects/librsb/' +description = """A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3fc024a410f94aca2a7139ae79f4d713b11fa83304293630c363786874c17db4'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('zlib', '1.2.11') +] + +configopts = '--enable-openmp --enable-fortran-module-install' + +sanity_check_paths = { + 'files': ['bin/rsbench', 'lib/librsb.a', 'lib/librsb.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From dc65cf2d30a7ab3bfee75c6b1dcea442cb8b774d Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 3 May 2022 14:55:07 +0200 Subject: [PATCH 1970/2365] adding easyconfigs: popt-1.16-GCC-10.2.0.eb --- .../p/popt/popt-1.16-GCC-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb new file mode 100644 index 0000000000..5d58b1b1a3 --- /dev/null +++ b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'popt' +version = "1.16" + +homepage = "http://freecode.com/projects/popt" +description = """Popt is a C library for parsing command line parameters.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://src.fedoraproject.org/repo/pkgs/popt/popt-1.16.tar.gz/3743beefa3dd6247a73f8f7a32c14c33/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['e728ed296fe9f069a0e005003c3d6b2dde3d9cad453422a10d6558616d304cc8'] + +toolchainopts = {'optarch': False} +sanity_check_paths = { + 'files': ['include/popt.h', + ('lib/libpopt.a', 'lib64/libpopt.a'), + ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], + 'dirs': [], +} + +maxparallel = 1 + +moduleclass = 'lib' From 75eb3b61e31a34c04298d7740fad22c150789630 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 May 2022 11:23:11 +0200 Subject: [PATCH 1971/2365] adding easyconfigs: MUSCLE-3.8.1551-GCC-10.2.0.eb --- .../m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb new file mode 100644 index 0000000000..75cf15432a --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = "3.8.1551" + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.drive5.com/muscle/'] +sources = ['%(namelower)s_src_%(version)s.tar.gz'] +checksums = ['c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e'] + +# use correct compiler flags + +# don't use -static when linking, since that implies requiring glibc-static to be installed +buildopts = 'CFLAGS="$CXXFLAGS" LDLIBS="-lm"' + +files_to_copy = [(["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%(namelower)s"], + 'dirs': [], +} + +moduleclass = 'bio' From 026112893e3f74a0cdbad73ada9111825f07f97a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 May 2022 11:16:18 +0200 Subject: [PATCH 1972/2365] adding easyconfigs: MrBayes-3.2.6-gompi-2020b.eb --- .../m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb new file mode 100644 index 0000000000..417331a216 --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb @@ -0,0 +1,26 @@ +name = 'MrBayes' +version = '3.2.6' + +homepage = "https://nbisweden.github.io/MrBayes/" +description = """MrBayes is a program for Bayesian inference and model choice across + a wide range of phylogenetic and evolutionary models.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +# add -fcommon as workaround for 'multiple definition' linking errors; +# see also https://www.gnu.org/software/gcc/gcc-10/porting_to.html +toolchainopts = {'usempi': True, 'extra_cflags': '-fcommon'} + +source_urls = ['https://github.com/NBISweden/MrBayes/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f8fea43b5cb5e24a203a2bb233bfe9f6e7f77af48332f8df20085467cc61496d'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('libreadline', '8.0'), + ('beagle-lib', '3.1.2'), +] + +moduleclass = 'bio' From 1a9be29d8a41d041198f5497e731df21cb2c4f13 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 31 May 2022 14:16:12 +0200 Subject: [PATCH 1973/2365] tcsh: add softlink for csh --- easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb index 46a56b3bba..b317cef498 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb @@ -35,8 +35,10 @@ builddependencies = [('binutils', '2.35')] dependencies = [('ncurses', '6.2')] +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + sanity_check_paths = { - 'files': ["bin/tcsh"], + 'files': ["bin/tcsh", "bin/csh"], 'dirs': [] } From 2178f991292b6d516a7dc23a35f54d5a3c2e1c99 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Jun 2022 12:51:41 +0100 Subject: [PATCH 1974/2365] remove unused WITH_BLAS and WITH_LAPACK options for CGAL 5 --- easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb index c03d9e13b1..875af6f2dc 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb @@ -32,7 +32,6 @@ configopts = "-DCGAL_HEADER_ONLY=OFF " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT -configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " -configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON -DWITH_GMPXX=ON" moduleclass = 'numlib' From affb7f2d5edd4c24644009cd063776015ea15624 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Jun 2022 18:01:54 +0200 Subject: [PATCH 1975/2365] remove commented out lines + fix minor style issues in easyconfig for RepeatMaster v4.1.2-p1 --- .../r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb index 7b7bd2f8ef..f342fbdcfe 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb @@ -36,16 +36,12 @@ dependencies = [ local_default_search_engine = 'RMBlast' -#preinstall_cmd = './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' -#preinstall_cmd += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' -#preinstall_cmd += '-default_search_engine %s' % local_default_search_engine.lower() - local_config_command = 'cd %(installdir)s &&' local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() -postinstallcmds = [ local_config_command, ] +postinstallcmds = [local_config_command] fix_perl_shebang_for = ['RepeatMasker'] From 7d288fd31c9982c797e79d2c2fcfb8fd58347e18 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 5 Jun 2022 08:45:36 +0100 Subject: [PATCH 1976/2365] add Bison and flex build dependencies to SCOTCH 6.1.x --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb | 5 +++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb index 08a103b4d3..82ed7faf68 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb @@ -12,6 +12,11 @@ source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] +builddependencies = [ + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb index 6e94531d82..01d6e5e9fa 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb @@ -12,6 +12,11 @@ source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] +builddependencies = [ + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + dependencies = [ ('zlib', '1.2.11'), ] From e8c8a7e287b69da765753bc19382fd4edfa9f299 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jun 2022 10:30:54 +0200 Subject: [PATCH 1977/2365] add missing dependencies + switch to non-static build for Arriba v2.1.0 --- easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb index 2eea4c45f1..05191b206c 100644 --- a/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb @@ -20,11 +20,18 @@ checksums = ['21c46121e00cf84ad471b2b22fca722d37e55bbdf9e7118978dc250754a264bb'] dependencies = [ ('bzip2', '1.0.8'), + ('HTSlib', '1.11'), + ('libdeflate', '1.7'), ('STAR', '2.7.7a'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), ] +# make target with dynamically linked libraries is called bioconda, default is a statically linked binary +build_cmd_targets = 'bioconda' +# otherwise it fails to find sam.h +buildopts = 'CPATH=${EBROOTHTSLIB}/include/htslib:CPATH' + postinstallcmds = ['mkdir %(installdir)s/database'] files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', 'LICENSE', 'README.md', 'run_%(namelower)s.sh'] From bf286b0ab32a124d600d0b433c83bb8ec7b4e46d Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 8 Jun 2022 15:37:41 +0200 Subject: [PATCH 1978/2365] match patched jorg version renamed easyconfig in order to match patched Jorg 1.0.1 version --- .../j/Jorg/Jorg-1.0.1-foss-2020b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb new file mode 100644 index 0000000000..11b8affb4e --- /dev/null +++ b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb @@ -0,0 +1,33 @@ +# Author: Ben Langenberg ben.langenberg@ufz.de +# Helmholtz-Centre for Environmental Research +# Leipzig - Germany + +easyblock = 'PackedBinary' + +name = 'Jorg' +version = '1.0.1' + +homepage = 'https://github.com/lmlui/Jorg' +description = "A MAG Circularization Method By Lauren Lui, Torben Nielsen, and Adam Arkin" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'Helmholtz-UFZ' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['74b1c455ba57ab240921966255ca059840b97c47efcd16e9e66b9b6a8a136ee2'] +prepend_to_path = ['.'] + +dependencies = [ + ('MIRA', '5.0rc2'), + ('seqtk', '1.3'), +] + +sanity_check_paths = { + 'files': ['jorg'], + 'dirs': [], +} + +sanity_check_commands = ['jorg --help'] + +moduleclass = 'bio' From ffdffeeaf2ae23defdbff57349f28b1c41cd33f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Jun 2022 20:08:53 +0200 Subject: [PATCH 1979/2365] avoid that pygmo v2.18.0 installs stuff in Python installation directory (fixes #15631) + add custom sanity check paths to pygmo easyconfigs --- easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb index 9b5c672dad..8e5e9cc501 100644 --- a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb @@ -46,6 +46,11 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pygmo'], +} + sanity_pip_check = True moduleclass = 'lib' From 1798aea51b33f8679acbf1898bca9195f95693d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jun 2022 14:58:50 +0200 Subject: [PATCH 1980/2365] add missing Python dependency for HPDBSCAN to fix unresolved %(pyshortver)s template --- easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb index f106d8a227..b96581acb3 100644 --- a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb @@ -20,6 +20,7 @@ builddependencies = [ dependencies = [ ('HDF5', '1.10.7'), + ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), # for mpi4py ('SWIG', '4.0.2'), ] From 3cfd04906c21ce398eb046db3b206844e92d3588 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 20 Jun 2022 13:16:26 +0200 Subject: [PATCH 1981/2365] Update Jorg-1.0.1-foss-2020b.eb adjust checksum to version jorg 1.0.1 --- easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb index 11b8affb4e..582026b28f 100644 --- a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} github_account = 'Helmholtz-UFZ' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['74b1c455ba57ab240921966255ca059840b97c47efcd16e9e66b9b6a8a136ee2'] +checksums = ['90a63d9dcd32fe7f65946798c98f1551cea20ceab6446e9e5898cbbe6f0be52d'] prepend_to_path = ['.'] dependencies = [ From 2b465358008c4995df18a692eb1762abd43d9a93 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 20 Jun 2022 15:10:29 +0200 Subject: [PATCH 1982/2365] adding easyconfigs: poppler-21.06.1-GCC-10.2.0.eb --- .../p/poppler/poppler-21.06.1-GCC-10.2.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.2.0.eb b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..50d2925719 --- /dev/null +++ b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'poppler' +version = '21.06.1' + +homepage = 'https://poppler.freedesktop.org' +description = "Poppler is a PDF rendering library" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('freetype', '2.10.3'), + ('fontconfig', '2.13.92'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('NSS', '3.57'), + ('LibTIFF', '4.1.0'), + ('Qt5', '5.14.2'), + ('Boost', '1.74.0'), + ('cairo', '1.16.0'), + ('OpenJPEG', '2.4.0'), + ('zlib', '1.2.11'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['86b09e5a02de40081a3916ef8711c5128eaf4b1fc59d5f87d0ec66f04f595db4'], + 'configopts': "-DENABLE_BOOST=ON", + }), + ('poppler-data', '0.4.10', { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['6e2fcef66ec8c44625f94292ccf8af9f1d918b410d5aa69c274ce67387967b30'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdfinfo', 'lib/libpoppler.%s' % SHLIB_EXT, 'lib/libpoppler-cpp.%s' % SHLIB_EXT, + 'lib/libpoppler-glib.%s' % SHLIB_EXT, 'lib/libpoppler-qt5.%s' % SHLIB_EXT], + 'dirs': ['include/poppler', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = ["pdfinfo --help"] + +moduleclass = 'lib' From 49cd44f56437ae64389901891a373027b4f24fe2 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 20 Jun 2022 15:12:21 +0200 Subject: [PATCH 1983/2365] adding easyconfigs: graphite2-1.3.14-GCCcore-10.2.0.eb --- .../graphite2-1.3.14-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0a3fc8da20 --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' From 5031f8d01f6c9d5b553dbc3f695db3d684d49e89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Jun 2022 19:53:55 +0200 Subject: [PATCH 1984/2365] adding easyconfigs: SUNDIALS-6.2.0-intel-2020b.eb, SUNDIALS-6.2.0-foss-2020b.eb --- .../s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb | 38 +++++++++++++++++++ .../s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb | 38 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb new file mode 100644 index 0000000000..794ce9c825 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '6.2.0' + +homepage = 'https://computing.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['195d5593772fc483f63f08794d79e4bab30c2ec58e6ce4b0fb6bcc0e0c48f31d'] + +# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, +# other for new source tarball downloaded from GitHub + +builddependencies = [('CMake', '3.18.4')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb new file mode 100644 index 0000000000..332c5869a4 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '6.2.0' + +homepage = 'https://computing.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['195d5593772fc483f63f08794d79e4bab30c2ec58e6ce4b0fb6bcc0e0c48f31d'] + +# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, +# other for new source tarball downloaded from GitHub + +builddependencies = [('CMake', '3.18.4')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From 3c9b4ea802d8e50ac7a9cfb48ca6bd5b20950fe9 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 10:58:30 +0200 Subject: [PATCH 1985/2365] adding easyconfigs: ecFlow-5.7.0-GCC-10.2.0.eb --- .../e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..e9de3754b2 --- /dev/null +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = "CMakeMake" + +name = 'ecFlow' +version = '5.7.0' + +homepage = "https://confluence.ecmwf.int/display/ECFLOW/ecflow+home" +description = """ecFlow is a client/server workflow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides reasonable tolerance for hardware and software failures, combined with restart capabilities. It is used at ECMWF to run all our operational suites across a range of platforms.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/8650755/'] +sources = ['%(name)s-%(version)s-Source.tar.gz'] +checksums = ['70cbabde5da705239a9e27b1e053dae4bdbee6c604c571a5ff07b47d0a84732f'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Boost', '1.74.0'), + ('Boost.Python', '1.74.0'), + ('Qt5', '5.14.2'), + ('OpenSSL', '1.1.1h'), +] + +configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " +prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_commands = ['ecflow_client --help'] + +moduleclass = "vis" From f32f3e330a213f15582354ffce020e89cbe36212 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 10:59:41 +0200 Subject: [PATCH 1986/2365] adding easyconfigs: EIGENSOFT-7.2.1-foss-2020b.eb --- .../e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb new file mode 100644 index 0000000000..6199519bcc --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 6.1.4 modified by: +# Adam Huffman +# The Francis Crick Institute +# 7.2.1 modified by: +# Tom Strempel +# Helmholtz-Centre for Environmental Research - UFZ + +easyblock = 'MakeCp' + +name = 'EIGENSOFT' +version = '7.2.1' + +homepage = 'https://www.hsph.harvard.edu/alkes-price/software/' +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. +2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal +components analysis to explicitly model ancestry differences between cases and controls along continuous axes of +variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral +populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT +package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/DReichLab/EIG/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_Fix_makefile_openblas.patch'] +checksums = [ + 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz + 'e49e3754f2326210114fe5a731a77c7ffd240c8a9134eb8e8e1517bfe06c71e1', # EIGENSOFT-7.2.1_Fix_makefile_openblas.patch +] + +dependencies = [ + ('GSL', '2.6'), + ('Perl', '5.32.0'), +] + +start_dir = 'src' + +# Run "make install" after make to copy all binaries to the bin dir +buildopts = ' && make install' + +files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] + +fix_perl_shebang_for = ['bin/*.perl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'dirs': [] +} + +moduleclass = 'bio' From 71943c083bc1e3750cf6860663fc7654bf92e24c Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 13:31:12 +0200 Subject: [PATCH 1987/2365] adding easyconfigs: jq-1.5-GCCcore-10.2.0.eb --- .../easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..139e674e29 --- /dev/null +++ b/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'jq' +version = '1.5' + +homepage = 'https://stedolan.github.io/jq/' +description = """jq is a lightweight and flexible command-line JSON processor.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/stedolan/jq/releases/download/jq-%(version)s'] +sources = ['jq-%(version)s.tar.gz'] +checksums = ['c4d2bfec6436341113419debf479d833692cc5cdab7eb0326b5a4d4fbe9f493c'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['bin/jq'], + 'dirs': [], +} + +moduleclass = 'tools' From f4875ab7c7b43f8e343f6087a8f5612d5a113c77 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 13:52:20 +0200 Subject: [PATCH 1988/2365] adding easyconfigs: libSBML-5.19.0-GCC-10.2.0.eb --- .../l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb | 82 +++++++++++++++++++ 1 file changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..ea2d22663c --- /dev/null +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb @@ -0,0 +1,82 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# Modified by: Toni Harzendorf +# +# Notes:: Patch libsbml-fix_install_libpaths.patch comes from Fedora +# https://src.fedoraproject.org/rpms/libsbml/blob/rawhide/f/libsbml-fix_install_libpaths.patch +## +easyblock = 'CMakeMake' + +name = 'libSBML' +version = '5.19.0' + +# NOTE not in the license list of EB +# software_license = 'LGPLv2+' +software_license_urls = ['http://sbml.org/Software/libSBML/LibSBML_License'] +docurls = [ + 'https://github.com/sbmlteam/libsbml/releases/tag/v%(version)s', + 'http://sbml.org/Software/libSBML', +] + +homepage = 'http://sbml.org/Software/libSBML' +description = """libSBML (Systems Biology Markup Language library) is a free, open-source +programming library to help you read, write, manipulate, translate, and +validate SBML files and data streams. It's not an application itself (though +it does come with example programs), but rather a library you embed in your +own applications.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://downloads.sourceforge.net/project/sbml/libsbml/%(version)s/stable/'] +sources = ['libSBML-%(version)s-core-plus-packages-src.tar.gz'] +patches = [ + 'libsbml-fix_install_libpaths.patch', # Fix some installation library paths (from Fedora) + 'libsbml-fix_perl_auto_case.patch', # Fix the misname for Perl .so binding folder + # (https://sourceforge.net/p/sbml/libsbml/476/) +] +checksums = [ + 'a7f0e18be78ff0e064e4cdb1cd86634d08bc33be5250db4a1878bd81eeb8b547', # libSBML-5.19.0-core-plus-packages-src.tar.gz + '1975b9372be00c5056e1f3408b8829e749adb1edb3345fd109d5c802b5219e45', # libsbml-fix_install_libpaths.patch + '52b3274ce1fdfb329bc53feb67b9862833a1240539eca2f137fcdca00800e34e', # libsbml-fix_perl_auto_case.patch +] + + +builddependencies = [ + ('CMake', '3.18.4'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Perl', '5.32.0'), +] + +# Java jar, Ruby or Octave can also be build here. +# Python libSBML binding better done from https://pypi.org/project/python-libsbml/ +configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' +configure_cmd += '-DWITH_CHECK=ON -DWITH_SWIG=ON -DWITH_PERL=ON -DWITH_PYTHON=OFF ' +configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF ' +configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' +configure_cmd += '../libSBML-%(version)s-Source/' + + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib64/libsbml.so', 'lib64/perl5/vendor_perl/LibSBML.pm'], + 'dirs': ['lib64', 'include', 'share'] +} + +modextrapaths = { + 'PERL5LIB': 'lib64/perl5/vendor_perl/', +} + + +moduleclass = 'bio' From 3f140e8d95820dd2ff7b4fb13be6eaec69408957 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 14:05:41 +0200 Subject: [PATCH 1989/2365] adding easyconfigs: Mesquite-2.3.0-GCCcore-10.2.0.eb --- .../Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5121180a91 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Mesquite' +version = '2.3.0' + +homepage = 'https://software.sandia.gov/mesquite/' + +description = """Mesh-Quality Improvement Library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://software.sandia.gov/mesquite/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4ab4ceadfa596e16c00dbb0e8b830a9112fa1b73291ca07633ec379a39b8bb28'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/msqquality', 'bin/msqshape', 'lib/libmesquite.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From 26c225e1982813c674ad6cbbd3a3f2ddadabc5b7 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 14:14:12 +0200 Subject: [PATCH 1990/2365] adding easyconfigs: MITObim-1.9.1-foss-2020b.eb --- .../m/MITObim/MITObim-1.9.1-foss-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb b/easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb new file mode 100644 index 0000000000..6711cda43d --- /dev/null +++ b/easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = "CmdCp" + +name = 'MITObim' +version = '1.9.1' + +homepage = "https://github.com/chrishah/MITObim" +description = """The MITObim procedure (mitochondrial baiting and iterative mapping) represents + a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms + directly from total genomic DNA derived NGS reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'chrishah' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['8f7d47eb6ea677ca152492a477ee6c7542c0f853e921675b81be509ddd4f75bf'] + +dependencies = [ + ('Perl', '5.32.0'), + ('MIRA', '5.0rc2'), +] + +skipsteps = ['build'] + +files_to_copy = [ + (['MITObim.pl'], 'bin'), +] + +sanity_check_paths = { + 'files': ["bin/MITObim.pl"], + 'dirs': [] +} + +moduleclass = "bio" From dcb9a67e1a3c3d34e69ab244733b885b5475872b Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 14:54:20 +0200 Subject: [PATCH 1991/2365] adding easyconfigs: OpenFOAM-v2112-foss-2020b.eb --- .../o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb new file mode 100644 index 0000000000..4455c12e40 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb @@ -0,0 +1,44 @@ +## +# Author: Robert Mijakovic +## +name = 'OpenFOAM' +version = 'v2112' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = [ + '3e838731e79db1c288acc27aad8cc8a43d9dac1f24e5773e3b9fa91419a8c3f7', # OpenFOAM-v2112.tgz +] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('CGAL', '5.2'), + ('ParaView', '5.8.1', '-mpi'), + ('gnuplot', '5.4.1'), +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['%(installdir)s/%(name)s-%(version)s/platforms/linux64GccDPInt32Opt/lib/dummy/libscotchDecomp.so'], + 'dirs': ['%(installdir)s/%(name)s-%(version)s/platforms/linux64GccDPInt32Opt/lib/dummy'], +} + +moduleclass = 'cae' From a2dc60fb8b9af0ca2d64e31f6bce54f669f51f5f Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 22 Jun 2022 08:28:42 +0200 Subject: [PATCH 1992/2365] adding easyconfigs: RapidJSON-1.1.0-GCCcore-10.2.0.eb --- .../RapidJSON-1.1.0-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0fd88903d3 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +version = '1.1.0' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-compiler-errors.patch'] +checksums = [ + 'bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e', # v1.1.0.tar.gz + # %(name)s-%(version_major_minor)s.0_fix-compiler-errors.patch + '2e40ef6c46bf355feac16cd84faad5b7aca0ad54273117b85534b1b781f411c7', +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' From 240237823b7ccf2b4c3cdb267b3de0e4d7da5ff6 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 22 Jun 2022 15:05:19 +0200 Subject: [PATCH 1993/2365] take over suggested changes --- .../f/FSON/FSON-1.0.5-GCC-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSON/FSON-1.0.5-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FSON/FSON-1.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/f/FSON/FSON-1.0.5-GCC-10.2.0.eb new file mode 100644 index 0000000000..c81063b3dd --- /dev/null +++ b/easybuild/easyconfigs/f/FSON/FSON-1.0.5-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = "CMakeMake" + +name = 'FSON' +version = '1.0.5' + +homepage = "https://github.com/josephalevin/fson" +description = "Fortran 95 JSON Parser" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/josephalevin/fson/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d52f928d59b090eb47ed2bc880ee58d46cd8dd7e554e3df03c7c517d7a6b6012'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['lib64/libFSON.%s' % SHLIB_EXT], + 'dirs': ['include/fson'], +} + +moduleclass = "lib" From 6ed1dd0d5ea9021ed31e7576cda9a4afbb138e14 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 24 Jun 2022 09:17:42 +0200 Subject: [PATCH 1994/2365] take over @akesandgren suggestions --- .../o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb | 27 ++++++++++--------- 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb index 4455c12e40..edf177d599 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb @@ -1,6 +1,8 @@ ## # Author: Robert Mijakovic ## +# Modified by: Ben Langenberg +## name = 'OpenFOAM' version = 'v2112' @@ -11,12 +13,24 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'cstd': 'c++11'} +toolchainopts = {'cstd': 'c++11', 'vectorize': False} source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2012-cleanup.patch', 1), + 'OpenFOAM-v1906-wmake-ompi.patch', +] checksums = [ '3e838731e79db1c288acc27aad8cc8a43d9dac1f24e5773e3b9fa91419a8c3f7', # OpenFOAM-v2112.tgz + 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), ] dependencies = [ @@ -30,15 +44,4 @@ dependencies = [ ('gnuplot', '5.4.1'), ] -builddependencies = [ - ('Bison', '3.7.1'), - ('CMake', '3.18.4'), - ('flex', '2.6.4'), -] - -sanity_check_paths = { - 'files': ['%(installdir)s/%(name)s-%(version)s/platforms/linux64GccDPInt32Opt/lib/dummy/libscotchDecomp.so'], - 'dirs': ['%(installdir)s/%(name)s-%(version)s/platforms/linux64GccDPInt32Opt/lib/dummy'], -} - moduleclass = 'cae' From 995e5aa62ec3885bd791a2da4b0534132e76e73c Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 24 Jun 2022 13:49:54 +0200 Subject: [PATCH 1995/2365] remove python version suffix --- .../t/Trinity/Trinity-2.9.1-foss-2020b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb new file mode 100644 index 0000000000..25ad6257c8 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb @@ -0,0 +1,49 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.9.1' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +checksums = ['98d98bc21cd5dd32b408ed52586d01a15873b49b96de3264d42616bdcfc9d455'] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Java', '11', '', True), + ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Bowtie2', '2.4.2'), + ('HTSlib', '1.12'), + ('Jellyfish', '2.3.0'), + ('kallisto', '0.46.2'), + ('ncurses', '6.2'), + ('Salmon', '1.4.0'), + ('SAMtools', '1.11'), + ('zlib', '1.2.11'), +] + +withsampledata = True + +moduleclass = 'bio' From 81d28c9b16eef62ab2abd90c7bf185f295cc65bb Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 24 Jun 2022 14:58:51 +0200 Subject: [PATCH 1996/2365] stay with HTSlib 1.11 for foss/2020b --- easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb index 25ad6257c8..f2e75d3871 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb @@ -35,7 +35,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('Bowtie2', '2.4.2'), - ('HTSlib', '1.12'), + ('HTSlib', '1.11'), ('Jellyfish', '2.3.0'), ('kallisto', '0.46.2'), ('ncurses', '6.2'), From 6bdd69004793bcf452db7de91461d34a590f4083 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Jun 2022 20:42:18 +0200 Subject: [PATCH 1997/2365] adding easyconfigs: WPS-3.9.1-foss-2020b-dmpar.eb and patches: WPS-3.9.1_fix-JasPer-2.x.patch, WPS-3.9.1_fix-intmath.patch --- .../w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb new file mode 100644 index 0000000000..9755379bfa --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb @@ -0,0 +1,47 @@ +name = 'WPS' +version = '3.9.1' +buildtype = 'dmpar' +versionsuffix = '-%s' % buildtype + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] +sources = ['%(name)sV%(version)s.TAR.gz'] +patches = [ + 'WPS-3.8.0_netCDF-Fortran_seperate_path.patch', + 'WPS-3.9.1_fix-intmath.patch', + 'WPS-3.9.1_fix-JasPer-2.x.patch', +] +checksums = [ + '48a05cb25d6dcfaf4ba6fc63719b361ae240c79aad8066412646c936eecfcf90', # WPSV3.9.1.TAR.gz + '7ff73248b55eff304bcfd0f7b9e936c4c460dcc351088a15c2c4ac22622b9d41', # WPS-3.8.0_netCDF-Fortran_seperate_path.patch + 'f0c440db2c50cf67b3ee04eff349127d0b5f3b6bed79d136db5e6dcaf11e0e29', # WPS-3.9.1_fix-intmath.patch + '41a82492d230178278da138c5ab530e5084e861147fd98b792392d769ad38091', # WPS-3.9.1_fix-JasPer-2.x.patch +] + +dependencies = [ + ('WRF', '3.9.1.1', versionsuffix), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('JasPer', '2.0.24'), +] + +# required to ensure that netcdf.mod is found +prebuildopts = "sed -i 's@-I\$(NETCDF)/include@-I\$(NETCDF)/include -I\$(NETCDFF)/include@g' configure.wps && " + +# workaround for "Type mismatch between actual argument" compiler errors, +# see also https://www.gnu.org/software/gcc/gcc-10/porting_to.html +prebuildopts += "sed -i 's/ -O / -O -fallow-argument-mismatch /g' configure.wps && " + +moduleclass = 'geo' From f58a645455d042877f289be06a58f1408390ecb2 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 1 Jul 2022 09:55:14 +0200 Subject: [PATCH 1998/2365] adding easyconfigs: gdbm-1.21-GCCcore-10.2.0.eb --- .../g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b28c2fd68d --- /dev/null +++ b/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'gdbm' +version = '1.21' + +homepage = "https://www.gnu.org.ua/software/gdbm/gdbm.html" +description = """GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing + and work similar to the standard UNIX dbm. + These routines are provided to a programmer needing to create and manipulate a hashed database.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/gdbm'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['b0b7dbdefd798de7ddccdd8edf6693a30494f7789777838042991ef107339cc2'] + +builddependencies = [ + ('binutils', '2.35') +] + +dependencies = [ + ('libreadline', '8.0') +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gdbm_dump', 'gdbm_load', 'gdbmtool']] + + ['include/gdbm.h', 'lib/libgdbm.%s' % SHLIB_EXT], + 'dirs': ['share/man'] +} + +moduleclass = "lib" From 39ffe95c3dd440835afe9857ec5255931c00d211 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 5 Jul 2022 12:39:49 +0200 Subject: [PATCH 1999/2365] adding easyconfigs: makedepend-1.0.6-GCCcore-10.2.0.eb --- .../makedepend-1.0.6-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3295f02cc8 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.6' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['845f6708fc850bf53f5b1d0fb4352c4feab3949f140b26f71b22faba354c3365'] + +builddependencies = [ + ('binutils', '2.35'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' From 17fc8339d72c0a73e07d36fe45985edeaf17cf33 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 5 Jul 2022 12:42:29 +0200 Subject: [PATCH 2000/2365] adding easyconfigs: g2lib-3.2.0-GCCcore-10.2.0.eb --- .../g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9f965a3a42 --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +name = 'g2lib' +version = '3.2.0' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = [ + '%(name)s-%(version)s_makefile.patch', +] +checksums = [ + '9d3866de32e13e80798bfb08dbbea9223f32cec3fce3c57b6838e76f27d5a1d3', # g2lib-3.2.0.tar + 'e434394a6ec8bd68dbd57e3fdb44c47372b07380e362ed955bb038b78dd81812', # g2lib-3.2.0_makefile.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('JasPer', '2.0.24'), + ('libpng', '1.6.37'), +] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FC=$FC CC=$CC ' +buildopts += 'FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -fallow-argument-mismatch -I."' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' From 0c38d66944b4bb947f898ab395817fe5a8b0239a Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 5 Jul 2022 12:44:12 +0200 Subject: [PATCH 2001/2365] adding easyconfigs: g2clib-1.6.3-GCCcore-10.2.0.eb --- .../g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1ccb3cd073 --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +name = 'g2clib' +version = '1.6.3' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['83e4f2061b3d4a8bd431ba860dda8c5cf103b25f42d265b7b724b9acafad177c'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('JasPer', '2.0.24'), + ('libpng', '1.6.37'), +] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' From cca03869b3c69c20ad06adfe856114dbc27ae8a3 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 5 Jul 2022 12:46:16 +0200 Subject: [PATCH 2002/2365] adding easyconfigs: NCL-6.6.2-foss-2020b.eb --- .../easyconfigs/n/NCL/NCL-6.6.2-foss-2020b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2020b.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2020b.eb new file mode 100644 index 0000000000..898a5271a1 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2020b.eb @@ -0,0 +1,57 @@ +name = 'NCL' +version = '6.6.2' + +homepage = 'https://www.ncl.ucar.edu' +description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = { + 'cstd': 'c99', 'openmp': True, 'pic': True, + 'extra_fflags': '-fallow-invalid-boz -fallow-argument-mismatch', +} + +source_urls = ['https://github.com/NCAR/ncl/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'NCL-6.4.0_fix-types.patch', + 'NCL-6.6.2_header_and_operands.patch', + 'NCL-6.6.2_multiple_definitions.patch', +] +checksums = [ + 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e', # 6.6.2.tar.gz + 'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f', # NCL-6.4.0_fix-types.patch + '5cb62d9a37de8af485b94487692f7e739ca5eb103a6b447e0290a68a6c094808', # NCL-6.6.2_header_and_operands.patch + 'e21503dc46fe6fd360ba7ca4897aa93bf9ec2961bc48634ca46de582710448f7', # NCL-6.6.2_multiple_definitions.patch +] + +builddependencies = [ + ('makedepend', '1.0.6'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] +dependencies = [ + ('cURL', '7.72.0'), + ('JasPer', '2.0.24'), + ('g2lib', '3.2.0'), + ('g2clib', '1.6.3'), + ('HDF', '4.2.15'), + ('HDF5', '1.10.7'), + ('HDF-EOS', '2.20'), + ('HDF-EOS5', '1.16'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('Szip', '2.1.1'), + ('freetype', '2.10.3'), + ('zlib', '1.2.11'), + ('GDAL', '3.2.1'), + ('UDUNITS', '2.2.26'), + ('ESMF', '8.0.1'), + ('bzip2', '1.0.8'), + ('cairo', '1.16.0'), + ('libiconv', '1.16'), + ('GSL', '2.6'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), +] + +moduleclass = 'data' From 84c48e7b03b02bd0b5a3f9c68942591558b990bb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Jul 2022 14:43:28 +0200 Subject: [PATCH 2003/2365] Fix BLIS build on PPC --- .../b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb index 58742db0fc..4e65c62993 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb @@ -15,7 +15,17 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e'] +patches = [ + '%(name)s-0.8.1_enable_ppc_autodetect.patch', + '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', +] +checksums = [ + 'dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e', # 3.0.1.tar.gz + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', + # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch + '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', +] builddependencies = [ ('binutils', '2.35'), From 9b7b96f354504fb4322a1bfd1444565f19548445 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Jul 2022 12:48:59 +0200 Subject: [PATCH 2004/2365] downgrade Globus-CLI from v3.1.2 to v3.1.1 in GCCcore/10.2.0 --- .../Globus-CLI-3.1.1-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..30bc7bbffd --- /dev/null +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'Globus-CLI' +version = '3.1.1' + +homepage = "https://docs.globus.org/cli/" +description = """A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services + from the shell, and is suited to both interactive and simple scripting use cases.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), + ('OpenSSL', '1.1', '', True), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('click', '8.0.3', { + 'checksums': ['410e932b050f5eed773c4cda94de75971c89cdb3155a72a0831139a79e5ecb5b'], + }), + ('PyJWT', '2.3.0', { + 'modulename': 'jwt', + 'checksums': ['b888b4d56f06f6dcd777210c334e69c737be74755d3e5e9ee3fe67dc18a0ee41'], + }), + ('globus-sdk', '3.0.3', { + 'checksums': ['f608ce7772dca3c2c8de22b4e89fadae82de7e326f18df3440c99ecac0ae5f55'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + (name, version, { + 'modulename': 'globus_cli', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['480876fd45f5921369854197a7b6681df1d67831d8c5f503f5d44b8cf39d4e7a'], + }), +] + +fix_python_shebang_for = ['bin/globus', 'bin/jp.py', 'bin/pyjwt'] + +sanity_check_commands = ['globus --help'] + +moduleclass = 'data' From 8a9383ed378725534efc4f0cab171dea156960b1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Jul 2022 13:04:13 +0200 Subject: [PATCH 2005/2365] restore build dependency on binutils to Globus-CLI v3.1.1 --- .../g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb index 30bc7bbffd..b8e860947d 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb @@ -10,6 +10,10 @@ description = """A Command Line Wrapper over the Globus SDK for Python, which pr toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [ + ('binutils', '2.35'), +] + dependencies = [ ('Python', '3.8.6'), ('OpenSSL', '1.1', '', True), From 1e9887413b4a3a2184c3f0a88dcae6b1dd3e9a66 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 13 Jul 2022 19:29:30 +0000 Subject: [PATCH 2006/2365] Add CVE patch, attempt to fix symbol patch for all OSes --- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index 264331a9b0..e54a2560c6 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -20,10 +20,14 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['XZ-5.2.2_compat-libs.patch'] +patches = [ + 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5-cve-2022-1271.patch', +] checksums = [ '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch + '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch + '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch ] builddependencies = [ From df39a495d01519df4bb4f472a9f6df308be73637 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Jul 2022 12:25:25 +0200 Subject: [PATCH 2007/2365] use build enviroment from EB and add missing dependency on zlib to minimap2 --- .../easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb | 4 ++++ .../easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb index 9f7b208cc9..d159c3b396 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb @@ -26,6 +26,10 @@ checksums = ['7a55101d58ecaec545db51079ad82b214632dc697ee67290b6dc34cc70dbeeb4'] builddependencies = [('binutils', '2.35')] +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + files_to_copy = [ (['%(name)s'], 'bin'), (['lib%(name)s.a'], 'lib'), diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb index 5cff5bf900..8ba21e5c0f 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb @@ -26,6 +26,10 @@ checksums = ['f9eff90a7f14f999df93dff6ed4e3428277edbbd6bda6bdb1800e8d57c9135e3'] builddependencies = [('binutils', '2.35')] +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + files_to_copy = [ (['%(name)s'], 'bin'), (['lib%(name)s.a'], 'lib'), From b5cac4a0ddced4dfb126a052d38231d7ff842b40 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Jul 2022 14:47:04 +0200 Subject: [PATCH 2008/2365] Explicitly enable HDF5 --- easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb index aa268d4e37..d57bbc1de7 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb @@ -25,6 +25,7 @@ builddependencies = [ dependencies = [('HDF5', '1.10.7')] preconfigopts = "cd ../%(name)s-%(version)s/ext/htslib/ && autoreconf && cd - &&" +configopts = '-DUSE_HDF5=ON' parallel = 1 From 1e2bbc2052e8e874303ca1975a8b1953302e97c6 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Fri, 22 Jul 2022 14:19:30 +0000 Subject: [PATCH 2009/2365] Add alternate download URL for Voro++ --- .../easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb index 6eb0971906..b23389e4e9 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb @@ -16,7 +16,10 @@ to analyze a system of particles.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] builddependencies = [('binutils', '2.35')] From c64f828fed25ad27f5b9fe1194c1f9293d8e6ba2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 23 Jul 2022 23:57:30 +0200 Subject: [PATCH 2010/2365] add extra symlinks and sanity checks for libtinfo --- .../n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb index 5044d91b4c..1f706304c6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -22,25 +22,25 @@ builddependencies = [('binutils', '2.35')] local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build + # build ncurses: serial build in default paths with shared libraries local_common_configopts, - # the UTF-8 enabled version (ncursesw) + # build ncursesw: serial with UTF-8 local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] -local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } From df3102cecc0c0f9fd28e8abc52f1a1ddf211a946 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 24 Jul 2022 01:15:45 +0200 Subject: [PATCH 2011/2365] exclude libncurses++ from libtinfo symlinks --- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb index 1f706304c6..d0f8980031 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ configopts = [ # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] From 3959a1f738275cdeb1abbbe0bc06286655f8f5a4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 8 Jul 2021 10:26:32 +0200 Subject: [PATCH 2012/2365] Remove superflous -DCMAKE_BUILD_TYPE --- .../double-conversion-3.1.5-GCCcore-10.2.0.eb | 4 ---- .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb | 3 +-- .../q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb | 4 ---- easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb | 3 --- 6 files changed, 2 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb index 23fc1b1e9f..ba6b262e5e 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb @@ -17,10 +17,6 @@ builddependencies = [ ('CMake', '3.18.4'), ] -separate_build_dir = True - -build_type = 'Release' - # Build static lib, static lib with -fPIC and shared lib configopts = [ '', diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index d871b75c78..2a82e9c481 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -23,8 +23,6 @@ dependencies = [ ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] -build_type = 'Release' - exts_defaultclass = 'PythonPackage' exts_default_options = { 'download_dep_fail': True, diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb index db3b9cf4a4..6fe1eb0f6c 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb @@ -47,8 +47,7 @@ dependencies = [ local_pcre2_path = '%%(builddir)s/pcre2-%s.zip' % local_pcre2_ver preconfigopts = "sed -i 's@http://.*.zip@file://%s@g' ../mariadb-%%(version)s/cmake/pcre.cmake && " % local_pcre2_path -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) configopts += "-DWITH_PCRE=bundled " # using an external PCRE is broken, see https://bugs.exim.org/show_bug.cgi?id=2173 configopts += "-DWITH_ZLIB=system " diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb index 0fff752203..d3095e4a6c 100644 --- a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb @@ -43,7 +43,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.5'), ] -configopts = "-G Ninja -DPORT=Qt -DCMAKE_BUILD_TYPE=Release -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " +configopts = "-DPORT=Qt -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " sanity_check_paths = { 'files': [ diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb index b18fbb2c5f..9510c0e8ee 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb @@ -62,10 +62,6 @@ builddependencies = [ configopts = '-DUSE_MPI=ON ' configopts += '-DUSE_GMP=ON ' -build_type = 'Release' - -separate_build_dir = True - # too much parallellism makes the build fail with: # No rule to make target 'localdeps/lib/libterraces.a'; # see https://github.com/amkozlov/raxml-ng/issues/108 diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb index c9423b441d..b6179c2306 100644 --- a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb @@ -17,9 +17,6 @@ builddependencies = [ ('CMake', '3.18.4') ] -separate_build_dir = True -build_type = 'release' - modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} sanity_check_paths = { From 1dce3163f893db5ee362870a3e4634c3180ec6f4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Jul 2022 15:55:46 +0200 Subject: [PATCH 2013/2365] PyTorch 1.9.0: Fix PPC patch --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 +- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 34f2218ba3..bec52561d8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -46,7 +46,7 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', - '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index a05a60e0fd..f08d6445a4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -64,7 +64,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', - '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index 0fc9595a1b..e075328d5f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -63,7 +63,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', - '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch From cc943d89ecb05e52034f474352224f57f4c4132d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 29 Jul 2022 15:43:55 +0200 Subject: [PATCH 2014/2365] Actually fix the patch --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 +- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index bec52561d8..5931428b70 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -46,7 +46,7 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', - 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index f08d6445a4..b66e358649 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -64,7 +64,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', - 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index e075328d5f..0b4f5b7fb3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -63,7 +63,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', - 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch From 19c35a6737997461466d48bec231b725451fa7de Mon Sep 17 00:00:00 2001 From: easybuild Date: Sat, 30 Jul 2022 12:34:34 +0800 Subject: [PATCH 2015/2365] Add libffi and elfutils as dependencies --- easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb index a7ec71f94d..6d6f037e9e 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb @@ -52,6 +52,8 @@ dependencies = [ ('ncurses', '6.2'), ('GMP', '6.2.0'), ('Z3', '4.8.10'), + ('libffi', '3.3'), + ('elfutils', '0.183'), ] builddependencies = [ From 1bc02ba55ea7eb927f1b8fdfa4e2011660253a5e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 4 Aug 2022 12:05:43 +0200 Subject: [PATCH 2016/2365] adding easyconfigs: Blitz++-1.0.2-GCCcore-10.2.0.eb --- .../b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d6dde31b47 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'Blitz++' +version = '1.0.2' + +homepage = 'https://github.com/blitzpp/blitz' + +description = """ + Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation + in C++ with a speed comparable to Fortran implementations, while preserving an + object-oriented interface +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [('https://github.com/blitzpp/blitz/archive/')] +sources = ['%(version)s.tar.gz'] +checksums = ['500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'] + +builddependencies = [('CMake', '3.18.4'), ('binutils', '2.35')] + +separate_build_dir = True + +postinstallcmds = ['mkdir %(installdir)s/lib64/blitz'] + +sanity_check_paths = { + 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], + 'dirs': ['include/blitz/array', 'include/blitz/meta', + 'include/random', 'lib64/pkgconfig'], +} + +configopts = '--enable-shared' + +moduleclass = 'lib' From b1da9a110aebf792c7a2aaf3641765a9f5475f19 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 5 Aug 2022 14:35:54 +0200 Subject: [PATCH 2017/2365] Fix some test failures --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 6 ++++++ .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 ++ .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 6 ++++++ 3 files changed, 14 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 5931428b70..4f48922d68 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -26,6 +26,7 @@ patches = [ 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', + 'PyTorch-1.9.0_fix-kineto-crash.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', ] @@ -46,6 +47,7 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', + '1ed5e125f7922ea577d43053a6652aedc21cc036157e101c0e3b9aee9029d3b0', # PyTorch-1.9.0_fix-kineto-crash.patch 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', @@ -79,6 +81,10 @@ excluded_tests = { # Bad tests: https://github.com/pytorch/pytorch/issues/60260 'distributed/elastic/utils/distributed_test', 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index b66e358649..11fe7f4935 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -32,6 +32,7 @@ patches = [ 'PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch', 'PyTorch-1.9.0_fix-testnn-on-A100.patch', 'PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.9.0_fix-kineto-crash.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', @@ -64,6 +65,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', + '1ed5e125f7922ea577d43053a6652aedc21cc036157e101c0e3b9aee9029d3b0', # PyTorch-1.9.0_fix-kineto-crash.patch 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index 0b4f5b7fb3..4aac578561 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -31,6 +31,7 @@ patches = [ 'PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch', 'PyTorch-1.9.0_fix-testnn-on-A100.patch', 'PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.9.0_fix-kineto-crash.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', @@ -63,6 +64,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', + '1ed5e125f7922ea577d43053a6652aedc21cc036157e101c0e3b9aee9029d3b0', # PyTorch-1.9.0_fix-kineto-crash.patch 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', @@ -111,6 +113,10 @@ excluded_tests = { # Bad tests: https://github.com/pytorch/pytorch/issues/60260 'distributed/elastic/utils/distributed_test', 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', ] From 8265d241ab94caedb48ce8d6f9568672774efda3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 Aug 2022 10:40:44 +0200 Subject: [PATCH 2018/2365] add missing SciPy-bundle dependency for rMATS-turbo --- .../easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb index 41bc0020a7..9f2bd8d726 100644 --- a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb @@ -13,6 +13,7 @@ builddependencies = [ ] dependencies = [ ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), ('GSL', '2.6'), ('SAMtools', '1.11'), ('STAR', '2.7.6a'), From 7a75386add003b3335f3cd8d89554663c5a39bbf Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 9 Aug 2022 16:57:44 +0200 Subject: [PATCH 2019/2365] Improved EB file for Blitz++ v1.0.2 for GCCcore/1[01].[23].0 --- .../easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb index d6dde31b47..b43168655a 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb @@ -20,16 +20,10 @@ checksums = ['500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'] builddependencies = [('CMake', '3.18.4'), ('binutils', '2.35')] -separate_build_dir = True - -postinstallcmds = ['mkdir %(installdir)s/lib64/blitz'] - sanity_check_paths = { 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], 'dirs': ['include/blitz/array', 'include/blitz/meta', 'include/random', 'lib64/pkgconfig'], } -configopts = '--enable-shared' - moduleclass = 'lib' From 7331429d5b129e54756ecc31d8c792834d919f4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Aug 2022 22:00:39 +0200 Subject: [PATCH 2020/2365] {lib}[GCCcore/10.2.0,GCCcore/10.3.0,GCCcore/11.2.0,GCCcore/11.3.0] scikit-build v0.15.0 w/ Python 3.8.6 + 3.9.5 + 3.9.6 + 3.10.4 --- .../scikit-build-0.15.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb new file mode 100755 index 0000000000..459369823e --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.15.0' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.7.0', { + 'checksums': ['151aeccf60c216402932b52e40ee477a939f8d58898927378a02abbe852c1c39'], + }), + (name, version, { + 'checksums': ['e723cd0f3489a042370b9ea988bbb9cfd7725e8b25b20ca1c7981821fcf65fb9'], + 'modulename': 'skbuild', + }), +] + +moduleclass = 'lib' From ba621cd9012760508eb0f232c58ee060e587bf05 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 10 Aug 2022 21:35:31 +0100 Subject: [PATCH 2021/2365] Add missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2021 versions --- easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb | 2 ++ .../easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb index 5a529a9533..706f52ed24 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb @@ -40,6 +40,7 @@ patches = [ 'GROMACS-2019_increase_test_timeout_for_GPU.patch', 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021_add-missing-sync.patch', ] checksums = [ 'efa78ab8409b0f5bf0fbca174fb8fbcf012815326b5c71a9d7c385cde9a8f87b', # gromacs-2021.tar.gz @@ -51,6 +52,7 @@ checksums = [ 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', + '52ee257309ff7761c2dd5b26de7dbc63f8ba698082adb88e2843f90e3f9168bf', # GROMACS-2021_add-missing-sync.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb index 13d039f411..abde5c2363 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb @@ -40,6 +40,7 @@ patches = [ 'GROMACS-2019_increase_test_timeout_for_GPU.patch', 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021_add-missing-sync.patch', ] checksums = [ 'd940d865ea91e78318043e71f229ce80d32b0dc578d64ee5aa2b1a4be801aadb', # gromacs-2021.2.tar.gz @@ -51,6 +52,7 @@ checksums = [ 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', + '52ee257309ff7761c2dd5b26de7dbc63f8ba698082adb88e2843f90e3f9168bf', # GROMACS-2021_add-missing-sync.patch ] builddependencies = [ From 6af4bcef0b38ece9c16658e6c92bf8f4f5f0297c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 11 Aug 2022 11:59:10 +0100 Subject: [PATCH 2022/2365] remove unecessary patch in recent JupyterLab --- .../j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) mode change 100644 => 100755 easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb old mode 100644 new mode 100755 index ce2bcb29a8..1f63a8e302 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb @@ -29,13 +29,8 @@ exts_list = [ 'checksums': ['5431d9dde96659364b7cc877693d5d21e7b80cea7ae3959ecc2b87518e5f5d8c'], }), (name, version, { - 'patches': ['%(name)s-1.2.5_set-app-path-for-easybuild.patch'], 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': [ - 'c8377bee30504919c1e79949f9fe35443ab7f5c4be622c95307e8108410c8b8c', # jupyterlab-2.2.8.tar.gz - # JupyterLab-1.2.5_set-app-path-for-easybuild.patch - 'a219b1071f37f848f7e79c6800149c0b2386a2b748be43288bc32af8e7dab668', - ], + 'checksums': ['c8377bee30504919c1e79949f9fe35443ab7f5c4be622c95307e8108410c8b8c'], }), ] From 5a6d61029e520d1079151d6f4620bcbbdf7a2f76 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 15 Aug 2022 17:00:34 +0200 Subject: [PATCH 2023/2365] Skip failing test_optim/test_tensorpipe_agent --- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 8 +++++++- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 6 +++++- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 8 +++++++- 3 files changed, 19 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 4f48922d68..68f81ba8ce 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -85,9 +85,15 @@ excluded_tests = { # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html 'distributed/test_distributed_fork', 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', - ] + ], + 'POWER': [ + # Works when run alone, fails when run as part of the suite. So far only observed on PPC + 'distributed/rpc/test_tensorpipe_agent', + ], } runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index 11fe7f4935..b4662e2722 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -123,7 +123,11 @@ excluded_tests = { 'test_optim', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', - ] + ], + 'POWER': [ + # Works when run alone, fails when run as part of the suite. So far only observed on PPC + 'distributed/rpc/test_tensorpipe_agent', + ], } runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index 4aac578561..e7070b8d18 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -117,9 +117,15 @@ excluded_tests = { # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html 'distributed/test_distributed_fork', 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', - ] + ], + 'POWER': [ + # Works when run alone, fails when run as part of the suite. So far only observed on PPC + 'distributed/rpc/test_tensorpipe_agent', + ], } runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' From dd1aef69d43b2aafee8fa74646d13712274e7366 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 15 Aug 2022 17:17:20 +0200 Subject: [PATCH 2024/2365] Exclude failing test in TensorFlow 2.4.1 --- .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 5 +++-- .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index 2342aee9b6..b37d88e8be 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -165,10 +165,10 @@ exts_list = [ 'TensorFlow-2.4.0_fix-eigen-on-power.patch', 'TensorFlow-2.4.0_downgrade-required-versions.patch', 'TensorFlow-2.4.0_add-protobuf-deps.patch', - 'TensorFlow-2.4.0_add-ldl.patch', 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', 'TensorFlow-2.4.0_fix-absl-on-power.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_add-ldl.patch', 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -190,6 +190,7 @@ exts_list = [ '-//tensorflow/c/eager:c_api_distributed_test_gpu', # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test', '-//tensorflow/c/eager:c_api_remote_function_test_gpu', '-//tensorflow/c/eager:c_api_remote_test_gpu', # Invalid alignment: https://github.com/tensorflow/tensorflow/issues/46460 @@ -216,13 +217,13 @@ exts_list = [ 'ac8f53662ad0bb660089c17bb433faf1ce3c2238234a2c3be7d92c8e02c1a8d6', # TensorFlow-2.4.0_add-protobuf-deps.patch '0ae2f4f1f1dc5b85f61edbe8a4a91dcffd5cf7588fa46c6a143455e4bc41a64e', - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch # TensorFlow-2.4.0_add-missing-llvm-deps.patch 'ce8c41e75f9854e547d03de99ae72cf41afa967b20439e864bc4af3dd4f565c7', # TensorFlow-2.4.0_fix-absl-on-power.patch 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', # TensorFlow-2.4.0_dont-use-var-lock.patch 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + 'ab57637e3e64a5ff8345573effed2b229c33579b9ac3c8ceb7e554d236890d4a', # TensorFlow-2.4.1_add-ldl.patch # TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch 'f384cd97e004673ae530b6e5cc826f8fddb46646991f1a228fc07b2aac87ee80', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index ea58071275..0feb8006d4 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -166,10 +166,10 @@ exts_list = [ 'TensorFlow-2.4.0_fix-eigen-on-power.patch', 'TensorFlow-2.4.0_downgrade-required-versions.patch', 'TensorFlow-2.4.0_add-protobuf-deps.patch', - 'TensorFlow-2.4.0_add-ldl.patch', 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', 'TensorFlow-2.4.0_fix-absl-on-power.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_add-ldl.patch', 'TensorFlow-2.4.1_fix-min-priority-test.patch', 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', ], @@ -193,6 +193,7 @@ exts_list = [ '-//tensorflow/c/eager:c_api_distributed_test_gpu', # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test', '-//tensorflow/c/eager:c_api_remote_function_test_gpu', '-//tensorflow/c/eager:c_api_remote_test_gpu', # Invalid alignment: https://github.com/tensorflow/tensorflow/issues/46460 @@ -221,13 +222,13 @@ exts_list = [ 'ac8f53662ad0bb660089c17bb433faf1ce3c2238234a2c3be7d92c8e02c1a8d6', # TensorFlow-2.4.0_add-protobuf-deps.patch '0ae2f4f1f1dc5b85f61edbe8a4a91dcffd5cf7588fa46c6a143455e4bc41a64e', - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch # TensorFlow-2.4.0_add-missing-llvm-deps.patch 'ce8c41e75f9854e547d03de99ae72cf41afa967b20439e864bc4af3dd4f565c7', # TensorFlow-2.4.0_fix-absl-on-power.patch 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', # TensorFlow-2.4.0_dont-use-var-lock.patch 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + 'ab57637e3e64a5ff8345573effed2b229c33579b9ac3c8ceb7e554d236890d4a', # TensorFlow-2.4.1_add-ldl.patch # TensorFlow-2.4.1_fix-min-priority-test.patch '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', # TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch From 1b07a43284dcbde59d0b0c74199f5054e2c74aad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 18 Aug 2022 10:45:12 +0200 Subject: [PATCH 2025/2365] add pigz as dependency --- easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb index f3ffcc20e0..31fce71f99 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb @@ -23,6 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} builddependencies = [('binutils', '2.35')] dependencies = [ + ('pigz', '2.6'), ('Python', '3.8.6'), ('python-isal', '0.11.1'), ] From 8025d5a5ad6a2959567c832bfa0daefd816b3426 Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 18 Aug 2022 12:49:31 +0100 Subject: [PATCH 2026/2365] Turned tcsh into runtime dependency --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb index b7b2e5f300..69bd6e602f 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb @@ -17,11 +17,8 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] -builddependencies = [ - ('tcsh', '6.22.03'), -] - dependencies = [ + ('tcsh', '6.22.03'), ('Tcl', '8.6.10'), ] From ca88d056850bb4e5028ccc281eaa9fcbfe050a09 Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 18 Aug 2022 12:50:17 +0100 Subject: [PATCH 2027/2365] Turned tcsh into runtime dependency --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb index b938c172e6..bb7d42b87f 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb @@ -20,12 +20,9 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] -builddependencies = [ - ('tcsh', '6.22.03'), -] - # support for GCC 8+ on POWER dependencies = [ + ('tcsh', '6.22.03'), ('Tcl', '8.6.10'), ] From aba308fed77422e3f5bb052cf75a68bd75c09034 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2022 12:13:03 +0200 Subject: [PATCH 2028/2365] add sanity check commands for recent gettext versions (>= 0.20.x) --- .../easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb index e0d0f8a84f..1303c6d192 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb @@ -29,4 +29,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + moduleclass = 'tools' From 50237ac398025535159e2fa182ef7c74c579ac91 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 23 Aug 2022 16:44:01 +0200 Subject: [PATCH 2029/2365] Patch pkgconfig file for Blitz++ v1.0.2 --- .../easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb index b43168655a..8dfa22d145 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb @@ -16,7 +16,11 @@ toolchainopts = {'pic': True} source_urls = [('https://github.com/blitzpp/blitz/archive/')] sources = ['%(version)s.tar.gz'] -checksums = ['500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'] +patches = ['blitz-%(version)s_pkgconfig.patch'] +checksums = [ + '500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2', # 1.0.2.tar.gz + 'd15fb397e75eb009809ecacdd7f2f154ff05e6586895f3b0511d0b53a6e3b9fe', # blitz-1.0.2_pkgconfig.patch +] builddependencies = [('CMake', '3.18.4'), ('binutils', '2.35')] From 8ea0a08c1420ebd51fa4aa4d32353d44d0cafb03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2022 19:28:00 +0200 Subject: [PATCH 2030/2365] add missing BCFtools dependency for recent medaka versions (+ run medaka_version_report to catch missing required dependencies) --- easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 6619e4a1e9..a6ccdd5505 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -36,6 +36,7 @@ dependencies = [ ('pyspoa', '0.0.8'), ('pyfaidx', '0.5.9.5'), ('python-isal', '0.11.1'), + ('BCFtools', '1.11'), ] use_pip = True @@ -83,10 +84,13 @@ exts_list = [ sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["medaka --help"] +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] moduleclass = 'bio' From 5fe7091226629f604b31506a77e25c65917dede4 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 25 Aug 2022 14:05:26 +0200 Subject: [PATCH 2031/2365] adding easyconfigs: Emacs-28.1-GCCcore-10.2.0.eb --- .../e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9bfb1e644e --- /dev/null +++ b/easybuild/easyconfigs/e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +# +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Robert Mijakovic +# reciPY derived from preexisting reciPy for GCCcore-9.2.0. +# Modder: Ben Langenberg +# +easyblock = 'ConfigureMake' + +name = 'Emacs' +version = '28.1' + +homepage = 'https://www.gnu.org/software/emacs/' +description = """GNU Emacs is an extensible, customizable text editor--and more. + At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming + language with extensions to support text editing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] +checksums = ['1439bf7f24e5769f35601dbf332e74dfc07634da6b1e9500af67188a92340a28'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('ncurses', '6.2'), + ('LibTIFF', '4.1.0'), + ('X11', '20201008'), + ('GTK+', '3.24.23'), +] + +# If you want to use Emacs plugins you must install the gnutls command line tools +# osdependencies = [('gnutls-utils')] + +configopts = '--with-gif=no --with-tiff=yes --with-x-toolkit=yes --with-xpm=yes --with-gnutls=no ' + +sanity_check_paths = { + 'files': ["bin/emacs", "bin/emacs-%(version)s", "bin/emacsclient", "bin/etags"], + 'dirs': [] +} + +moduleclass = 'tools' From 05b1cba1acf287a27f38e4abf140e91a79c0c2c6 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 26 Aug 2022 07:37:00 +0200 Subject: [PATCH 2032/2365] working sanity checks --- .../o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb index edf177d599..38e19f85b0 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb @@ -13,18 +13,18 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'cstd': 'c++11', 'vectorize': False} +toolchainopts = {'cstd': 'c++14', 'vectorize': False} source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] patches = [ - ('OpenFOAM-v2012-cleanup.patch', 1), - 'OpenFOAM-v1906-wmake-ompi.patch', + ('OpenFOAM-v2112-cleanup.patch', 1), + 'OpenFOAM-v2112-wmake-ompi.patch', ] checksums = [ '3e838731e79db1c288acc27aad8cc8a43d9dac1f24e5773e3b9fa91419a8c3f7', # OpenFOAM-v2112.tgz - 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch - '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch + 'e883f628cb393b3ab60317304d7085d0a6ba7b8992feb12c2fab20389af34f1c', # OpenFOAM-v2112-cleanup.patch + '8cc2d9feac07b564abb4a16614f142a7c1aceedc4ad6ee02836e7d4f654410cd', # OpenFOAM-v2112-wmake-ompi.patch ] builddependencies = [ From a6e4f81f7eff47328a048a35c910e37d14eac660 Mon Sep 17 00:00:00 2001 From: fizwit Date: Sat, 27 Aug 2022 07:31:23 -0700 Subject: [PATCH 2033/2365] {math}[foss/2020b]PyStan v2.19.1.1 --- .../p/PyStan/PyStan-2.19.1.1-foss-2020b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb new file mode 100644 index 0000000000..67938571cc --- /dev/null +++ b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'PyStan' +version = '2.19.1.1' + +homepage = 'https://github.com/stan-dev/pystan' +description = """Python interface to Stan, a package for Bayesian inference + using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From dbd4af8a952fb7573ac70dcf587f041042fdc0ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Aug 2022 16:26:44 +0200 Subject: [PATCH 2034/2365] adding easyconfigs: spaln-2.4.12-GCC-10.2.0.eb --- .../s/spaln/spaln-2.4.12-GCC-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb new file mode 100644 index 0000000000..364c2101be --- /dev/null +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'spaln' +version = '2.4.12' + +homepage = 'https://github.com/ogotoh/spaln' +description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps + and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h; +# see also https://github.com/ogotoh/spaln/issues/56 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/ogotoh/spaln/archive/'] +sources = ['ver%(version)s.tar.gz'] +checksums = ['0c5f842131409686dbaad01778960f53f1ebba8dd83d55b454ec4bf1b6bde2af'] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +# we need to make sure not to pass --prefix, otherwise the configure script gets stuck in an infinite loop... +prefix_opt = '--exec_prefix=' + +configopts = "--exec_prefix=%(installdir)s/bin --table_dir=%(installdir)s/table --alndbs_dir=%(installdir)s/seqdb " +configopts += "--use_zlib=1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], + 'dirs': ['seqdb', 'table'], +} + +sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] + +moduleclass = 'bio' From 86bbaaed117cada834353a257d3559b518a80f22 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 29 Aug 2022 14:46:04 -0700 Subject: [PATCH 2035/2365] convert to PythonBundle --- .../p/PyStan/PyStan-2.19.1.1-foss-2020b.eb | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb index 67938571cc..766b4a7e03 100644 --- a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'PyStan' version = '2.19.1.1' @@ -9,16 +9,20 @@ description = """Python interface to Stan, a package for Bayesian inference toolchain = {'name': 'foss', 'version': '2020b'} -sources = [SOURCELOWER_TAR_GZ] -checksums = ['fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038'] - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True +exts_list = [ + (name, version, { + 'modulename': '%(namelower)s', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038'] + }), +] + moduleclass = 'math' From d53d98b14f336edfccedb90257aa196f4d7b02d5 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 2 Sep 2022 10:54:18 +0200 Subject: [PATCH 2036/2365] codestyle and use OpenSSL Wrapper - thx to jfgrimm and boegelbot --- .../easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index e9de3754b2..8e39c2882d 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -1,10 +1,16 @@ +# Written by Tom Strempel +# Modified by Ben Langenberg easyblock = "CMakeMake" name = 'ecFlow' version = '5.7.0' homepage = "https://confluence.ecmwf.int/display/ECFLOW/ecflow+home" -description = """ecFlow is a client/server workflow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides reasonable tolerance for hardware and software failures, combined with restart capabilities. It is used at ECMWF to run all our operational suites across a range of platforms.""" +description = """ecFlow is a client/server workflow package that enables users + to run a large number of programs (with dependencies on each other and on time) + in a controlled environment. It provides reasonable tolerance for hardware and + software failures, combined with restart capabilities. + It is used at ECMWF to run all our operational suites across a range of platforms.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} @@ -22,7 +28,7 @@ dependencies = [ ('Boost', '1.74.0'), ('Boost.Python', '1.74.0'), ('Qt5', '5.14.2'), - ('OpenSSL', '1.1.1h'), + ('OpenSSL', '1.1', '', True), ] configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " From af88b19d2aa5f16874920da61a0b6bca4a248584 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 2 Sep 2022 12:42:46 +0200 Subject: [PATCH 2037/2365] add sanity_check_paths --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 8e39c2882d..4c712180e7 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -37,5 +37,9 @@ prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_commands = ['ecflow_client --help'] +sanity_check_paths = { + 'files': ['bin/ecflow_client', 'bin/ecflow_server'] + 'dirs': ['lib/python3.8/site-packages/ecflow', 'share/ecflow/etc'] +} moduleclass = "vis" From f9633f4a284e08b05c5ae32e182d5d4547b2bab8 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 2 Sep 2022 13:28:19 +0200 Subject: [PATCH 2038/2365] corrected syntax error --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 4c712180e7..15338b73d9 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -38,8 +38,8 @@ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_commands = ['ecflow_client --help'] sanity_check_paths = { - 'files': ['bin/ecflow_client', 'bin/ecflow_server'] - 'dirs': ['lib/python3.8/site-packages/ecflow', 'share/ecflow/etc'] + 'files': ['bin/ecflow_client', 'bin/ecflow_server'], + 'dirs': ['lib/python3.8/site-packages/ecflow', 'share/ecflow/etc'], } moduleclass = "vis" From c0e54f7c574411f89fc009c98e96072ce1d1b720 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 2 Sep 2022 13:56:46 +0200 Subject: [PATCH 2039/2365] no more Python suffix --- .../m/MUST/MUST-1.7.1-foss-2020b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb new file mode 100644 index 0000000000..6fd80a401d --- /dev/null +++ b/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = "CMakeMake" + +name = 'MUST' +version = '1.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://hpc.rwth-aachen.de/must/" +description = """MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. + As MPI calls are complex and usage errors common, this functionality is extremely helpful for application developers + that want to develop correct MPI applications. + This includes errors that already manifest – segmentation faults or incorrect results – as well as many errors + that are not visible to the application developer or do not manifest on a certain system or MPI implementation.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://hpc.rwth-aachen.de/must/files/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['de3f6144a433035d24952c1acdf1acac47bcd843b24243bd8c0467a0567b1ed6'] + +builddependencies = [ + ('CMake', '3.18.4') +] + +dependencies = [ + ('Python', '3.8.6'), + ('libxml2', '2.9.10'), + ('Graphviz', '2.47.0', '-Java-11'), +] + +sanity_check_paths = { + 'files': ["bin/mustrun", "bin/wrap.py", "include/mustConfig.h", "lib/libpnmpif.so", "lib/libpnmpi.so"], + 'dirs': ["include/pnmpi", "lib64/pnmpi-modules", "modules", "share", "specifications", "src"], +} + +moduleclass = "perf" From 2d7d08a5a1dd24c2d71c38450518d3194a4ac788 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 2 Sep 2022 16:08:16 +0200 Subject: [PATCH 2040/2365] remove versionsuffix config --- easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb index 6fd80a401d..b7aef9fc7f 100644 --- a/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb @@ -2,7 +2,6 @@ easyblock = "CMakeMake" name = 'MUST' version = '1.7.1' -versionsuffix = '-Python-%(pyver)s' homepage = "https://hpc.rwth-aachen.de/must/" description = """MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. From 6f08ac007e97cb7e30e8e32635e66ceb599e5931 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 1 Sep 2022 17:42:02 +0200 Subject: [PATCH 2041/2365] adding easyconfigs: tox-3.25.1-GCCcore-10.2.0.eb, tox-3.25.1-GCCcore-11.3.0.eb --- .../t/tox/tox-3.25.1-GCCcore-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d6014a40f3 --- /dev/null +++ b/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'tox' +version = '3.25.1' + +homepage = 'https://tox.wiki' +description = "tox aims to automate and standardize testing in Python" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c138327815f53bc6da4fe56baec5f25f00622ae69ef3fe4e1e385720e22486f9'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 47378d3f2e943bda86a6ffa88a6bd7ad0e2cd23b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 6 Sep 2022 16:58:12 +0200 Subject: [PATCH 2042/2365] Fix miscomputation in OpenBLAS on POWER --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index f3346d9db0..a0d4dffee1 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -15,7 +15,8 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-%(version)s_add-missing-params-for-power.patch', '%(name)s-0.3.15_icelake-detection.patch', ] checksums = [ @@ -24,6 +25,8 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch '4b3ab7260975ea2cfd7460731c0201b2c1e374cd83ae90d55b8da3e670633ba0', + # OpenBLAS-0.3.12_add-missing-params-for-power.patch + '4454af07290d1fe33e414023a41bb8999d6ee31887e194daa72bd23d46a0072a', '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', # OpenBLAS-0.3.15_icelake-detection.patch ] From c0b7c44d3d3c85b12b84b236b5069bbf5876214a Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 15:27:17 +0100 Subject: [PATCH 2043/2365] adding easyconfigs: x13as-1-1-b59-GCCcore-10.2.0.eb --- .../x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b3b916d640 --- /dev/null +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'x13as' +version = '1-1-b59' + +homepage = 'https://www.census.gov/data/software/x13as.About_X-13.html' + +description = """ +X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, +and maintained by the Census Bureau. + +Features of X-13ARIMA-SEATS include: + - Extensive time series modeling and model selection capabilities for + linear regression models with ARIMA errors (regARIMA models); + - The capability to generate ARIMA model-based seasonal adjustment + using a version of the SEATS software originally developed by Victor + Gómez and Agustín Maravall at the Bank of Spain, as well as nonparametric + adjustments from the X-11 procedure; + - Diagnostics of the quality and stability of the adjustments + achieved under the options selected; + - The ability to efficiently process many series at once. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://www2.census.gov/software/x-13arima-seats/x13as/unix-linux/program-archives', +] +sources = ['%(name)s_asciisrc-v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + '256ee87f326ef6e0ac33a806812d614a5584c6b9e1f2a67ec06af52f2c3be85d', # x13as_asciisrc-v1-1-b59.tar.gz + 'cbde094a2396c256e9ac996cd539806bb0274e569d578ad42c4879f0e02c5ef3', # x13as-v1-1_makefile.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +build_cmd = 'make -f makefile.gf' + +files_to_copy = [(["x13as"], "bin")] + +sanity_check_paths = { + 'files': ['bin/x13as'], + 'dirs': [], +} + +moduleclass = 'tools' From b5cdc9409a151fbbdff64b7db402c14d9735ae33 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Sep 2022 19:50:57 +0200 Subject: [PATCH 2044/2365] consistently add libffi + elfutils dependencies to recent Clang easyconfigs --- easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb index 34cb362004..d5b83b6bd5 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb @@ -52,13 +52,14 @@ dependencies = [ ('ncurses', '6.2'), ('GMP', '6.2.0'), ('Z3', '4.8.10'), + ('libffi', '3.3'), + ('elfutils', '0.183'), ] builddependencies = [ ('CMake', '3.18.4'), ('Python', '3.8.6'), ('Perl', '5.32.0'), - ('elfutils', '0.183'), ] assertions = True From abb1b2025c8b4ac6c6944ededc6ea5496608776b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Sep 2022 21:53:02 +0200 Subject: [PATCH 2045/2365] add direct Pango dependency in recent ImageMagick easyconfigs (fixes #16236) --- .../i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb index 980874e68b..f0077dead9 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb @@ -24,6 +24,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.5'), ('LibTIFF', '4.1.0'), ('LittleCMS', '2.11'), + ('Pango', '1.47.0'), ] builddependencies = [ From de611ac565edaa68e1f42c2e0f18e792ef5ce4d4 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Sep 2022 09:58:58 +0100 Subject: [PATCH 2046/2365] Name of module class changed to math --- easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb index b3b916d640..0687aee7c0 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -48,4 +48,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'math' From 682a0d1ba6c23ef00c7b0f22feaaaaf860b67ab9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Sep 2022 16:10:51 +0200 Subject: [PATCH 2047/2365] configure recent pocl versions to -DLLC_HOST_CPU=native to avoid CPU auto-detection --- easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb | 4 +++- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb index 7f2991f31f..949bd6168a 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb @@ -30,7 +30,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb index d5d54b8902..b6ff23250e 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb @@ -30,7 +30,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb index 4dc3a0dc23..257dcb0f4d 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb @@ -30,7 +30,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], From 6e8feb78e1f9353e79f62f5faf0a1357f220f1af Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 19 Sep 2022 17:10:09 +0200 Subject: [PATCH 2048/2365] skip flaky test in PyTorch 1.9 --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 68f81ba8ce..000f5a2c4f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -28,6 +28,7 @@ patches = [ 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', 'PyTorch-1.9.0_fix-kineto-crash.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', ] checksums = [ @@ -49,6 +50,8 @@ checksums = [ 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', '1ed5e125f7922ea577d43053a6652aedc21cc036157e101c0e3b9aee9029d3b0', # PyTorch-1.9.0_fix-kineto-crash.patch 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + # PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch + '94957de0fd5bcbea37482cb6d0d12b4608dccf50a10da0836e151b414954ccc3', # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index b4662e2722..12f7239095 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -37,6 +37,7 @@ patches = [ 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] @@ -73,6 +74,8 @@ checksums = [ '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch + '94957de0fd5bcbea37482cb6d0d12b4608dccf50a10da0836e151b414954ccc3', # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index e7070b8d18..0982b4f230 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -36,6 +36,7 @@ patches = [ 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] @@ -72,6 +73,8 @@ checksums = [ '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch + '94957de0fd5bcbea37482cb6d0d12b4608dccf50a10da0836e151b414954ccc3', # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch From 3714ee78c8f481ebb6d742ea2338d58bbe28ca2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 20 Sep 2022 17:45:08 +0200 Subject: [PATCH 2049/2365] Add --with-versioned-syms to ncurses 6.2 and 6.3 --- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb index d0f8980031..2ef2ac3431 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.35')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, From f5f1510019e5e59df9022b96fdf3117ff4afd094 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 24 Sep 2022 18:17:22 +0200 Subject: [PATCH 2050/2365] adding easyconfigs: SuperLU-5.3.0-foss-2020b.eb, SuperLU-5.3.0-foss-2022a.eb, SuperLU-5.3.0-intel-2020b.eb, SuperLU-5.3.0-intel-2022a.eb --- .../s/SuperLU/SuperLU-5.3.0-foss-2020b.eb | 21 +++++++++++++++++++ .../s/SuperLU/SuperLU-5.3.0-intel-2020b.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb new file mode 100644 index 0000000000..41d145da7e --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.18.4')] + +runtest = " test" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb new file mode 100644 index 0000000000..2328a04942 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.18.4')] + +runtest = " test" + +moduleclass = 'numlib' From 0e56971d1d425194571b9c210c964ad00394e360 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 30 Sep 2022 16:00:33 +0200 Subject: [PATCH 2051/2365] add patches for ambertools to work with new easyblock --- .../Amber-20.11-foss-2020b-AmberTools-21.3.eb | 38 ++++++++++++++++--- 1 file changed, 33 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb index ee8d80b627..1f0d542911 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb @@ -15,21 +15,49 @@ toolchainopts = {'usempi': True, 'openmp': True} sources = [ '%%(name)s%s.tar.bz2' % local_amber_ver, - 'AmberTools%s.tar.bz2' % local_ambertools_ver, + {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'} ] patches = [ - 'AmberTools-20_cmake-locate-netcdf.patch', - 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', - 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', 'alt_location': 'AmberTools'}, ] checksums = [ 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch - '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch + # AmberTools-21_dont_include_config.h_in_top_Makefile.patch + 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', ] builddependencies = [ From bf963cd490b739d2faa6c0e2670ecd6b18328dd0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 6 Oct 2022 11:20:33 +0200 Subject: [PATCH 2052/2365] use Intel MPI from EasyBuild toolchain in AMS (#16363) --- .../easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb index 0e032547e3..0d9ba4e2d4 100644 --- a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb +++ b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb @@ -30,6 +30,11 @@ modextrapaths = { 'AMSRESOURCES': 'atomicdata', } +modextravars = { + # use Intel MPI from EasyBuild + 'SCM_USE_LOCAL_IMPI': '1', +} + modloadmsg = """These environment variables need to be defined before using AMS: * $SCMLICENSE: path to AMS license file * $SCM_TMPDIR: path to user scratch directory From 4472c99187cd792fe1fb042905ccdf95e48e8c64 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 11 Oct 2022 11:04:26 +0100 Subject: [PATCH 2053/2365] update easyconfigs to use SYSTEM instead of True in dependencies --- easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb | 4 ++-- .../AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb | 2 +- .../easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb | 2 +- .../a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb | 2 +- .../a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 4 ++-- easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb | 2 +- .../c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb | 2 +- .../CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 4 ++-- .../easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb | 4 ++-- easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb | 2 +- .../easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb | 2 +- .../c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb | 2 +- easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb | 4 ++-- easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb | 2 +- .../cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb | 4 ++-- easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb | 4 ++-- .../easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb | 2 +- .../g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb | 2 +- .../easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb | 2 +- .../g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb | 2 +- .../g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb | 2 +- easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb | 2 +- easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb | 2 +- easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb | 2 +- .../g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb | 2 +- .../g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb | 2 +- .../g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb | 2 +- .../h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb | 4 ++-- .../easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb | 2 +- .../h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb | 2 +- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb | 2 +- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb | 2 +- .../m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb | 4 ++-- .../n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb | 4 ++-- easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb | 2 +- .../easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb | 4 ++-- .../o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb | 4 ++-- .../easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 2 +- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 2 +- .../easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb | 2 +- easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb | 4 ++-- .../q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb | 2 +- easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb | 2 +- .../q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb | 2 +- easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 2 +- .../s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb | 2 +- .../easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb | 2 +- .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 2 +- .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 2 +- .../easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb | 2 +- .../Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb | 4 ++-- .../easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb | 2 +- .../easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb | 2 +- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb | 2 +- 90 files changed, 104 insertions(+), 104 deletions(-) diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb index f62a0b1e28..b06c4f9ab4 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb @@ -16,10 +16,10 @@ checksums = [ '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch ] -builddependencies = [('Maven', '3.6.3', '', True)] +builddependencies = [('Maven', '3.6.3', '', SYSTEM)] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('BWA', '0.7.17'), ] diff --git a/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb b/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb index c9a3002ee8..176bd70202 100644 --- a/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb +++ b/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb @@ -21,7 +21,7 @@ checksums = ['2d361fcc2b800c3daaf25692988af6105669cba2ff513aba82f36089beb2839f'] dependencies = [ ('Perl', '5.32.0'), - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('BioPerl', '1.7.8'), ('HMMER', '3.3.2'), ('EMBOSS', '6.6.0', local_javasuffix), diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb index 7f7064ef51..740009f42a 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb @@ -21,7 +21,7 @@ checksums = [ ] builddependencies = [('binutils', '2.35')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb index fc45e8660c..638decc861 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb @@ -53,7 +53,7 @@ dependencies = [ ('PnetCDF', '1.12.2'), ('Tkinter', '3.8.6'), ('X11', '20201008'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', SYSTEM), ] # Some CUDA tests differs from expected results diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index c499524697..80e2cc8068 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -33,8 +33,8 @@ dependencies = [ ('python-parasail', '1.2.4'), ('PhyML', '3.3.20200621'), ('nodejs', '12.19.0'), - ('goalign', '0.3.2', '', True), - ('gotree', '0.4.0', '', True), + ('goalign', '0.3.2', '', SYSTEM), + ('gotree', '0.4.0', '', SYSTEM), ('rampart', '1.2.0'), ('libdeflate', '1.7'), ('nanopolish', '0.13.3'), diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb index 94e6c8540f..d0f16e3b3b 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb index 64cebdfa53..3c49531cee 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Python', '3.8.6'), ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb index 6b259a49b4..f540819325 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('Python', '3.8.6'), ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb index c20e3f3948..7924ce6969 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ checksums = ['34e201d963156618a0ea5bc87220f660a1e08403dd3c7c7903d4f38db3f40039'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb index 55d04ef9b9..8edc3c84d8 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ checksums = ['1dd952839cf0d5a8178c691eeae40dc48fa50d18dcce648b1ad9ae0195367d13'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb index f40b3b1712..e676c19b2a 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pkg-config', '0.29.2'), ('pocl', '1.6'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb index c3fb942ee7..43435891a6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.1'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb index 9c7b23d10c..e8a5cb71f3 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb @@ -25,7 +25,7 @@ dependencies = [ ('GSL', '2.6'), ('MEGAHIT', '1.2.9', versionsuffix), ('parallel', '20210322'), - ('picard', '2.25.0', '-Java-11', True), + ('picard', '2.25.0', '-Java-11', SYSTEM), ('Pysam', '0.16.0.1', versionsuffix), ('SAMtools', '1.11'), ('scikit-learn', '0.20.4', versionsuffix), diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb index 4024c882cd..e815134c6e 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -24,11 +24,11 @@ checksums = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '2.7.18'), ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'), ('matplotlib', '2.2.5', '-Python-%(pyver)s'), - ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', SYSTEM), ('FLASH', '2.2.00'), ('SAMtools', '1.11'), ('Bowtie2', '2.4.2'), diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb index 10d20ead47..e1a264c229 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb @@ -23,11 +23,11 @@ checksums = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('matplotlib', '3.3.3'), - ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', SYSTEM), ('FLASH', '2.2.00'), ('SAMtools', '1.11'), ('Bowtie2', '2.4.2'), diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb index d6d90b8133..02cea32f4a 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'GCC', 'version': '10.2.0'} -dependencies = [('CUDAcore', version, '', True)] +dependencies = [('CUDAcore', version, '', SYSTEM)] altroot = 'CUDAcore' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb index c9848f3232..60c8e70673 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -dependencies = [('CUDAcore', version, '', True)] +dependencies = [('CUDAcore', version, '', SYSTEM)] altroot = 'CUDAcore' diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb index b5127b17c5..3930c1d64b 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb @@ -32,7 +32,7 @@ checksums = [ dependencies = [ ('Python', '2.7.18'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), ('SciPy-bundle', '2020.11', versionsuffix), diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb index 7a92cacfd6..dddce517cb 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb @@ -13,9 +13,9 @@ builddependencies = [('Cython', '0.29.22')] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), - ('cuTENSOR', '1.2.2.5', '-CUDA-%(cudaver)s', True), + ('cuTENSOR', '1.2.2.5', '-CUDA-%(cudaver)s', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb index 7a7d3c59ec..1a81cacc46 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.0'), ('gnuplot', '5.4.1'), ] diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 7d60fb1c61..8356b39778 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -18,7 +18,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('SciPy-bundle', '2020.11'), ('leidenalg', '0.8.3'), ('hyperopt', '0.2.5'), diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb index 020b8f5f67..e06ee84b7f 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -13,7 +13,7 @@ dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), ('tMAE', '1.0.0', '-R-%(rver)s'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('GATK', '4.2.0.0', '-Java-%(javaver)s'), ('Graphviz', '2.47.0', '-Java-%(javaver)s'), ('Python', '3.8.6'), @@ -23,7 +23,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix ('SAMtools', '1.11'), ('BCFtools', '1.11'), - ('Pandoc', '2.13', '', True), + ('Pandoc', '2.13', '', SYSTEM), ] # postinstallcmds for pandoc are required to avoid that import fails because pandoc/definitions dir is not installed diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb index 014ae7c311..8091ae5611 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb @@ -13,7 +13,7 @@ dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), ('tMAE', '1.0.0', '-R-%(rver)s'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('GATK', '4.2.0.0', '-Java-%(javaver)s'), ('Graphviz', '2.47.0', '-Java-%(javaver)s'), ('Python', '3.8.6'), @@ -23,7 +23,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix ('SAMtools', '1.11'), ('BCFtools', '1.11'), - ('Pandoc', '2.13', '', True), + ('Pandoc', '2.13', '', SYSTEM), ] exts_list = [ diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb index eaf6f22dc1..e32b7fad6c 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb @@ -42,7 +42,7 @@ builddependencies = [('CMake', '3.18.4')] dependencies = [ ('X11', '20201008'), ('libharu', '2.3.0'), - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb index d6bae199dd..f9dd97bb26 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.1'), ('help2man', '1.47.16'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb index 610d9d24aa..097bd00e48 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb @@ -34,7 +34,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb index f11ab54125..515f6cea9b 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb @@ -34,7 +34,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb index ecc2aa7e0a..c99c15a13e 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', local_cudaversion, '', True), # needed by GDRCopy binaries, which are tools for testing + ('CUDAcore', local_cudaversion, '', SYSTEM), # needed by GDRCopy binaries, which are tools for testing ('Check', '0.15.2'), ] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb index 4e78c65fb6..accc04a5bd 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', local_cudaversion, '', True), # needed by GDRCopy binaries, which are tools for testing + ('CUDAcore', local_cudaversion, '', SYSTEM), # needed by GDRCopy binaries, which are tools for testing ('Check', '0.15.2'), ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb index 1b32207461..6758eb6089 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ ('ASE', '3.20.1'), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb index 861a80e2fd..0714f4060f 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('ASE', '3.20.1'), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb index 7a2e4989e8..7c88872300 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb @@ -29,7 +29,7 @@ dependencies = [ ('ASE', _aseversion), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb index 1f22f89cc8..978ddc9ef5 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb @@ -28,7 +28,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('ASE', _aseversion), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb index 582e90ea73..465fd9c9b0 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('ASE', _aseversion), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb index bba61ad120..5688561947 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('ASE', _aseversion), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb index 0ff0be7b62..5f2ae47346 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.56.2'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb index d0bc5d3e52..d40e1ff699 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.56.2'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb index 2e0232fed4..4d81bd500b 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.56.2'), diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb index 095a77b88c..2eabe89e52 100644 --- a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb @@ -15,7 +15,7 @@ checksums = ['ee3dc807e0fb59c1788717a155238115d7a860191f686ef2c5a5b685aa2a2948'] dependencies = [ ('Python', '3.8.6'), - ('Bandage', '0.8.1', '_Centos', True), + ('Bandage', '0.8.1', '_Centos', SYSTEM), ('SciPy-bundle', '2020.11'), ('sympy', '1.7.1'), ('SPAdes', '3.15.2'), diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb index b8e860947d..65e2cb1163 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb index fe7ec68c3f..740e71bf49 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb @@ -33,7 +33,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.6'), ('FriBidi', '1.0.10'), ('Gdk-Pixbuf', '2.40.0'), diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb index cb15f9404e..795f421b23 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb @@ -29,7 +29,7 @@ checksums = [ builddependencies = [ ('binutils', '2.35'), - ('Maven', '3.6.3', '', True), + ('Maven', '3.6.3', '', SYSTEM), ('protobuf', '2.5.0'), # *must* be this version - https://issues.apache.org/jira/browse/HADOOP-13363 ('CMake', '3.18.4'), ('snappy', '1.1.8'), @@ -39,7 +39,7 @@ builddependencies = [ # https://cwiki.apache.org/confluence/display/HADOOP/Hadoop+Java+Versions dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libtirpc', '1.3.1'), ] diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb index 16eb74c38c..48daa7126a 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ checksums = ['3ef8580c5b86e32ca092ce8de43df204f5e6f714b0cd32bc6237e6cd0f34a8f4'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb index d06d9b20df..ee5c6c8ec6 100644 --- a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('Clang', '11.0.1'), - # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), + # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', SYSTEM), # ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index fa2d35b964..d3a1580f52 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -34,7 +34,7 @@ checksums = [ dependencies = [ ('LibTIFF', '4.1.0'), ('Qt5', '5.14.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('HDF5', '1.10.7'), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index d2bc021cbb..1f1c6e82c8 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -37,7 +37,7 @@ checksums = [ dependencies = [ ('LibTIFF', '4.1.0'), ('Qt5', '5.14.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('HDF5', '1.10.7'), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index f138187813..039ed9bd0d 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('flatbuffers-python', '1.12'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb index f509313572..a022ed94c4 100644 --- a/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('CMake', '3.18.4'), ('Ninja', '1.10.1'), # building LDC from source required LDC 0.17.x - ('LDC', '0.17.6', '-%(arch)s', True), + ('LDC', '0.17.6', '-%(arch)s', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index 50594f87ec..40d8acc91a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.35', '', True)] +builddependencies = [('binutils', '2.35', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb index 4f2bf4aeab..0bbb8322a6 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb @@ -34,7 +34,7 @@ checksums = ['5a1b952f46816e396b918b92fcb118376c02be3636371bd6fcef00f315685b8d'] # of MotionCor2 builddependencies = [ ('binutils', '2.35'), - ('CUDAcore', '11.1.1', '', True), + ('CUDAcore', '11.1.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb index ed127443bf..836b2d4668 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # of MotionCor2 builddependencies = [ ('binutils', '2.35'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb index bb979fb26e..382b15693e 100644 --- a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb @@ -17,7 +17,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['ffdbccf340dc0b1ebd0ad6f222e3bdef1e22bbd6e4e5156bf93500a3a834dd52'] builddependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] # see https://github.com/bxlab/metaWRAP/blob/master/installation/dependancies.md @@ -30,7 +30,7 @@ dependencies = [ ('Bowtie2', '2.4.2'), ('BWA', '0.7.17'), ('CheckM', '1.0.18', versionsuffix), - ('FastQC', '0.11.9', '-Java-11', True), + ('FastQC', '0.11.9', '-Java-11', SYSTEM), ('Kraken', '1.1.1'), ('KronaTools', '2.8'), ('MEGAHIT', '1.2.9', versionsuffix), diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb index cbf8532c70..81fa9b3dfa 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -10,8 +10,8 @@ communication primitives that are performance optimized for NVIDIA GPUs.""" toolchain = {'name': 'GCCcore', 'version': local_gcc_ver} -builddependencies = [('GCC', local_gcc_ver, '', True)] -dependencies = [('CUDAcore', local_cuda_version, '', True)] +builddependencies = [('GCC', local_gcc_ver, '', SYSTEM)] +dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb index 3ca4af87ce..3ef383ecc8 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('Perl', '5.32.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb index 3da5bd86b4..03e6837966 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.2'), ('gnuplot', '5.4.1'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '20.2.1'), ('libGLU', '9.0.1'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb index cf24b5ca03..f866015943 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb @@ -45,8 +45,8 @@ dependencies = [ ('libwebp', '1.1.0'), ('OpenEXR', '2.5.5'), ('JasPer', '2.0.24'), - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.66.1'), ('GTK+', '3.24.23'), ('HDF5', '1.10.7'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb index 5fe200231f..6bd1dad125 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb @@ -45,8 +45,8 @@ dependencies = [ ('libwebp', '1.1.0'), ('OpenEXR', '2.5.5'), ('JasPer', '2.0.24'), - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.66.1'), ('GTK+', '3.24.23'), ('HDF5', '1.10.7'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index a7ff2a282f..938b94c4f9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -86,7 +86,7 @@ dependencies = [ ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), ('expecttest', '0.1.3'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb index 20dd004271..1e64c9e1b9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb @@ -277,7 +277,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 5b00155d13..63ff087989 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -28,7 +28,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index a32c54ea29..90e96f96e0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -97,7 +97,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index b4662e2722..bcfc0d48d2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -99,7 +99,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('imkl', '2020.4.304'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index e7070b8d18..55ca64a602 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -98,7 +98,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb index a782c5e9a6..b84ba84bea 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Biopython', '1.78'), - ('gofasta', '0.0.5', '', True), + ('gofasta', '0.0.5', '', SYSTEM), ('minimap2', '2.18'), ('Pysam', '0.16.0.1'), ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb index 8f30af1ba5..d5adf00b38 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -22,10 +22,10 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] dependencies = [ ('BioPerl', '1.7.8'), ('BLAST+', '2.11.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bio-SearchIO-hmmer', '1.7.3'), ('parallel', '20210322'), - ('tbl2asn', '20220427', '-linux64', True), + ('tbl2asn', '20220427', '-linux64', SYSTEM), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb index 58f9709a65..81762184ba 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '2.7.18'), ('Perl', '5.32.0'), ('matplotlib', '2.2.5', versionsuffix), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.74.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb index 53e95a0065..d0057cb1ac 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.8.6'), ('Perl', '5.32.0'), ('matplotlib', '3.3.3'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.74.0'), ] diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb index 4b25f9686c..70260a39f7 100644 --- a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb @@ -16,7 +16,7 @@ sources = ['qualimap_v%(version)s.zip'] checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', versionsuffix), ] diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 3226ee0f4b..782f039b49 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index d35824d64b..db5d9c9e47 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 26d6cbdb27..c7d07e5f2a 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -36,7 +36,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 9c612d32b9..afc6216b0b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index febdb0ca5e..bf2b31d78e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -33,7 +33,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index d1e5430a10..be10c211dc 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -33,7 +33,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index eaec7699da..7eab5f3ec8 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb index 41984431bd..3aac6838fb 100644 --- a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb @@ -15,7 +15,7 @@ checksums = ['93e6864b7ab18be96584950227426102b545db7d6d02762490a43e1610b7eb9b'] builddependencies = [('binutils', '2.35')] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('NGS', '2.10.9'), ('bzip2', '1.0.8'), ] diff --git a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb index 3781b94855..b6965d55e6 100644 --- a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb @@ -29,7 +29,7 @@ checksums = [ builddependencies = [ ('CMake', '3.18.4'), - ('Cereal', '1.3.0', '', True), + ('Cereal', '1.3.0', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb index 5cb1ec3c5e..c5815aa76a 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -19,7 +19,7 @@ checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] dependencies = [ ('Python', '3.8.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # ('Hadoop', '2.10.0', '-native'), ('Arrow', '0.17.1'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index b4585778e5..e08aae3577 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -19,7 +19,7 @@ checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] dependencies = [ ('Python', '3.8.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # ('Hadoop', '2.10.0', '-native'), ('Arrow', '0.17.1'), ] diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb index cfde903143..2e5679be3c 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb @@ -15,7 +15,7 @@ sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] checksums = ['85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d'] dependencies = [ - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('Python', '3.8.6'), ('Perl', '5.32.0'), ] diff --git a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb index 003fb9008b..fd54246780 100644 --- a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb @@ -27,7 +27,7 @@ parallel = 1 builddependencies = [ ('binutils', '2.35'), - ('Pandoc', '2.10', '', True), + ('Pandoc', '2.10', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 0feb8006d4..110b07df5a 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -19,7 +19,7 @@ builddependencies = [ ('UnZip', '6.0'), ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.6'), # Next 2 are for h5py diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index c1662ad3a3..b4daf67aaa 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -19,7 +19,7 @@ builddependencies = [ ('UnZip', '6.0'), ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.6'), ('h5py', '3.1.0'), diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb index c7c4aba1c1..7acce00ef7 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb @@ -19,7 +19,7 @@ checksums = ['5da6c2242ea72a991c8446d7fe7d35189ea346ef7d024c890397011114bf10fc'] dependencies = [ ('Python', '3.8.6'), ('libgpuarray', '0.7.6'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('SciPy-bundle', '2020.11'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb index add7564676..36e7345465 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb @@ -25,10 +25,10 @@ builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '2.7.18'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.6'), ('Perl', '5.32.0'), - ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ('cutadapt', '1.18', versionsuffix), ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb index 48c65be294..4f58f9acc8 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -30,7 +30,7 @@ osdependencies = [OS_PKG_IBVERBS_DEV] dependencies = [ ('numactl', '2.0.13'), - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', SYSTEM), ('GDRCopy', '2.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb index fd3d6e7b5d..11fabfc2ea 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -30,7 +30,7 @@ osdependencies = [OS_PKG_IBVERBS_DEV] dependencies = [ ('numactl', '2.0.13'), - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', SYSTEM), ('GDRCopy', '2.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb index 854dade5cb..0ad4daad39 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -52,7 +52,7 @@ dependencies = [ ('FFmpeg', '4.3.1'), ('ImageMagick', '7.0.10-35'), ('ACTC', '1.1'), - ('OptiX', '6.5.0', '', True), + ('OptiX', '6.5.0', '', SYSTEM), ('zlib', '1.2.11'), ('libpng', '1.6.37'), ('POV-Ray', '3.7.0.8'), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index e54a2560c6..2ba344e0ac 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.21', '', True), + ('gettext', '0.21', '', SYSTEM), ('binutils', '2.35'), ] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb index c26c13b8e5..5a346a38f1 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.35', '', True)] +builddependencies = [('binutils', '2.35', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], From 614bdf51a1e489a5aa90e0f138096d4c3b08e68e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2022 22:50:41 +0200 Subject: [PATCH 2054/2365] add sanity check command for x13as --- easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb index 0687aee7c0..efe8235a51 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -41,11 +41,13 @@ builddependencies = [ build_cmd = 'make -f makefile.gf' -files_to_copy = [(["x13as"], "bin")] +files_to_copy = [(['x13as'], 'bin')] sanity_check_paths = { 'files': ['bin/x13as'], 'dirs': [], } +sanity_check_commands = ["x13as --help"] + moduleclass = 'math' From 672d5312c760ada58e1ab1a299168f7d14ebc90b Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 12 Oct 2022 18:49:19 +0200 Subject: [PATCH 2055/2365] Style fixes. --- .../p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb new file mode 100644 index 0000000000..8173740a5a --- /dev/null +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonPackage' + +name = 'PyMOL' +version = '2.5.0' + +homepage = 'https://github.com/schrodinger/pymol-open-source' +description = """ +PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D +visualization of proteins, small molecules, density, surfaces, and trajectories. +It also includes molecular editing, ray tracing, and movies. Open Source PyMOL +is free to everyone! +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"] +sources = ['v%(version)s.tar.gz'] +checksums = ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('Pmw', '2.0.1', { + 'buildopts': '', + 'installopts': '', + 'modulename': 'Pmw', + 'sources': [{ + 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', + 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], + 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], + 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], + }), +] +exts_default_options = { + 'use_pip': True, + 'download_dep_fail': True, +} + +download_dep_fail = True +use_pip = False + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyQt5', '5.15.1'), + ('glew', '2.1.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.10'), + ('freetype', '2.10.3'), + ('GLM', '0.9.9.8'), + ('netCDF', '4.7.4'), + ('Tkinter', '%(pyver)s'), +] + +buildopts = '' +buildopts += '--use-msgpackc=no ' +installopts = buildopts + +modextravars = {'PYMOL_PATH': 'lib/python%(pyshortver)s/site-packages/pymol/pymol_path'} + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/pymol'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'vis' From 6f97142a28ffe4bf9867242821392191df9b01da Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 13 Oct 2022 15:31:32 +0200 Subject: [PATCH 2056/2365] adding easyconfigs: motif-2.3.8-GCCcore-11.3.0.eb, motif-2.3.8-GCCcore-10.2.0.eb --- .../m/motif/motif-2.3.8-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..63dcdcf5ab --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'https://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +builddependencies = [ + ('Autotools', '20200321'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('util-linux', '2.36'), +] + +dependencies = [ + ('X11', '20201008'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('libjpeg-turbo', '2.0.5'), + ('bzip2', '1.0.8'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' From efc7c468889be03e1653fd38e4b451090605498c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 09:40:05 +0200 Subject: [PATCH 2057/2365] stick to http in source URL for stride.tar.gz in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb | 2 +- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb index e2b6645847..b170a6dc5f 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', - 'https://webclu.bio.wzw.tum.de/stride/' + 'http://webclu.bio.wzw.tum.de/stride/' ] sources = [ 'vmd-%(version)s.src.tar.gz', diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb index 0ad4daad39..6a7845eece 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = [ 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', - 'https://webclu.bio.wzw.tum.de/stride/' + 'http://webclu.bio.wzw.tum.de/stride/' ] sources = [ 'vmd-%(version)s.src.tar.gz', From 8f4ec8a3420a80942ebdb817d56315ef1ff28fa6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 13:52:18 +0200 Subject: [PATCH 2058/2365] make requested changes to spaln 2.4.12 easyconfig --- easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb index 364c2101be..6012bf6434 100644 --- a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb @@ -16,7 +16,10 @@ source_urls = ['https://github.com/ogotoh/spaln/archive/'] sources = ['ver%(version)s.tar.gz'] checksums = ['0c5f842131409686dbaad01778960f53f1ebba8dd83d55b454ec4bf1b6bde2af'] -dependencies = [('zlib', '1.2.11')] +dependencies = [ + ('zlib', '1.2.11'), + ('Perl', '5.32.0'), +] start_dir = 'src' @@ -26,6 +29,8 @@ prefix_opt = '--exec_prefix=' configopts = "--exec_prefix=%(installdir)s/bin --table_dir=%(installdir)s/table --alndbs_dir=%(installdir)s/seqdb " configopts += "--use_zlib=1" +fix_perl_shebang_for = ['seqdb/*.pl'] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], 'dirs': ['seqdb', 'table'], @@ -33,4 +38,6 @@ sanity_check_paths = { sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] +modextrapaths = {'PATH': 'seqdb'} + moduleclass = 'bio' From 1fc553840085806685b9dc028eccdadf6f77e6d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 13:58:10 +0200 Subject: [PATCH 2059/2365] also update $PERL5LIB to Perl module required by spaln Perl scripts are found --- easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb index 6012bf6434..1d2162cf61 100644 --- a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb @@ -38,6 +38,9 @@ sanity_check_paths = { sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] -modextrapaths = {'PATH': 'seqdb'} +modextrapaths = { + 'PATH': 'seqdb', + 'PERL5LIB': 'seqdb', +} moduleclass = 'bio' From 524bc417c70e5c7ba883abaa9108622594d57f24 Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 14 Oct 2022 17:00:05 +0200 Subject: [PATCH 2060/2365] Switch to PythonBundle. --- .../p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 53 ++++++++----------- 1 file changed, 21 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb index 8173740a5a..642fc01b62 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'PyMOL' version = '2.5.0' @@ -11,33 +11,6 @@ It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone! """ -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"] -sources = ['v%(version)s.tar.gz'] -checksums = ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'] - -exts_defaultclass = 'PythonPackage' -exts_list = [ - ('Pmw', '2.0.1', { - 'buildopts': '', - 'installopts': '', - 'modulename': 'Pmw', - 'sources': [{ - 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', - 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], - 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], - 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], - }), -] -exts_default_options = { - 'use_pip': True, - 'download_dep_fail': True, -} - -download_dep_fail = True -use_pip = False - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -51,13 +24,29 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ] -buildopts = '' -buildopts += '--use-msgpackc=no ' -installopts = buildopts +toolchain = {'name': 'foss', 'version': '2020b'} + +use_pip = False +sanity_pip_check = True + +exts_list = [ + ('Pmw', '2.0.1', { + 'modulename': 'Pmw', + 'source_tmpl': 'Pmw-patched-%(version)s-20200210-8bedfc8.zip', + 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], + 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], + }), + (name, version, { + 'buildopts': '--use-msgpackc=no', + 'installopts': '--use-msgpackc=no', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"], + 'checksums': ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'], + }), +] modextravars = {'PYMOL_PATH': 'lib/python%(pyshortver)s/site-packages/pymol/pymol_path'} -sanity_pip_check = True sanity_check_paths = { 'files': ['bin/pymol'], 'dirs': ['bin', 'lib'], From 62a2d22d229e71ba911e4059e19774b5ccfdf328 Mon Sep 17 00:00:00 2001 From: guacke Date: Sat, 15 Oct 2022 13:07:54 +0200 Subject: [PATCH 2061/2365] Fix download link Pmw. --- easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb index 642fc01b62..c96cc51c18 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -32,7 +32,7 @@ sanity_pip_check = True exts_list = [ ('Pmw', '2.0.1', { 'modulename': 'Pmw', - 'source_tmpl': 'Pmw-patched-%(version)s-20200210-8bedfc8.zip', + 'source_tmpl': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], }), From a5acee98271fd682fa3eef69b1a2107c764e075a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Jul 2022 09:15:03 +0200 Subject: [PATCH 2062/2365] Fix PyTorch 1.10.0 build on PPC --- .../PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 53 ++++++++++++------- 1 file changed, 34 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 938b94c4f9..450db866c3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -7,15 +7,9 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', @@ -23,18 +17,25 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_remove-vec-dump-functions.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', - 'PyTorch-1.10.0_skip_cmake_rpath.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '1970225700d1f9791eb553855ad3c22e7c9fd69cff2765d532506b33e449831e', # pytorch-v1.10.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch @@ -44,24 +45,38 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch + '0c8bf4b284c5c2cb4d175645d44bed674cca5218de741a8ea698cef2884a86da', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', - # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch - '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-faulty-asserts.patch + '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch + '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_remove-vec-dump-functions.patch + '5e796c83f74e77aa193fef2720a7a41e3e0eb39df726a6f0a2a1c55d37d8fcc8', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_failing_ops_tests.patch '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', - # PyTorch-1.10.0_skip_cmake_rpath.patch - 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', ] osdependencies = [OS_PKG_IBVERBS_DEV] From f5c726f11ea0214caa600629ad42972e4a96ec19 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Sep 2022 16:40:19 +0200 Subject: [PATCH 2063/2365] Fix FP16 quantization (fixes test_quantization) --- .../easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 450db866c3..412066dcf6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -20,6 +20,7 @@ patches = [ 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -51,6 +52,8 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts.patch '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch + 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch From 9174e90d657ec884afa528fd1497ffa9081a6cc6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 22 Sep 2022 11:04:57 +0200 Subject: [PATCH 2064/2365] Add PyTorch-1.10.0_fix-kineto-crash.patch --- .../easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 412066dcf6..ffbf98f586 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -21,6 +21,7 @@ patches = [ 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -54,6 +55,8 @@ checksums = [ '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch From fd40385de7721c7263ef7d7d2b63280a87549df4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 Oct 2022 11:33:16 +0100 Subject: [PATCH 2065/2365] update libxml2, libxslt sources to use gnome.org (#16419) --- .../l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb | 9 +++------ 2 files changed, 6 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb index 38a25e4b1a..aeed9cfa94 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb index d17aa440dc..fc7feb6f53 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.35')] From 433b28c05218e7e861d79b7706682525ad06c0dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 18:27:44 +0200 Subject: [PATCH 2066/2365] adding easyconfigs: CDBtools-0.99-GCC-10.2.0.eb --- .../c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb new file mode 100644 index 0000000000..11fc1a9fd9 --- /dev/null +++ b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'CDBtools' +version = '0.99' + +homepage = 'http://compbio.dfci.harvard.edu/tgi' +description = "CDB (Constant DataBase) indexing and retrieval tools for FASTA files" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta'] +sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c'] + +buildopts = 'CC="$CXX" DBGFLAGS="$CXXFLAGS"' + +files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cdbfasta', 'bin/cdbyank'], + 'dirs': [], +} + +sanity_check_commands = [ + "cdbfasta -v", + "cdbyank -v", +] + +moduleclass = 'bio' From 1bed3b341a7b7824c08f7953f8b33462ae933a9c Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 19 Oct 2022 16:39:37 +0200 Subject: [PATCH 2067/2365] adding easyconfigs: python-telegram-bot-20.0a0-GCCcore-10.2.0.eb --- ...thon-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..925a1086d5 --- /dev/null +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -0,0 +1,97 @@ +easyblock = 'PythonBundle' + +name = 'python-telegram-bot' +version = '20.0a0' + +homepage = 'https://python-telegram-bot.org/' +description = """This library provides a pure Python, asynchronous interface for the Telegram Bot API. + It's compatible with Python versions 3.7+.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('APScheduler', '3.9.1', { + 'checksums': ['65e6574b6395498d371d045f2a8a7e4f7d50c6ad21ef7313d15b1c7cf20df1e3'], + }), + ('anyio', '3.6.2', { + 'checksums': ['25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421'], + }), + ('backports.zoneinfo', '0.2.1', { + 'checksums': ['fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2'], + }), + ('cachetools', '5.0.0', { + 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], + }), + ('certifi', '2022.9.24', { + 'checksums': ['0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14'], + }), + ('charset-normalizer', '2.1.1', { + 'checksums': ['5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845'], + }), + ('flit_core', '3.7.1', { + 'checksums': ['14955af340c43035dbfa96b5ee47407e377ee337f69e70f73064940d27d0a44f'], + }), + ('h11', '0.12.0', { + 'checksums': ['47222cb6067e4a307d535814917cd98fd0a57b6788ce715755fa2b6c28b56042'], + }), + ('httpcore', '0.14.7', { + 'checksums': ['7503ec1c0f559066e7e39bc4003fd2ce023d01cf51793e3c173b864eb456ead1'], + }), + ('httpx', '0.22.0', { + 'checksums': ['d8e778f76d9bbd46af49e7f062467e3157a5a3d2ae4876a4bbfd8a51ed9c9cb4'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('pytz_deprecation_shim', '0.1.0.post0', { + 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], + }), + ('pytz', '2022.4', { + 'checksums': ['48ce799d83b6f8aab2020e369b627446696619e79645419610b9facd909b3174'], + }), + ('requests', '2.28.1', { + 'checksums': ['7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('ruffus', '2.8.4', { + 'checksums': ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'], + }), + ('setuptools', '65.5.0', { + 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('tzdata', '2022.5', { + 'checksums': ['e15b2b3005e2546108af42a0eb4ccab4d9e225e2dfbf4f77aad50c70a4b1f3ab'], + }), + ('tzlocal', '4.2', { + 'checksums': ['ee5842fa3a795f023514ac2d801c4a81d1743bbe642e3940143326b3a00addd7'], + }), + (name, version, { + 'modulename': 'telegram', + 'checksums': ['a182a3d081071f1ea34833bc68ed7d0843c1fe0d6dca1d260a0e2d253b150f71'], + }), +] + +sanity_check_commands = [ + "python -c 'from telegram import Update'", + "python -c 'from telegram.ext import ApplicationBuilder, CommandHandler, ContextTypes'", +] + +moduleclass = 'lib' From 0d5c8d3284d604276317ac61429a2a1647227c5e Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 19 Oct 2022 16:55:57 +0200 Subject: [PATCH 2068/2365] added binutils as builddependency --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index 925a1086d5..f98289dd3b 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -13,6 +13,8 @@ dependencies = [ ('Python', '3.8.6'), ] +builddependencies = [('binutils', '2.35')] + use_pip = True sanity_pip_check = True From 3295bbfdb0949a8b9c4610b82133dd33524e1d6c Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 20 Oct 2022 07:06:39 +0200 Subject: [PATCH 2069/2365] removed ruffus as dependency --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index f98289dd3b..34c1581e97 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -64,9 +64,6 @@ exts_list = [ ('rfc3986', '1.5.0', { 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], }), - ('ruffus', '2.8.4', { - 'checksums': ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'], - }), ('setuptools', '65.5.0', { 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], }), From b21f7ed2f7ac67bc089edf1ff320a607daa8eb15 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 20 Oct 2022 09:55:25 +0200 Subject: [PATCH 2070/2365] removed unnecessary dependencies --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index 34c1581e97..dfb7a16b6b 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -31,9 +31,6 @@ exts_list = [ ('cachetools', '5.0.0', { 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], }), - ('certifi', '2022.9.24', { - 'checksums': ['0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14'], - }), ('charset-normalizer', '2.1.1', { 'checksums': ['5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845'], }), @@ -55,21 +52,13 @@ exts_list = [ ('pytz_deprecation_shim', '0.1.0.post0', { 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], }), - ('pytz', '2022.4', { - 'checksums': ['48ce799d83b6f8aab2020e369b627446696619e79645419610b9facd909b3174'], - }), + # to overwrite Python's requests requirement which requires older version of idna ('requests', '2.28.1', { 'checksums': ['7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983'], }), ('rfc3986', '1.5.0', { 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], }), - ('setuptools', '65.5.0', { - 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], - }), - ('six', '1.16.0', { - 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], - }), ('sniffio', '1.3.0', { 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], }), From b7dbec47c90a4249203536de01c090aa1bdc7a73 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:55:27 +0100 Subject: [PATCH 2071/2365] adding easyconfigs: TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb and patches: tfea-1.1.4-README.md.patch --- .../TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb diff --git a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb new file mode 100644 index 0000000000..94610d8bfd --- /dev/null +++ b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -0,0 +1,67 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'TFEA' +version = '1.1.4' +_mumergever = '1.1.0' +versionsuffix = '-muMerge-%s' % _mumergever + + +homepage = 'https://github.com/Dowell-Lab/TFEA' +description = """Transcription Factor Enrichment Analysis """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.5.1'), + ('SciPy-bundle', '2020.11'), + ('pybedtools', '0.8.2'), + ('psutil', '5.9.3'), + ('SWIG', '4.0.2'), + ('ncurses', '6.2'), + ('cURL', '7.72.0'), + ('XZ', '5.2.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('ujson', '5.5.0', { + 'checksums': ['b25077a971c7da47bd6846a912a747f6963776d90720c88603b1b55d81790780'], + }), + ('pysam', '0.15.2', { + 'checksums': ['d049efd91ed5b1af515aa30280bc9cb46a92ddd15d546c9b21ee68a6ed4055d9'], + }), + ('HTSeq', '2.0.2', { + 'checksums': ['e2c7442d6ff3f97293cfa0da276576f0996eae0a66eb3c2006332ef198f7ea09'], + 'modulename': '%(name)s', + }), + ('mumerge', '1.1.0', { + 'source_urls': ['https://github.com/Dowell-Lab/mumerge/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['f8afd360800567ddb4e7b602ed63ef30d22eb41d7bfbd1dc323295cdc8a98bf3'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'patches': ['tfea-1.1.4-README.md.patch'], + 'checksums': [('fa74d0e4ab11fa7ca125d86b76ee1cb66480374a220ab01d61433d4302cb9b3a'), + ('92e53d05c2422e422e6744d42afdd04ffc267a743f6a39c9c6957be3c6bf3b30')], + 'modulename': 'TFEA' + }), +] + +sanity_check_paths = { + 'files': ['bin/TFEA', 'bin/TFEA-annotate', 'bin/TFEA-simulate'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "TFEA --help", + "TFEA-simulate -h", +] + +moduleclass = 'bio' From da98ab4a393a6f819df32c81c26d7127e0e55af4 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:34:55 +0100 Subject: [PATCH 2072/2365] download_dep_fail removed as PythonBundle --- .../easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb index 94610d8bfd..ef3a56457d 100644 --- a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb +++ b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -26,7 +26,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From 2713a6ac4ada3ac166ff0e3788aa5238c71111c8 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 12:13:47 +0100 Subject: [PATCH 2073/2365] GCCcore-10.2.0 EasyConfig file added --- .../p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9bae7e1c2b --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '5.9.3' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['7ccfcdfea4fc4b0a02ca2c31de7fcd186beb9cff8207800e14ab66f79c773af6'], + }), +] + +moduleclass = 'lib' From b1648c44de2231862b0419abe31dee87f0aaba25 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 15:58:10 +0100 Subject: [PATCH 2074/2365] download_dep_fail removed sanity_pip_check added --- easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb index 9bae7e1c2b..6cb55d2040 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] use_pip = True -download_dep_fail = True +sanity_pip_check = True exts_list = [ (name, version, { From db4c43364e05c3a9d998b5d20053969b3a7a76ae Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 25 Oct 2022 15:37:31 +0200 Subject: [PATCH 2075/2365] @jfgrimm added sanity check commands for tools pyuic5, pylupdate5, and pyrcc5; port changes to recent-ish easyconfigs. --- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb | 29 ++++++++++++++----- 1 file changed, 21 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb index b04ed87846..775d1c1a6e 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb @@ -19,20 +19,28 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - local_sipver = '5.5.0' - components = [ ('SIP', local_sipver, { 'source_urls': [PYPI_SOURCE], @@ -63,10 +71,10 @@ components = [ 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'Binary', + 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts }), ('PyQtWebEngine', version, { @@ -82,13 +90,18 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip-wheel'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip-wheel --help", + "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { From b54ae4f3806a9e6b1def90f88f4a939b962ab8eb Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 25 Oct 2022 17:17:07 +0200 Subject: [PATCH 2076/2365] Backport glibc-2.34 SIGSTKSZ patch --- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index 40d8acc91a..eb7a850b08 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain From bc29fa9913af88e6d24d85bbec6b6dfc3c1264b3 Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 25 Oct 2022 17:42:52 +0200 Subject: [PATCH 2077/2365] Fix mixed spaces/tabs --- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index eb7a850b08..a8d9bfb519 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ From 183547328af528d5c7ffbb0299a82adab16c64b7 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 25 Oct 2022 18:50:40 +0100 Subject: [PATCH 2078/2365] Patch added to ensure test-jobs are not failing due to blanks (https://github.com/pybind/pybind11/issues/3680) --- .../p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb index 60135a6d7f..8e9b6e72bf 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -1,3 +1,7 @@ +# include patch to fix failing test jobs due to additional white space +# see https://github.com/pybind/pybind11/issues/3680 +# Authors: J. Sassmannshausen / Alexander Grund + name = 'pybind11' version = '2.6.0' @@ -9,7 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/pybind/pybind11/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571'] +patches = ['1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch'] +checksums = [ + '90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571', + # 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch: + 'f0ff7416d14f9589b5d100ad021e18690cb08cb662df9d0ac21327d04bdb96fc', +] builddependencies = [ ('binutils', '2.35'), From 8853d6198b3d13ff013190397a956034b474ddff Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 26 Oct 2022 12:18:12 +0100 Subject: [PATCH 2079/2365] Name of patchfile changed --- .../easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb index 8e9b6e72bf..9eddf8c8ef 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -13,10 +13,10 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/pybind/pybind11/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch'] +patches = ['pybind11-2.6.0_fix-test-extra-whitespace.patch'] checksums = [ '90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571', - # 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch: + # pybind11-2.6.0_fix-test-extra-whitespace.patch: 'f0ff7416d14f9589b5d100ad021e18690cb08cb662df9d0ac21327d04bdb96fc', ] From 5a73934dd9e9b83e2edc1e0276dd874387ef8eaa Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 26 Oct 2022 20:38:38 +0100 Subject: [PATCH 2080/2365] adding easyconfigs: TBA-1.0-foss-2020b.eb --- .../easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb new file mode 100644 index 0000000000..d6d7f6ff55 --- /dev/null +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -0,0 +1,65 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'Tarball' + +name = 'TBA' +version = '1.0' + +homepage = 'https://github.com/jenhantao/tba' +description = """TBA (a Transcription factor Binding Analysis): +TBA is a multi-functional machine learning tool for identifying +transcription factors associated with genomic features""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/jenhantao/tba/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['97acb78e045bbd066d67213c84417f2af7f48fde1f513be22cbb46ad2966ae2c'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), + ('scikit-learn', '0.23.2'), + ('Seaborn', '0.11.1'), + ('matplotlib', '3.5.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('idr', '2.0.3', { + 'source_urls': ['https://github.com/nboley/idr/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['63e3be099b2deadfa8c7ccc3ab83659afe683f6a35bd41b2319c6ad58ca74de6'], + }), + ('joblib', '1.2.0', { + 'checksums': ['e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018'], + }), +] + +postinstallcmds = [ + "mv %(installdir)s/model_training/* %(installdir)s/bin ", + "mv %(installdir)s/default_motifs %(installdir)s/share ", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/train_model_default.sh', 'bin/train_classifier.py', + 'bin/create_features.py', 'bin/idr'], + 'dirs': ['share'], +} + +sanity_check_commands = [ + "idr --version", + "train_classifier.py -h", +] + +moduleclass = 'bio' From d76c2567ba8786deeecef2fd0b6f84c8a783e005 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Wed, 26 Oct 2022 21:40:11 +0100 Subject: [PATCH 2081/2365] Update TBA-1.0-foss-2020b.eb matplotlib demoted to 3.3.3 to avoid conflicts --- easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb index d6d7f6ff55..c3f0e23f2d 100644 --- a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('Biopython', '1.78'), ('scikit-learn', '0.23.2'), ('Seaborn', '0.11.1'), - ('matplotlib', '3.5.1'), + ('matplotlib', '3.3.3'), ] exts_defaultclass = 'PythonPackage' From 65bb94897f074c033355ea4ffb9c09ae08f7378a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 28 Oct 2022 08:45:04 +0100 Subject: [PATCH 2082/2365] fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x --- .../easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 36 ++++++++++--------- 1 file changed, 20 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index d6d21047a9..880ff3864f 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -39,24 +39,28 @@ patches = [ 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ - '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz - 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea', # gmp-6.2.0.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz - '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 - '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66', # newlib-3.3.0.tar.gz - 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # nvptx-tools-20180301.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch - 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCCcore-10.2.0_fix-has-include-Fortran.patch - '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278', # GCCcore-10.2.0_fix-ice-on-arm.patch - # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch - 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-10.2.0.tar.gz': '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d'}, + {'gmp-6.2.0.tar.bz2': 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.1.0.tar.gz': '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'}, + {'isl-0.22.1.tar.bz2': '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd'}, + {'newlib-3.3.0.tar.gz': '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66'}, + {'nvptx-tools-20180301.tar.gz': 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.3.0_nvptx_sm_35_default.patch': '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108'}, + {'GCCcore-10.2.0_fix-has-include-Fortran.patch': + 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6'}, + {'GCCcore-10.2.0_fix-ice-on-arm.patch': '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278'}, + {'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch': + 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, ] builddependencies = [ From 2539d0d6228ceed537c2e9e3424dc4238d2bc5a7 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 18:31:57 +0100 Subject: [PATCH 2083/2365] adding easyconfigs: svist4get-1.3.1-foss-2020b.eb --- .../s/svist4get/svist4get-1.3.1-foss-2020b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb new file mode 100644 index 0000000000..8ec2b2b006 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -0,0 +1,59 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'svist4get' +version = '1.3.1' + +homepage = 'https://github.com/art-egorov/svist4get' +description = """Svist4get is a simple bioinformatics tool for visualization of +genomic signal tracks in user-defined genomic windows, either arbitrary selected +by genomic coordinates or anchored to particular transcripts or genes.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('pybedtools', '0.8.2'), + ('Biopython', '1.78'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('reportlab', '3.6.9', { + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84'], + }), + + ('configs', '3.0.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('Wand', '0.6.10', { + 'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + + (name, version, { + 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/svist4get', 'bin/svist4get_copier'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "svist4get --help", + "svist4get -v", +] + +moduleclass = 'bio' From 74a0f81cf147f9dc785e254462cfa998175f3b79 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 18:33:08 +0100 Subject: [PATCH 2084/2365] adding easyconfigs: TOBIAS-0.14.0-foss-2020b.eb --- .../t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb new file mode 100644 index 0000000000..124583e843 --- /dev/null +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -0,0 +1,83 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'TOBIAS' +version = '0.14.0' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools +for performing footprinting analysis on ATAC-seq data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Seaborn', '0.11.1'), + ('pybedtools', '0.8.2'), + ('pyBigWig', '0.3.18'), + ('scikit-learn', '0.23.2'), + ('PyYAML', '5.3.1'), + ('XlsxWriter', '1.4.0'), + ('svist4get', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('adjustText', '0.7.3', { + 'checksums': ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'], + 'modulename': 'adjustText', + }), + ('botocore', '1.28.2', { + 'checksums': ['9890005735652555d1183b44bad729603d26922dc08e261e1e0a35a7bf26ba38'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.6.0', { + 'checksums': ['2ed07d3866f523cc561bf4a00fc5535827981b117dd7876f036b0c1aca42c947'], + }), + ('boto3', '1.25.2', { + 'checksums': ['43a93f8cecd882cccb2815cd76fc07a73b076027ab092a1c7cede89cb9b075f8'], + }), + ('kneed', '0.7.0', { + 'checksums': ['340d67fa183a72b0afae19846dd246a6fb7204e8d54243d8b8d3d9932f887c6e'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('MOODS-python', '1.9.4.1', { + 'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'], + 'modulename': 'MOODS', + }), + ('flit_core', '3.7.1', { + 'checksums': ['14955af340c43035dbfa96b5ee47407e377ee337f69e70f73064940d27d0a44f'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('PyPDF2', '2.11.1', { + 'checksums': ['3c7badd512c21711eb1789c2eadbf96279289c0f94452ee54a86473bfbefd732'], + 'modulename': 'PyPDF2', + }), + + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['ac74c35f981d499425147054f82142d22e52858d402d0c63ab7e8481bd156589'], + }), +] + +sanity_check_paths = { + 'files': ['bin/TOBIAS', 'bin/cluster_sites_by_overlap.py', 'bin/moods-dna.py', 'bin/jp.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "TOBIAS --help", +] + +moduleclass = 'bio' From a24de0e00bcc9816ef61d847286089c99614dd0d Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:37:54 +0100 Subject: [PATCH 2085/2365] reportlab patched so it finds EB fontconfig instead system one --- .../s/svist4get/svist4get-1.3.1-foss-2020b.eb | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index 8ec2b2b006..c228ca9af4 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -16,17 +16,19 @@ dependencies = [ ('Python', '3.8.6'), ('pybedtools', '0.8.2'), ('Biopython', '1.78'), - ('Pillow', '8.0.1'), + ('Pillow', '9.2.0'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('reportlab', '3.6.9', { - 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84'], + ('reportlab', '3.6.12', { + 'patches': ['reportlab-3.6.12-fontconfig.patch'], + 'checksums': ['b13cebf4e397bba14542bcd023338b6ff2c151a3a12aabca89eecbf972cb361a', + # reportlab-3.6.12-fontconfig.patch: + '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], }), - ('configs', '3.0.3', { 'sources': ['%(name)s-%(version)s.zip'], 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], @@ -40,7 +42,6 @@ exts_list = [ ('statistics', '1.0.3.5', { 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], }), - (name, version, { 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], }), @@ -52,7 +53,7 @@ sanity_check_paths = { } sanity_check_commands = [ - "svist4get --help", + "svist4get --help", "svist4get -v", ] From c75cda1078025a5f0cacac8d2496960b794eafd2 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:39:29 +0100 Subject: [PATCH 2086/2365] adding easyconfigs: Pillow-9.2.0-GCCcore-10.2.0.eb --- .../p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..38e7492daf --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '9.2.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = [ + '75e636fd3e0fb872693f23ccb8a5ff2cd578801251f3a4f6854c6a5d437d3c04', # Pillow-8.0.1.tar.gz +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.1.0'), + ('freetype', '2.10.3') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From d134a2123b80cf1348167c3c7612e5df5f8b688d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 00:38:28 +0100 Subject: [PATCH 2087/2365] Update svist4get-1.3.1-foss-2020b.eb Missing ImageMagick added (picked up OS installation before) --- easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index c228ca9af4..d9b689ae40 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -17,6 +17,7 @@ dependencies = [ ('pybedtools', '0.8.2'), ('Biopython', '1.78'), ('Pillow', '9.2.0'), + ('ImageMagick', '7.0.10-35'), ] use_pip = True From 32272acc6f4666f2c88bc20b6675db810767dad8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 00:53:11 +0100 Subject: [PATCH 2088/2365] Update svist4get-1.3.1-foss-2020b.eb Pillow downgraded to 8.0.1, reportlab downgraded to 3.6.9 due to conflicts with TOBIAS --- .../easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index d9b689ae40..a6339d51f1 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.8.6'), ('pybedtools', '0.8.2'), ('Biopython', '1.78'), - ('Pillow', '9.2.0'), + ('Pillow', '8.0.1'), ('ImageMagick', '7.0.10-35'), ] @@ -24,9 +24,9 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('reportlab', '3.6.12', { + ('reportlab', '3.6.9', { 'patches': ['reportlab-3.6.12-fontconfig.patch'], - 'checksums': ['b13cebf4e397bba14542bcd023338b6ff2c151a3a12aabca89eecbf972cb361a', + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84', # reportlab-3.6.12-fontconfig.patch: '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], }), From dd39e446310a5af0bcca037375da6f10f5ebd89a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 09:12:32 +0100 Subject: [PATCH 2089/2365] Update TOBIAS-0.14.0-foss-2020b.eb Empty line removed --- easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb index 124583e843..862d4fe55c 100644 --- a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -64,7 +64,6 @@ exts_list = [ 'checksums': ['3c7badd512c21711eb1789c2eadbf96279289c0f94452ee54a86473bfbefd732'], 'modulename': 'PyPDF2', }), - (name, version, { 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'checksums': ['ac74c35f981d499425147054f82142d22e52858d402d0c63ab7e8481bd156589'], From c042470e1ada7d803505ec0acddd05f67ad389b6 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 31 Oct 2022 13:35:42 +0100 Subject: [PATCH 2090/2365] favor decision in https://github.com/easybuilders/easybuild-easyconfigs/issues/16330 --- easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb index f2e75d3871..fabca76f18 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb @@ -29,8 +29,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('Perl', '5.32.0'), ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), From 4a64e22e235ad383066cfb3610734ce8fa5e001f Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 31 Oct 2022 13:41:08 +0100 Subject: [PATCH 2091/2365] Update easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb thanks for the hint Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 15338b73d9..96cb3e1828 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -7,10 +7,10 @@ version = '5.7.0' homepage = "https://confluence.ecmwf.int/display/ECFLOW/ecflow+home" description = """ecFlow is a client/server workflow package that enables users - to run a large number of programs (with dependencies on each other and on time) - in a controlled environment. It provides reasonable tolerance for hardware and - software failures, combined with restart capabilities. - It is used at ECMWF to run all our operational suites across a range of platforms.""" + to run a large number of programs (with dependencies on each other and on time) + in a controlled environment. It provides reasonable tolerance for hardware and + software failures, combined with restart capabilities. + It is used at ECMWF to run all our operational suites across a range of platforms.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} From 00f8532c72e98fe7f0039111083cc1c812e3cb48 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 31 Oct 2022 13:44:32 +0100 Subject: [PATCH 2092/2365] favor decision in https://github.com/easybuilders/easybuild-easyconfigs/issues/16330 --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 96cb3e1828..fa918e8234 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -28,7 +28,7 @@ dependencies = [ ('Boost', '1.74.0'), ('Boost.Python', '1.74.0'), ('Qt5', '5.14.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " From 47bec6f29076a69a4f7b70db4e54cdaafb26bedd Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 1 Nov 2022 08:37:25 +0100 Subject: [PATCH 2093/2365] add missing build dependency on Perl for GStreamer. And make sure to not make files suid. --- .../g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb index a4c5be9091..cc7e4f4623 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.18.4.tar.xz': '9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.55.3'), ('Ninja', '1.10.1'), + ('Perl', '5.32.0'), ('Bison', '3.7.1'), ('flex', '2.6.4'), ('GObject-Introspection', '1.66.1'), From a2fc3e2d5443146800fc9563c9748802b8da7f85 Mon Sep 17 00:00:00 2001 From: eb-test Date: Tue, 8 Nov 2022 12:55:52 +0100 Subject: [PATCH 2094/2365] include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 --- .../easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb index d156b3c22f..2b39682fdb 100644 --- a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb @@ -19,15 +19,17 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), ('coverage', '5.5'), - ('tqdm', '4.60.0'), ] use_pip = True exts_list = [ ('pytest-runner', '5.3.0', { - 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], 'modulename': 'ptr', + 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], + }), + ('tqdm', '4.60.0', { + 'checksums': ['ebdebdb95e3477ceea267decfc0784859aa3df3e27e22d23b83e9b272bf157ae'], }), (name, version, { 'checksums': ['590980baaf810c8a02705efd50eb4ace644c360470fc3dc4491d077bbb6b26fc'], From fde1376fa7710e810504d23cc84c427be243dbd7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 17:30:32 +0100 Subject: [PATCH 2095/2365] avoid that zlib + htslib are downloaded and built during installation of MetaBAT --- .../m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index 827c80520e..d8416cf32d 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ @@ -29,9 +30,11 @@ dependencies = [ ('bzip2', '1.0.8'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], From 33e13ab2f4f0aaf382e976c6e16409d015731cc0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 18:10:03 +0100 Subject: [PATCH 2096/2365] add checksum for MetaBAT patch --- .../m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index d8416cf32d..de52566483 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] -checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] +checksums = [ + {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, +] builddependencies = [ ('binutils', '2.35'), From c69c68b3022b9f5d7ac6a9e8786e4500db409163 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Nov 2022 17:53:44 +0100 Subject: [PATCH 2097/2365] add patch to fix installation of MetaBAT 2.15 on aarch64 --- .../m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index de52566483..0852b759a0 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -11,10 +11,14 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] -patches = ['MetaBAT-2.15_zlib-htslib.patch'] +patches = [ + 'MetaBAT-2.15_zlib-htslib.patch', + 'MetaBAT-2.15_fix-aarch64.patch', +] checksums = [ {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, + {'MetaBAT-2.15_fix-aarch64.patch': '061b43d6c0ac4a9acf3bd7cf3c62efc856661993a61e7d4652ed68aafb7aa7af'}, ] builddependencies = [ From 7fc385f12694d718bdc68c5e9efd812e63c4c0f8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 02:26:55 +0100 Subject: [PATCH 2098/2365] update MATLAB-Engine v2021a to PyPI package v2021a-9.10.1 --- ...TLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..97c48e8fad --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'MATLAB-Engine' +_matlab_version = '2021a' +_engine_version = '9.10.1' +version = "%s-%s" % (_matlab_version, _engine_version) + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('MATLAB', _matlab_version, '', SYSTEM), + ('Python', '3.8.6'), +] + +use_pip = True + +exts_list = [ + ('matlabengine', '9.10.1', { + 'modulename': 'matlab.engine', + 'checksums': ['c1610690dbe58ac00e74e8cbb20406208235ede47da7960238e0c2fd3bd496c0'], + }), +] + +sanity_pip_check = True + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +# Systems with old glibc (e.g. CentOS7) need to preload shim library +# modluafooter = """ +# setenv("LD_PRELOAD", pathJoin(os.getenv("EBROOTMATLAB"), "bin", "glnxa64", "glibc-2.17_shim.so")) +# """ + +moduleclass = 'math' From b344e06c3d5b622b0216ca722a97e0c1497ac4cf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 16:39:26 +0100 Subject: [PATCH 2099/2365] replace hardcoded versions for matlabengine extensions --- .../MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb index 97c48e8fad..d559c0538d 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ use_pip = True exts_list = [ - ('matlabengine', '9.10.1', { + ('matlabengine', _engine_version, { 'modulename': 'matlab.engine', 'checksums': ['c1610690dbe58ac00e74e8cbb20406208235ede47da7960238e0c2fd3bd496c0'], }), From cacdde346d66327d84f38435d7d2b37397f97ec6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 22:45:24 +0100 Subject: [PATCH 2100/2365] add build dependency on binutils to MATLAB-Engine v2021a-9.10.1 --- .../MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb index d559c0538d..f9fc548a6e 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -11,6 +11,8 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] + dependencies = [ ('MATLAB', _matlab_version, '', SYSTEM), ('Python', '3.8.6'), From 18baaba9127214a6986f1f2d5ad1a31b23b64088 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 18 Nov 2022 18:39:40 +0100 Subject: [PATCH 2101/2365] Update easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb index 63dcdcf5ab..29f68f317f 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ('Autotools', '20200321'), ('flex', '2.6.4'), ('Bison', '3.7.1'), + ('binutils', '2.35'), ('util-linux', '2.36'), ] From b7192bd2137bd6286f38abc883df78f800d2bad0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 21 Nov 2022 13:20:13 +0100 Subject: [PATCH 2102/2365] rename hyperopt to Hyperopt --- ...cell2location-0.05-alpha-fosscuda-2020b.eb | 2 +- .../Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb | 49 +++++++++++++++++++ 2 files changed, 50 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 8356b39778..23a780fa2a 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -21,7 +21,7 @@ dependencies = [ ('Java', '11', '', SYSTEM), ('SciPy-bundle', '2020.11'), ('leidenalg', '0.8.3'), - ('hyperopt', '0.2.5'), + ('Hyperopt', '0.2.5'), ('CMake', '3.18.4'), ('dill', '0.3.3'), ('IPython', '7.18.1'), diff --git a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..e78c32c265 --- /dev/null +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb @@ -0,0 +1,49 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'Hyperopt' +version = '0.2.5' + +homepage = 'https://github.com/hyperopt/hyperopt' +description = "Distributed Asynchronous Hyperparameter Optimization in Python" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy, scipy + ('networkx', '2.5'), + ('scikit-learn', '0.23.2'), + ('tqdm', '4.56.2'), + ('Java', '11', '', SYSTEM), + ('Spark', '3.1.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('pymongo', '3.11.3', { + 'checksums': ['db5098587f58fbf8582d9bda2462762b367207246d3e19623782fb449c3c5fcc'], + }), + ('lightgbm', '3.2.0', { + 'checksums': ['000c6e0e225834a8a94a84571cf41e4b7c7b97a0db6d286c1237de8ba6066726'], + }), + ('py4j', '0.10.9.2', { + 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], + }), + ('hyperopt', version, { + 'use_pip_extras': 'SparkTrials,MongoTrials,ATPE', + 'checksums': ['bc6047d50f956ae64eebcb34b1fd40f186a93e214957f20e87af2f10195295cc'], + }), +] + +moduleclass = 'math' From 43f3352f78f67d9d317a213e6a1f83f47ef901fc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Nov 2022 15:53:21 +0100 Subject: [PATCH 2103/2365] adding easyconfigs: Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb --- .../Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0a9f224eba --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx-RTD-Theme' +version = '1.1.1' + +homepage = 'https://sphinx-rtd-theme.readthedocs.io' +description = """Sphinx theme was designed to provide a great reader experience + for documentation users on both desktop and mobile devices""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [('Python', '3.8.6')] + +use_pip = True +exts_download_dep_fail = True + +exts_list = [ + ('sphinx_rtd_theme', version, { + 'checksums': ['6146c845f1e1947b3c3dd4432c28998a1693ccc742b4f9ad7c63129f0757c103'], + }), +] + +moduleclass = 'vis' From 834e75cc50844994987e597702e63c7e77e8658e Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 24 Nov 2022 16:43:37 +0000 Subject: [PATCH 2104/2365] Make sure VTK finds the specified Python --- easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb index b4161f95ea..c92d21af64 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -54,6 +54,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Other configopts += "-DVTK_USE_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" From c967178dd6847338f3a729c79ddc3d0dddf507ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 18:55:56 +0100 Subject: [PATCH 2105/2365] fix checksum for cell2location 0.05-alpha --- .../c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 8356b39778..7f105e3eeb 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -119,7 +119,7 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/BayraktarLab/cell2location/archive/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['2df1fe2b2b4ec5fcebc6c1d6146ce0cd79115bd14059b0ae882a41f1029a4efc'], + 'checksums': ['b1d4fc0e1eb8292457793d6af8228189bd24dd87837b8f4435d0a0312ed20c6b'], }), ] From feee074db9d5bce3ceb47ba28e349f5246abc7d1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 15:01:31 +0100 Subject: [PATCH 2106/2365] add flex as build dependency of cell2location v0.05 --- .../c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 7f105e3eeb..1f400b6850 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ ('Bison', '3.7.1'), + ('flex', '2.6.4'), # needed by louvain ] dependencies = [ From 56650ca267a958d96fcdbbebe2d21bc91440f753 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 10 Dec 2022 01:05:25 +0100 Subject: [PATCH 2107/2365] fix parameters of Sphinx-RTD-Theme v1.1.1 PythonBundle --- .../Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb index 0a9f224eba..b47eb8e0a2 100644 --- a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -4,15 +4,14 @@ name = 'Sphinx-RTD-Theme' version = '1.1.1' homepage = 'https://sphinx-rtd-theme.readthedocs.io' -description = """Sphinx theme was designed to provide a great reader experience - for documentation users on both desktop and mobile devices""" +description = """Sphinx theme designed to provide a great reader experience + for documentation users on both desktop and mobile devices.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [('Python', '3.8.6')] use_pip = True -exts_download_dep_fail = True exts_list = [ ('sphinx_rtd_theme', version, { @@ -20,4 +19,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'vis' From d1d4e33b78cf2993514a67e32244284ca03fab9d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 10 Dec 2022 01:33:08 +0100 Subject: [PATCH 2108/2365] add binutils as build dependecy of Sphinx-RTD-Theme v1.1.1 --- .../s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb index b47eb8e0a2..76924dcf22 100644 --- a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -9,6 +9,8 @@ description = """Sphinx theme designed to provide a great reader experience toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] + dependencies = [('Python', '3.8.6')] use_pip = True From 8c97a0800d6a16697f1701f30f5664c0a1b96b24 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 17 Dec 2022 10:11:30 +0000 Subject: [PATCH 2109/2365] update source_urls in MUMPS 5.3.*, 5.4.*, and 5.5.* --- easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb index c3b9ed471b..788e37ba40 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb index 3e9e86cfe0..2ccfcf5826 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD From 79e413eb229f978e563999c77c6685f0ffa94921 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 19 Dec 2022 15:22:53 +0800 Subject: [PATCH 2110/2365] adding easyconfigs: alsa-lib-1.2.8-GCCcore-10.2.0.eb --- .../alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a96a6a054d --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.8' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347'] + +dependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' From d93465467a50adbc81aa5dc94b014cab6cdfd86b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 19 Dec 2022 15:27:17 +0800 Subject: [PATCH 2111/2365] adding easyconfigs: umap-learn-0.4.6-foss-2020b.eb --- .../umap-learn/umap-learn-0.4.6-foss-2020b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb new file mode 100644 index 0000000000..80d6fbc581 --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb @@ -0,0 +1,32 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'umap-learn' +version = '0.4.6' + +homepage = 'https://pypi.org/project/umap-learn/' +description = """Uniform Manifold Approximation and Projection (UMAP) is a +dimension reduction technique that can be used for visualisation similarly to t-SNE, +but also for general non-linear dimension reduction.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('numba', '0.52.0'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'umap'} + +sanity_pip_check = True + +moduleclass = 'tools' From 4ed70ce522e4952382730861c4f9d980753a6ad4 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 19 Dec 2022 15:29:21 +0800 Subject: [PATCH 2112/2365] adding easyconfigs: scikit-bio-0.5.7-foss-2020b.eb --- .../scikit-bio/scikit-bio-0.5.7-foss-2020b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb new file mode 100644 index 0000000000..7ce9ef45be --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scikit-bio' +version = '0.5.7' + +homepage = 'http://scikit-bio.org' +description = """scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms +and educational resources for bioinformatics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('scikit-learn', '0.23.2'), + ('IPython', '7.18.1'), + ('h5py', '3.1.0'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('msgpack', '1.0.1', { + 'checksums': ['7033215267a0e9f60f4a5e4fb2228a932c404f237817caff8dc3115d9e7cd975'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('hdmedians', '0.14.2', { + 'checksums': ['b47aecb16771e1ba0736557255d80ae0240b09156bff434321de559b359ac2d6'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + (name, version, { + 'modulename': 'skbio', + 'checksums': ['6343ca0c621e2fcc5d1c042c8be3200664c5325956a83bea751cf1bcc75d1da9'], + }), +] + +moduleclass = 'bio' From 0beb597e8c3304cbac8f26f389c5e82e459ece0a Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:45:21 +0000 Subject: [PATCH 2113/2365] Updating download links to 'official home on GitHub' according to pcre.org --- easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb index af6d2eaca8..b44919660c 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['8fdcef8c8f4cd735169dd0225fd010487970c1bcadd49e9b90e26c7250a33dc9'] From 22ca3029252092b34cb27243ec3a70da49974812 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 13 Jul 2022 20:33:16 +1000 Subject: [PATCH 2114/2365] Update checksum also in OpenBLAS-0.3.12-GCC-10.2.0.eb. --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index a0d4dffee1..e9601f06ac 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -27,7 +27,8 @@ checksums = [ '4b3ab7260975ea2cfd7460731c0201b2c1e374cd83ae90d55b8da3e670633ba0', # OpenBLAS-0.3.12_add-missing-params-for-power.patch '4454af07290d1fe33e414023a41bb8999d6ee31887e194daa72bd23d46a0072a', - '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', # OpenBLAS-0.3.15_icelake-detection.patch + # OpenBLAS-0.3.15_icelake-detection.patch + 'aa96e1c3b1532dbafe4b6e8591688ef200e99304a902851f342cb9d467219762', ] # extensive testing can be enabled by uncommenting the line below From 408cf6d54958622f331b73273fb1d2eb28b49e04 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Thu, 22 Dec 2022 14:05:58 +1100 Subject: [PATCH 2115/2365] Use the unmodified version of the patch for OpenBLAS-0.3.12-GCC-10.2.0.eb --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index e9601f06ac..c98d769985 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -17,7 +17,7 @@ patches = [ ('timing.tgz', '.'), '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', '%(name)s-%(version)s_add-missing-params-for-power.patch', - '%(name)s-0.3.15_icelake-detection.patch', + '%(name)s-0.3.12_icelake-detection.patch', ] checksums = [ '65a7d3a4010a4e3bd5c0baa41a234797cd3a1735449a4a5902129152601dc57b', # v0.3.12.tar.gz @@ -27,8 +27,8 @@ checksums = [ '4b3ab7260975ea2cfd7460731c0201b2c1e374cd83ae90d55b8da3e670633ba0', # OpenBLAS-0.3.12_add-missing-params-for-power.patch '4454af07290d1fe33e414023a41bb8999d6ee31887e194daa72bd23d46a0072a', - # OpenBLAS-0.3.15_icelake-detection.patch - 'aa96e1c3b1532dbafe4b6e8591688ef200e99304a902851f342cb9d467219762', + # OpenBLAS-0.3.12_icelake-detection.patch + '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', ] # extensive testing can be enabled by uncommenting the line below From d2bc87fbf60ca4d6504e0009f68b6ceafb1b919a Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 23 Dec 2022 10:57:56 +0000 Subject: [PATCH 2116/2365] matplotlib version changed to 3.3.3 --- .../easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb index ef3a56457d..37bf2e3548 100644 --- a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb +++ b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), - ('matplotlib', '3.5.1'), + ('matplotlib', '3.3.3'), ('SciPy-bundle', '2020.11'), ('pybedtools', '0.8.2'), ('psutil', '5.9.3'), From fcfd36ffb04d60b80923d23dec6c1f0e2dfb8295 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 6 Jan 2023 10:03:46 +0100 Subject: [PATCH 2117/2365] take over @jfgrimm suggested change --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index fa918e8234..25947a6df2 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -32,6 +32,7 @@ dependencies = [ ] configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 90311ef9be9dc8bba4abbceeba6a507a818e6d99 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 13 Jan 2023 16:21:18 +0100 Subject: [PATCH 2118/2365] fix patch for TensorFlow 2.5+ on ARM The patch is actually wrong and may yield wrong results. Use the upstream patch from TF 2.10 --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 2 +- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index b7a9a39b86..2840f4d3d7 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -180,7 +180,7 @@ exts_list = [ # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', ], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index b4daf67aaa..3136244b06 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -189,7 +189,7 @@ exts_list = [ # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', # TensorFlow-2.5.0_fix-crash-on-shutdown.patch '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch From 11926134dc80938f8c437b008470331471202b87 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 18 Jan 2023 12:26:07 +0100 Subject: [PATCH 2119/2365] sources of p7zip v17.x moved to p7zip-project repo --- easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb index 8c1b293c37..9ceffd4c10 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'MakeCp' name = 'p7zip' version = '17.03' -homepage = 'https://github.com/jinfeihan57/p7zip/' +homepage = 'https://github.com/p7zip-project/p7zip/' description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -github_account = 'jinfeihan57' +github_account = 'p7zip-project' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['bb4b9b21584c0e076e0b4b2705af0dbe7ac19d378aa7f09a79da33a5b3293187'] From f612c5cd1db9b2cc6153acb1210519d877e3aa67 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 19 Jan 2023 14:26:09 +0100 Subject: [PATCH 2120/2365] Fix AARCH64 build --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 3 +++ .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 2840f4d3d7..503325ea6d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -161,6 +161,7 @@ exts_list = [ 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.3_fix-aarch64-build.patch', ], 'checksums': [ '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz @@ -181,6 +182,8 @@ exts_list = [ '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', + {'TensorFlow-2.5.3_fix-aarch64-build.patch': + '9bfd9a3586bb04c131c4d07a40b0ef5c2e7f474dc986449fc68817d927af0c6d'}, ], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 3136244b06..3ca12b1e63 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -167,6 +167,7 @@ exts_list = [ 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.5.3_fix-aarch64-build.patch', ], 'checksums': [ '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz @@ -194,6 +195,8 @@ exts_list = [ '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', + {'TensorFlow-2.5.3_fix-aarch64-build.patch': + '9bfd9a3586bb04c131c4d07a40b0ef5c2e7f474dc986449fc68817d927af0c6d'}, ], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', From 02887d33ab3f4b036960d5e2b0ae0bcb3585557d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Jan 2023 23:15:51 +0100 Subject: [PATCH 2121/2365] adding easyconfigs: umap-learn-0.5.3-foss-2020b.eb --- .../umap-learn/umap-learn-0.5.3-foss-2020b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb new file mode 100644 index 0000000000..e3de10224d --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb @@ -0,0 +1,41 @@ +# Author: Denis Krišťák (INUITS) +# This is a contribution from HPCNow! (http://hpcnow.com) +# Update: Erica Bianco +# License:: GPL-v3.0 +easyblock = "PythonBundle" + +name = 'umap-learn' +version = '0.5.3' + +homepage = 'https://umap-learn.readthedocs.io/en/latest/' +description = """ +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique +that can be used for visualisation similarly to t-SNE, but also for general non-linear +dimension reduction. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('numba', '0.53.1'), + ('LLVM', '11.0.0'), + ('tqdm', '4.56.2'), +] + +use_pip = True + +exts_list = [ + ('pynndescent', '0.5.7', { + 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], + }), + (name, version, { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From b13b7762085f37e654b741885ffd6a4b198269a0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Jan 2023 14:47:12 +0100 Subject: [PATCH 2122/2365] remove dependency on Pillow from scikit-bio v0.5.7 --- .../easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb index 7ce9ef45be..aeec62fa9d 100644 --- a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb @@ -16,7 +16,6 @@ dependencies = [ ('scikit-learn', '0.23.2'), ('IPython', '7.18.1'), ('h5py', '3.1.0'), - ('Pillow', '8.0.1'), ] use_pip = True From fc9c97f842d1224ebd920713b073212215a8830f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 23 Jan 2023 19:13:29 +0100 Subject: [PATCH 2123/2365] Brotli-python-1.0.9-GCCcore-10.2.0.eb --- .../Brotli-python-1.0.9-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b08a96811d --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Brotli-python' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/B/Brotli'] +sources = ['Brotli-%(version)s.zip'] +checksums = ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'brotli'} + +moduleclass = 'tools' From 055a144146b1fa72a3b2f0050047dcf7fcb7763b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Feb 2023 10:40:23 +0000 Subject: [PATCH 2124/2365] add alternative source_url for MariaDB > 10.4 --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb index 6fe1eb0f6c..0b8c7c5e09 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} local_pcre2_ver = '10.34' source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', 'https://downloads.sourceforge.net/project/pcre/pcre2/%s/' % local_pcre2_ver, ] From ca60a1dadfe59dbbacbe50133206d42e303c4724 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Feb 2023 13:21:26 +0000 Subject: [PATCH 2125/2365] remove use of rysnc in building Kent_tools --- easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb index f9110e0bf8..49423ef592 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb @@ -23,6 +23,7 @@ dependencies = [ ('util-linux', '2.36'), ] +prebuildopts = 'sed -i "s/rsync -a /cp /" %(builddir)s/userApps/kent/src/parasol/makefile && ' buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' buildopts += 'MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' From 1860aa9457f4941ed94b99b35b32f1d8e52b6ab2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 3 Feb 2023 15:40:14 +0100 Subject: [PATCH 2126/2365] Add Score-P and dependencies for 2019a/b, 2020a/b, 2021b, 2022a (CUDA) --- .../s/Score-P/Score-P-7.0-gompi-2020b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2020b.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2020b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2020b.eb new file mode 100644 index 0000000000..f24cb4ef9f --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2020b.eb @@ -0,0 +1,57 @@ +# # +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Alexander Grund +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'Score-P' +version = '7.0' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['68f24a68eb6f94eaecf500e17448f566031946deab74f2cba072ee8368af0996'] + +dependencies = [ + ('CubeLib', '4.6'), + ('CubeWriter', '4.6'), + ('libunwind', '1.4.0'), + ('OPARI2', '2.0.6'), + ('OTF2', '2.3'), + # Hardware counter support (optional): + ('PAPI', '6.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 754ee0c0ab0ca46a82051ca55457b43bf9bdc93c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Feb 2023 17:18:00 +0100 Subject: [PATCH 2127/2365] Fixes #17202 --- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb index fc7feb6f53..2c20332345 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb @@ -13,7 +13,10 @@ source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor sources = [SOURCE_TAR_XZ] checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] -builddependencies = [('binutils', '2.35')] +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] dependencies = [ ('zlib', '1.2.11'), From 597b36844556762d439c136f728e065bdfdd5d96 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Aug 2020 16:44:22 +0200 Subject: [PATCH 2128/2365] Fix invalid escape sequences in ECs --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb | 4 ++-- easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb | 2 +- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb | 2 +- easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb | 4 +++- .../l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 2 +- .../s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb | 2 +- .../s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb | 2 +- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 5 +++-- easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb | 2 +- 11 files changed, 16 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb index edbae709f1..b6a06a8326 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -40,13 +40,13 @@ start_dir = 'src' # check versions of libxml2 and libxslt from EB local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' -local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +local_sed_libver = r'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} # remove hardcoded compilation flags local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' -preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx +preconfigopts += r'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb index 875af6f2dc..0ee32908a0 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ ] configopts = "-DCGAL_HEADER_ONLY=OFF " -configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON -DWITH_GMPXX=ON" diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb index 71748cbee2..2484b33b3c 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -45,7 +45,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb index 606bd64d0d..a2b483559e 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb @@ -45,7 +45,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb index 09c2c1bb82..1168e3faf6 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb @@ -49,7 +49,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb index e7a9e16bb5..40c4ad0139 100644 --- a/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb @@ -32,6 +32,8 @@ sanity_check_paths = { 'dirs': ['share'], } -sanity_check_commands = [("prover9 -h 2>&1 | grep 'Usage: prover9 \[-h\] \[-x\] \[-p\] \[-t \] \[-f \]'", '')] +sanity_check_commands = [( + r"prover9 -h 2>&1 | grep 'Usage: prover9 \[-h\] \[-x\] \[-p\] \[-t \] \[-f \]'", '' +)] moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index 8b9541720e..1a6ef6836a 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -58,7 +58,7 @@ local_deps_patch = ( ) postinstallcmds = [ - 'find %(installdir)s -name "*.sh" -exec chmod +x {} \;', + 'find %(installdir)s -name "*.sh" -exec chmod +x {} \\;', 'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi', # Part of the installation process; longread uses porechop with custom adapters 'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/', diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb index 1f87241aa7..d37d76cfc3 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb @@ -48,7 +48,7 @@ exts_list = [ ('pandas', '1.1.4', { 'checksums': ['a979d0404b135c63954dea79e6246c45dd45371a88631cdbb4877d844e6de3b6'], # strip out use of -Werror to avoid failing compilation due to Intel compiler warning - 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, }), ('mpmath', '1.1.0', { 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb index 804efa8e74..d5dd17674e 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb @@ -48,7 +48,7 @@ exts_list = [ ('pandas', '1.1.4', { 'checksums': ['a979d0404b135c63954dea79e6246c45dd45371a88631cdbb4877d844e6de3b6'], # strip out use of -Werror to avoid failing compilation due to Intel compiler warning - 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, }), ('mpmath', '1.1.0', { 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 1d6bc7fb95..309b53a98c 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -46,12 +46,13 @@ dependencies = [ ('smithwaterman', '20160702'), ] -preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f -regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f " +preconfigopts += r"-regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" -preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " +preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \\; && " postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb index 9755379bfa..e0b1909d58 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb @@ -38,7 +38,7 @@ dependencies = [ ] # required to ensure that netcdf.mod is found -prebuildopts = "sed -i 's@-I\$(NETCDF)/include@-I\$(NETCDF)/include -I\$(NETCDFF)/include@g' configure.wps && " +prebuildopts = r"sed -i 's@-I\$(NETCDF)/include@-I\$(NETCDF)/include -I\$(NETCDFF)/include@g' configure.wps && " # workaround for "Type mismatch between actual argument" compiler errors, # see also https://www.gnu.org/software/gcc/gcc-10/porting_to.html From 0c61e8be974bfb483ce812a4418ffee26fcb624c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 7 Feb 2023 17:10:45 +0100 Subject: [PATCH 2129/2365] Make ECs consistent --- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 309b53a98c..e6a30f8717 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -52,7 +52,7 @@ preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" -preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \\; && " +preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] From 19ca4539d9ec27d47412e8f7e1f7bc23b7c50e32 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Feb 2023 16:48:31 +0100 Subject: [PATCH 2130/2365] Fix ELSI build and add missing foss versions --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 2 ++ easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 332df2352b..68020a6e29 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11 sources = [SOURCELOWER_TAR_GZ] patches = [ 'pexsi-1.2.0-mpi30.patch', + '%(name)s-%(version)s_fix-compiler-detection.patch', 'ELSI-2.7.1_bison_3.7_compat.patch', ] checksums = [ 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37', # ELSI-2.6.4_fix-compiler-detection.patch '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb index 800d33b16d..ff84be63e3 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb @@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11 sources = [SOURCELOWER_TAR_GZ] patches = [ 'pexsi-1.2.0-mpi30.patch', + '%(name)s-%(version)s_fix-compiler-detection.patch', 'ELSI-2.7.1_bison_3.7_compat.patch', ] checksums = [ 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37', # ELSI-2.6.4_fix-compiler-detection.patch '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] From 71de2974116625383426339ca07984252ae75a01 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 10 Feb 2023 14:05:07 +0100 Subject: [PATCH 2131/2365] adding easyconfigs: CHERAB-1.4.0-intel-2020b.eb, CHERAB-1.4.0-foss-2020b.eb --- .../c/CHERAB/CHERAB-1.4.0-foss-2020b.eb | 31 +++++++++++++++++++ .../c/CHERAB/CHERAB-1.4.0-intel-2020b.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb new file mode 100644 index 0000000000..e87a4eff59 --- /dev/null +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'CHERAB' +version = '1.4.0' + +homepage = 'https://cherab.github.io/documentation/index.html' + +description = """CHERAB is a python library for forward modelling diagnostics + based on spectroscopic plasma emission.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0b3c48e91582ca7e9aad0f45f982791820e070ad1c1fb17d41d58c35cadda8b'] + +builddependencies = [ + ('Cython', '3.0a5'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb new file mode 100644 index 0000000000..95c8e30c60 --- /dev/null +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'CHERAB' +version = '1.4.0' + +homepage = 'https://cherab.github.io/documentation/index.html' + +description = """CHERAB is a python library for forward modelling diagnostics + based on spectroscopic plasma emission.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0b3c48e91582ca7e9aad0f45f982791820e070ad1c1fb17d41d58c35cadda8b'] + +builddependencies = [ + ('Cython', '3.0a5'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'phys' From 5d06e81dd4656aca8dde70264c9f0b17500a2885 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 10 Feb 2023 16:27:49 +0000 Subject: [PATCH 2132/2365] remove commented out line and delete unused patch for TALON --- easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) mode change 100644 => 100755 easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb old mode 100644 new mode 100755 index 595fe31958..27cae837ee --- a/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/mortazavilab/%(name)s/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] -# patches = ['TALON-%(version)s_less_strict_deps.patch'] checksums = [ 'aeb1c1f46a4c757a8bb866b9a4446186f0f280e9391933a040de9dad30453649', # v5.0.tar.gz ] From f2c4dc413d25ff38bd67f61816c8e263f03f3e51 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Feb 2023 10:46:10 +0100 Subject: [PATCH 2133/2365] fix homepage + source URL for ELPA (due to switch to new domain) --- .../easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb | 10 +++++----- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb index 312d380e03..73968dfba3 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2020.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['15591f142eeaa98ab3201d27ca9ac328e21beabf0803b011a04183fcaf6efdde'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb index 209492c7de..36d6628f6c 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2020.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['15591f142eeaa98ab3201d27ca9ac328e21beabf0803b011a04183fcaf6efdde'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb index bd153664f9..03bbb92844 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb @@ -9,19 +9,19 @@ name = 'ELPA' version = '2021.05.002' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s_bugfix/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s_bugfix/'] sources = ['elpa-%(version)s_bugfix.tar.gz'] patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] checksums = [ - 'deabc48de5b9e4b2f073d749d335c8f354a7ce4245b643a23b7951cd6c90224b', # elpa-2021.05.002_bugfix.tar.gz - # ELPA-2021.05.002_fix_hardcoded_perl_path.patch - '69d2a7dcb61a7a699dd469a134a693e74c72b157dc72b3eba7a5dc12eb29893d', + {'elpa-2021.05.002_bugfix.tar.gz': 'deabc48de5b9e4b2f073d749d335c8f354a7ce4245b643a23b7951cd6c90224b'}, + {'ELPA-2021.05.002_fix_hardcoded_perl_path.patch': + '69d2a7dcb61a7a699dd469a134a693e74c72b157dc72b3eba7a5dc12eb29893d'}, ] builddependencies = [ From 069d486e47b4882cd1b68fb97b0a0c6e5f702720 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 16 Feb 2023 12:09:22 +0000 Subject: [PATCH 2134/2365] rename libpsml for consistency with libPSML --- .../l/libPSML/libPSML-1.1.10-GCC-10.2.0.eb | 25 +++++++++++++++++++ .../libPSML-1.1.10-iccifort-2020.4.304.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-10.2.0.eb new file mode 100644 index 0000000000..080cda40c5 --- /dev/null +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libPSML' +version = '1.1.10' + +homepage = 'https://launchpad.net/libpsml' +description = """LibPSML provides a Fortran API to parse files in the + PSeudopotential Markup Language (PSML) format.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/uploads/95c4d83d750d1ca87659b6395c8f7ea7/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['67c38b5bc26acbb77fd13794d1d92f41197a44311314f5453c82506205e0717b'] + +dependencies = [ + ('xmlf90', '1.5.4'), +] + +sanity_check_paths = { + 'files': ['include/m_psml.mod', 'lib/libpsml.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..ae80d7188d --- /dev/null +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-iccifort-2020.4.304.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libPSML' +version = '1.1.10' + +homepage = 'https://launchpad.net/libpsml' +description = """LibPSML provides a Fortran API to parse files in the + PSeudopotential Markup Language (PSML) format.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/uploads/95c4d83d750d1ca87659b6395c8f7ea7/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['67c38b5bc26acbb77fd13794d1d92f41197a44311314f5453c82506205e0717b'] + +dependencies = [ + ('xmlf90', '1.5.4'), +] + +sanity_check_paths = { + 'files': ['include/m_psml.mod', 'lib/libpsml.a'], + 'dirs': [], +} + +moduleclass = 'data' From 33757a8cf0cf4298de96ec7836096b986672ad28 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 16 Feb 2023 12:09:38 +0000 Subject: [PATCH 2135/2365] update dep name in ESL-Bundle --- .../easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb | 2 +- .../easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb index 640410c954..80ff5c2bd6 100644 --- a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('flook', '0.8.1'), ('libfdf', '0.2.2', '-serial'), ('libmbd', '0.10.4'), - ('libpsml', '1.1.10'), + ('libPSML', '1.1.10'), ('libpspio', '0.2.4'), ('libxc', '4.3.4'), ('libGridXC', '0.9.6'), diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb index e060b31d21..10c5d31e52 100644 --- a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('flook', '0.8.1'), ('libfdf', '0.2.2', '-serial'), ('libmbd', '0.10.4'), - ('libpsml', '1.1.10'), + ('libPSML', '1.1.10'), ('libpspio', '0.2.4'), ('libxc', '4.3.4'), ('libGridXC', '0.9.6'), From ca392adf53a2c51504c5d7d07b4059ee7f40fa43 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 23 Feb 2023 08:54:42 +0100 Subject: [PATCH 2136/2365] take EB Python3 root dir thx to @jfgrimm Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 25947a6df2..d699232fd9 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -33,6 +33,7 @@ dependencies = [ configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 8ffb118a21b26924bd8da6986d7490142afb7d31 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 23 Feb 2023 11:20:18 +0000 Subject: [PATCH 2137/2365] remove duplicated configopt --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index d699232fd9..25947a6df2 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -33,7 +33,6 @@ dependencies = [ configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From fac94ad0251880f4945f9809e0192a59bc634447 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 23 Feb 2023 15:14:56 +0100 Subject: [PATCH 2138/2365] adding easyconfigs: ROOT-6.22.08-foss-2020b.eb --- .../r/ROOT/ROOT-6.22.08-foss-2020b.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb new file mode 100644 index 0000000000..020ed48f66 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb @@ -0,0 +1,55 @@ +name = 'ROOT' +version = '6.22.08' + +homepage = 'https://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://root.cern.ch/download/'] +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +checksums = ['6f061ff6ef8f5ec218a12c4c9ea92665eea116b16e1cd4df4f96f00c078a2f6f'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GSL', '2.6'), + ('libxml2', '2.9.10'), + ('PCRE', '8.44'), + ('CFITSIO', '3.49'), + ('freetype', '2.10.3'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('zlib', '1.2.11'), + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('GL2PS', '1.4.2'), + ('FFTW', '3.3.8'), + ('SQLite', '3.33.0'), + ('XZ', '5.2.5'), + ('libpng', '1.6.37'), +] + +# NOTE: Ensure that each configopts string begins with a blank +# disable some components +configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" + +# make sure some components are enabled +configopts += " -Dpcre=ON -Dzlib=ON -Dpyroot=ON" +configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " + +# Add component-specific settings based on dependencies +configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' + +# Set C++ standard to C++17 for better stability +configopts += ' -DCMAKE_CXX_STANDARD=17' + +configopts += " -Dgallium-drivers=swrast" + +moduleclass = 'data' From 5c2ef825a88fea30072057e80b16aa538fb65998 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 28 Feb 2023 14:31:50 +0000 Subject: [PATCH 2139/2365] adding easyconfigs: mpmath-1.2.1-GCCcore-10.2.0.eb, mpmath-1.2.1-GCCcore-10.3.0.eb, mpmath-1.2.1-GCCcore-11.2.0.eb, mpmath-1.2.1-GCCcore-11.3.0.eb --- .../m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..60b2d1678d --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '1.2.1' + +homepage = 'https://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'] + +builddependencies = [ + ('binutils', '2.35') +] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From 40f57da61c60e41bb407d15eaa40218871de4717 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2023 16:40:56 +0100 Subject: [PATCH 2140/2365] add Math::Utils extension to recent Perl easyconfigs --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 515872cd4a..34e3a3e297 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -1796,6 +1796,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY/'], 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), ] moduleclass = 'lang' From 678995bf4d52ea9223d014587d8f6339088496c8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 8 Mar 2023 15:34:28 +0100 Subject: [PATCH 2141/2365] add missing zstd dep to Boost --- easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 1 + .../easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index faa5a1229d..963017ac24 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -23,6 +23,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.4.5'), ] configopts = '--without-libraries=python,mpi' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb index ab084d66fb..8a46e2591d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb @@ -21,6 +21,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.4.5'), ] configopts = '--without-libraries=python,mpi' From 575cac06c0596348284e7f55ff5a14df9eaf6bfb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2023 14:48:56 +0100 Subject: [PATCH 2142/2365] adding easyconfigs: eggnog-mapper-2.1.10-foss-2020b.eb --- .../eggnog-mapper-2.1.10-foss-2020b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb new file mode 100644 index 0000000000..8ebfa69235 --- /dev/null +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb @@ -0,0 +1,56 @@ +# Eggnog DB installation instructions: +# 1. 'export EGGNOG_DATA_DIR=//eggnog-mapper-data' +# 2. run 'download_eggnog_data.py' +# 3. Check the expected DB version with 'emapper.py --version' + +easyblock = 'PythonPackage' + +name = 'eggnog-mapper' +version = '2.1.10' + +homepage = 'https://github.com/eggnogdb/eggnog-mapper' +description = """EggNOG-mapper is a tool for fast functional annotation of novel +sequences. It uses precomputed orthologous groups and phylogenies from the +eggNOG database (http://eggnog5.embl.de) to transfer functional information from +fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation +of novel genomes, transcriptomes or even metagenomic gene catalogs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'eggnogdb' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e905b99ae81991aea696ba45587ae81c2dce5f03fe51d9c2a580cc2987976c8e'] + +dependencies = [ + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('HMMER', '3.3.2'), + ('DIAMOND', '2.0.7'), + ('prodigal', '2.6.3'), + ('wget', '1.20.3'), + ('MMseqs2', '13-45111'), + ('XlsxWriter', '1.4.0'), +] + +# strip out (too) strict version requirements for dependencies +preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'download_eggnog_data.py --help', + 'create_dbs.py --help', + 'emapper.py --version | grep %(version)s', +] + +options = {'modulename': 'eggnogmapper'} + +moduleclass = 'bio' From 6067f3a6f444a25172c8d4460c2d37e7422d0430 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 14 Mar 2023 13:43:52 +0100 Subject: [PATCH 2143/2365] update homepage and source url --- .../easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb index 113163554c..29e0a67ce6 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb @@ -3,13 +3,13 @@ easyblock = 'MakeCp' name = 'DFT-D3' version = '3.2.0' -homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +homepage = 'https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3' description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3'] +source_urls = ['https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3'] sources = [{'download_filename': 'dftd3.tgz', 'filename': SOURCELOWER_TGZ}] checksums = ['d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59'] From 484307680bb5d461b4479fef5a2815f2a7c55be0 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 17 Mar 2023 08:05:42 +0100 Subject: [PATCH 2144/2365] adding easyconfigs: FFTW-3.3.8-iomkl-2020b.eb --- .../f/FFTW/FFTW-3.3.8-iomkl-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iomkl-2020b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iomkl-2020b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iomkl-2020b.eb new file mode 100644 index 0000000000..a3012e1e59 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iomkl-2020b.eb @@ -0,0 +1,28 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'iomkl', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +patches = ['FFTW-%(version)s_fix-icc-no-gcc.patch'] +checksums = [ + '6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303', # fftw-3.3.8.tar.gz + '1b3319b98a2ca4ead68290b3229385c0573e22749a5a2ffb49486a0bbb37dc1e', # FFTW-3.3.8_fix-icc-no-gcc.patch +] +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' From 8f8766b1a1c7631617751b880b6ca0da09974c79 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 17 Mar 2023 13:35:38 +0100 Subject: [PATCH 2145/2365] adding easyconfigs: FFTW-3.3.8-iompi-2020b.eb --- .../f/FFTW/FFTW-3.3.8-iompi-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb new file mode 100644 index 0000000000..3c7c5f3084 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb @@ -0,0 +1,26 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'iompi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +patches = ['FFTW-%(version)s_fix-icc-no-gcc.patch'] +checksums = [ + '6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303', # fftw-3.3.8.tar.gz + '1b3319b98a2ca4ead68290b3229385c0573e22749a5a2ffb49486a0bbb37dc1e', # FFTW-3.3.8_fix-icc-no-gcc.patch +] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +runtest = 'check' + +moduleclass = 'numlib' From e03aee56db896a66e6ccb0458dd2b916abd3e8f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2023 18:48:26 +0200 Subject: [PATCH 2146/2365] adding easyconfigs: Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb --- ...s-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..f8e15be695 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Keras' +version = '2.4.3' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-2.5.0' + +homepage = 'https://keras.io/' +description = """ +Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Theano', '1.1.2', '-PyMC'), + ('PyYAML', '5.3.1'), + ('TensorFlow', local_tf_version), # provides h5py 2.1.0 +] + +use_pip = True + +exts_list = [ + ('Keras_Applications', '1.0.8', { + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'checksums': ['fedd729b52572fb108a98e3d97e1bac10a81d3917d2103cc20ab2a5f03beb973'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From cdbf62681f3932e750469484f10ba64fb7ea7511 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 07:48:24 +0200 Subject: [PATCH 2147/2365] add wrongly ommitted use_fma4 --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb index 3c7c5f3084..65082d495d 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb @@ -21,6 +21,9 @@ checksums = [ # http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html with_quad_prec = False +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + runtest = 'check' moduleclass = 'numlib' From 0d53fec444597009ed103f3825a2af56ccefc3ed Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 08:02:43 +0200 Subject: [PATCH 2148/2365] adding easyconfigs: argtable-2.13-GCCcore-10.2.0.eb --- .../argtable/argtable-2.13-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..896c622188 --- /dev/null +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'argtable' +version = '2.13' + +homepage = 'http://argtable.sourceforge.net/' +description = """ Argtable is an ANSI C library for parsing GNU style + command line options with a minimum of fuss. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] +checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['include/argtable2.h', 'lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.a'], + 'dirs': ['share'], +} + +moduleclass = 'lib' From 1f47f66d525290c553550bf9e06c515c192871d0 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 08:03:38 +0200 Subject: [PATCH 2149/2365] adding easyconfigs: Clustal-Omega-1.2.4-GCC-10.2.0.eb --- .../Clustal-Omega-1.2.4-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..df007a1ade --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by Adam Huffman +# Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Clustal-Omega' +version = '1.2.4' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee'] + +dependencies = [('argtable', '2.13')] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +sanity_check_commands = ["clustalo --help"] + +moduleclass = 'bio' From fbb560ff0a2de656999556f47ee261d87bbdd0db Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 08:21:02 +0200 Subject: [PATCH 2150/2365] adding easyconfigs: c-ares-1.17.2-GCCcore-10.2.0.eb --- .../c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6b168c4949 --- /dev/null +++ b/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'c-ares' +version = '1.17.2' + +homepage = 'https://c-ares.haxx.se' +description = "c-ares is a C library for asynchronous DNS requests (including name resolves)" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://c-ares.haxx.se/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4803c844ce20ce510ef0eb83f8ea41fa24ecaae9d280c468c582d2bb25b3913d'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['lib/libcares.a', 'lib/libcares.%s' % SHLIB_EXT, 'lib/pkgconfig/libcares.pc'], + 'dirs': ['include', 'share/man'], +} + +moduleclass = 'lib' From 3f69cae17426f46c6f01d94e19f2e4bad79972bd Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 08:25:20 +0200 Subject: [PATCH 2151/2365] adding easyconfigs: CppUnit-1.15.1-GCCcore-10.2.0.eb --- .../CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..61e5d8e491 --- /dev/null +++ b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CppUnit' +version = '1.15.1' + +homepage = 'https://freedesktop.org/wiki/Software/cppunit/' + +description = """ + CppUnit is the C++ port of the famous JUnit framework for unit testing. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://dev-www.libreoffice.org/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['89c5c6665337f56fd2db36bc3805a5619709d51fb136e51937072f63fcc717a7'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT, + 'lib/pkgconfig/cppunit.pc'], + 'dirs': ['bin', 'include/cppunit', 'share'], +} + +moduleclass = 'tools' From f33bdaf046b4681d3ce96dce9333dd748f787f43 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 8 Apr 2023 18:15:32 +0200 Subject: [PATCH 2152/2365] adding easyconfigs: astropy-4.2.1-foss-2020b.eb, astropy-4.2.1-intel-2020b.eb, astropy-5.2.2-gfbf-2022b.eb --- .../a/astropy/astropy-4.2.1-foss-2020b.eb | 40 +++++++++++++++++++ .../a/astropy/astropy-4.2.1-intel-2020b.eb | 40 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb new file mode 100644 index 0000000000..879b5774c3 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.2.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '1.7.3', { + 'modulename': 'erfa', + 'checksums': ['6cf3a645d63e0c575a357797903eac5d2c6591d7cdb89217c8c4d39777cf18cb'], + }), + ('extension-helpers', '0.1', { + 'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'], + }), + (name, version, { + 'checksums': ['ed483e472241153daec45f4b0c318c2c63d9f47305b78e6e63d32fc388c18427'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], +} + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb new file mode 100644 index 0000000000..878eb8ce9f --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.2.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '1.7.3', { + 'modulename': 'erfa', + 'checksums': ['6cf3a645d63e0c575a357797903eac5d2c6591d7cdb89217c8c4d39777cf18cb'], + }), + ('extension-helpers', '0.1', { + 'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'], + }), + (name, version, { + 'checksums': ['ed483e472241153daec45f4b0c318c2c63d9f47305b78e6e63d32fc388c18427'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], +} + +moduleclass = 'astro' From 80553e5ce2344c637b0a39b492cc2b48ef373474 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 20 Apr 2023 23:36:31 +0200 Subject: [PATCH 2153/2365] adding easyconfigs: AlphaPulldown-0.30.4-foss-2020b.eb, cctbx-base-2022.8-foss-2020b.eb, Kalign-2.0.4-GCCcore-11.2.0.eb and patches: AlphaPulldown-0.30.4_fix-deps.patch --- .../AlphaPulldown-0.30.4-foss-2020b.eb | 93 +++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb new file mode 100644 index 0000000000..e0c1549fb9 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -0,0 +1,93 @@ +# created by Denis Kristak (Inuits) +easyblock = "PythonBundle" + +name = "AlphaPulldown" +version = "0.30.4" + +homepage = "https://github.com/KosinskiLab/AlphaPulldown" +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '3.7.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ("OpenMM", "7.5.0"), + ("Kalign", "3.3.1"), + ('PyYAML', '5.3.1'), + ("cctbx-base", "2022.8"), + ('jax', '0.2.19'), # also provides absl-py + ('Biopython', '1.78'), + ('h5py', '3.1.0'), + ('IPython', '7.18.1'), + ('JupyterLab', '2.2.8'), + ('matplotlib', '3.3.3'), + ('TensorFlow', '2.4.1'), + ('tqdm', '4.56.2'), +] + +use_pip = True + +exts_list = [ + ('py3Dmol', '2.0.1.post1', { + 'modulename': 'py3Dmol', + 'checksums': ['add70ecf8f647970925eb8c1043c5c1343813fa49e613b77f0628e522c4148ac'], + }), + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('importlib-resources', '5.12.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_fix-deps.patch'], + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': [ + {'alphapulldown-0.30.4.tar.gz': '7797500abaee2e92d28034dc97844bca8c8d7281817e29dc110220824e9d1b5b'}, + {'AlphaPulldown-0.30.4_fix-deps.patch': 'c31cd3fcb6688f77a9277ccb779e54bb862c84e1cac485b03a9f00d10eb9ffe6'}, + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + "files": ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + "dirs": ["lib/python%(pyshortver)s/site-packages/alphapulldown"], +} + +sanity_check_commands = [('python -c "import alphapulldown"')] + +moduleclass = "data" From e45d58bc0fcd764e9d7f2dad0a2aedbc6df8573f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 23 Apr 2023 12:51:41 +0200 Subject: [PATCH 2154/2365] adding easyconfigs: Meep-1.26.0-foss-2020b.eb, Guile-3.0.9-GCCcore-10.2.0.eb, libGDSII-0.21-GCCcore-10.2.0.eb, libctl-4.5.1-GCCcore-10.2.0.eb, Harminv-1.4.2-foss-2020b.eb, MPB-1.11.1-foss-2020b.eb --- .../g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb | 46 ++++++++++++++++ .../h/Harminv/Harminv-1.4.2-foss-2020b.eb | 28 ++++++++++ .../libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb | 26 +++++++++ .../l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb | 31 +++++++++++ .../m/MPB/MPB-1.11.1-foss-2020b.eb | 48 +++++++++++++++++ .../m/Meep/Meep-1.26.0-foss-2020b.eb | 53 +++++++++++++++++++ 6 files changed, 232 insertions(+) create mode 100644 easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cd161186df --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.9' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['18525079ad29a0d46d15c76581b5d91c8702301bfd821666d2e1d13726162811'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('gc', '8.2.2'), + ('GMP', '6.2.0'), + ('libffi', '3.3'), + ('libunistring', '1.1'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb new file mode 100644 index 0000000000..7065f827a2 --- /dev/null +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Harminv' +version = '1.4.2' + +homepage = 'https://github.com/stevengj/harminv' +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'cstd': 'c99'} + +source_urls = ['https://github.com/stevengj/harminv/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5a9a1bf710972442f065d0d62c62d0c4ec3da4a3696d7160a35602c9470bc7a2'] + +builddependencies = [('pkg-config', '0.29.2')] + +configopts = "--with-pic --with-blas=openblas --with-lapack=openblas --enable-shared" + +sanity_check_paths = { + 'files': ['bin/harminv', 'lib/libharminv.a', 'lib/libharminv.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5ebb3d807a --- /dev/null +++ b/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libGDSII' +version = '0.21' + +homepage = 'https://github.com/HomerReid/libGDSII' +description = """libGDSII is a C++ library for working with GDSII binary data files, + intended primarily for use with the computational electromagnetism codes + scuff-em and meep but sufficiently general-purpose to allow other uses as well.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/HomerReid/libGDSII/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['31c90a4fb699746d051c0c597ef0543889c9f17b2a711fed398756ac4f1b1f4c'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/GDSIIConvert', 'include/libGDSII.h', 'lib/libGDSII.a', 'lib/libGDSII.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3dfc9fe295 --- /dev/null +++ b/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libctl' +version = '4.5.1' + +homepage = 'https://libctl.readthedocs.io/en/latest/' +description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/NanoComp/libctl/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['fcfeb2f13dda05b560f0ec6872757d9318fdfe8f4bc587eb2053a29ba328ae25'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), # required for libtool +] + +dependencies = [('Guile', '3.0.9')] + +configopts = '--with-pic --enable-shared' + +sanity_check_paths = { + 'files': ['bin/gen-ctl-io', 'lib/libctl.a', 'lib/libctlgeom.a', + 'lib/libctlgeom.%s' % SHLIB_EXT, 'lib/libctl.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb b/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb new file mode 100644 index 0000000000..bff6686a32 --- /dev/null +++ b/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'MPB' +version = '1.11.1' + +homepage = 'https://mpb.readthedocs.io/en/latest/' +description = """MPB is a free and open-source software package for computing + the band structures, or dispersion relations, and electromagnetic + modes of periodic dielectric structures, on both serial + and parallel computers. MPB is an acronym for MIT Photonic Bands.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://github.com/NanoComp/mpb/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dc55b081c56079727dac92d309f8e4ea84ca6eea9122ec24b7955f8c258608e1'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('HDF5', '1.10.7'), + ('libctl', '4.5.1'), + ('Guile', '3.0.9'), + ('libreadline', '8.0'), +] + +local_common_configopts = "--with-pic --with-blas=openblas --with-lapack=openblas " +local_common_configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " + +configopts = [ + local_common_configopts + " ", + local_common_configopts + " --with-inv-symmetry", + local_common_configopts + " --with-mpi ", + local_common_configopts + " --with-mpi --with-inv-symmetry", +] + +sanity_check_paths = { + 'files': ['bin/mpb%s' % x for x in ['', '-data', 'i', 'i-data', 'i-mpi', 'i-split', '-mpi', '-split']] + + ['lib/libmpb.a', 'lib/libmpbi_mpi.a', 'lib/libmpbi.a', 'lib/libmpb_mpi.a', 'lib/libmpb.%s' % SHLIB_EXT, + 'lib/libmpbi_mpi.%s' % SHLIB_EXT, 'lib/libmpbi.%s' % SHLIB_EXT, 'lib/libmpb_mpi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb new file mode 100644 index 0000000000..d7c07a5167 --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'Meep' +version = '1.26.0' + +homepage = 'https://meep.readthedocs.io/en/latest/' +description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package + developed at MIT to model electromagnetic systems.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['https://github.com/NanoComp/meep/releases/download/v%(version)s/'] +sources = ['meep-%(version)s.tar.gz'] +checksums = ['3f89f1bd781e46b938aa02e315a4526a4ae9896687db75c187b4f17febcbc301'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), + ('SWIG', '4.0.2') +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('MPB', '1.11.1'), + ('Harminv', '1.4.2'), + ('HDF5', '1.10.7'), + ('libctl', '4.5.1'), + ('libGDSII', '0.21'), + ('GSL', '2.6'), + ('Guile', '3.0.9'), +] + +configopts = "--with-pic --with-mpi --with-blas=openblas --with-lapack=openblas --without-gcc-arch " +configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " +configopts += "LDFLAGS=$LDFLAGS+' -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl -lmpi_mpifh'" + +sanity_check_paths = { + 'files': ['bin/meep', 'include/meep.hpp', 'lib/libmeep.a', 'lib/libpympb.a', + 'lib/libmeep.%s' % SHLIB_EXT, 'lib/libpympb.%s' % SHLIB_EXT], + 'dirs': ['include/meep', 'lib/python%(pyshortver)s/site-packages/meep', 'share/meep'], +} + +sanity_check_commands = [ + "meep --help", + "python -c 'import meep'", +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'phys' From 7b8952f46eb3fb69eeda114396a525839261374b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 24 Apr 2023 11:42:29 +0200 Subject: [PATCH 2155/2365] gc v8.0.4, libunistring v1.1 and update to Meep v1.26.0 --- .../g/gc/gc-8.2.2-GCCcore-10.2.0.eb | 42 +++++++++++++++++++ .../libunistring-1.1-GCCcore-10.2.0.eb | 31 ++++++++++++++ .../m/Meep/Meep-1.26.0-foss-2020b.eb | 1 - 3 files changed, 73 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5061399f2f --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.2' +local_libatomic_version = '7.8.0' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a + garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + {'gc-8.2.2.tar.gz': 'f30107bcb062e0920a790ffffa56d9512348546859364c23a14be264b38836a0'}, + {'libatomic_ops-7.8.0.tar.gz': '15676e7674e11bda5a7e50a73f4d9e7d60452271b8acf6fd39a71fefdf89fa31'}, +] + +builddependencies = [ + ('binutils', '2.35'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f93fd92279 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.1' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['827c1eb9cb6e7c738b171745dac0888aa58c5924df2e59239318383de0729b98'] + +builddependencies = [ + ('binutils', '2.35'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb index d7c07a5167..0b54a76009 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb @@ -35,7 +35,6 @@ dependencies = [ configopts = "--with-pic --with-mpi --with-blas=openblas --with-lapack=openblas --without-gcc-arch " configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " -configopts += "LDFLAGS=$LDFLAGS+' -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl -lmpi_mpifh'" sanity_check_paths = { 'files': ['bin/meep', 'include/meep.hpp', 'lib/libmeep.a', 'lib/libpympb.a', From 1e7611a8e027d84d7c78bf6fb80131c9a20fd80f Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Mon, 24 Apr 2023 17:51:43 +0200 Subject: [PATCH 2156/2365] adding easyconfigs: GLI-4.5.31-GCCcore-10.2.0.eb, GLI-4.5.31-GCCcore-12.2.0.eb --- .../g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7820338ddf --- /dev/null +++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +easyblock = "ConfigureMake" + +name = "GLI" +version = "4.5.31" + +homepage = "https://pgi-jcns.fz-juelich.de/portal/pages/gli.html" +description = "Graphics Language Interpreter" + +toolchain = {"name": "GCCcore", "version": "10.2.0"} +toolchainopts = {"pic": True} + +source_urls = ["http://iffwww.iff.kfa-juelich.de/gli/"] +sources = [SOURCELOWER_TAR_GZ] +checksums = ["13b7def217672ab4fa01e39977af26f3fbbe0f7bbe7e7c42c2c4aa0ea5fc8c05"] + +builddependencies = [("binutils", "2.35")] + +dependencies = [ + ('X11', '20201008'), + ('zlib', '1.2.11'), + ('Tk', '8.6.10'), + ('Tcl', '8.6.10'), + ('libtirpc', '1.3.1') +] + +preconfigopts = 'cd src && ' +configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc ' +configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib' + +prebuildopts = 'cd src &&' + +preinstallopts = 'cd src &&' + +parallel = 1 + +modextravars = { + "GLI_WSTYPE": "217", + "GLI_HOME": "%(installdir)s" +} + +modextrapaths = { + "PATH": "", + "LD_LIBRARY_PATH": "", +} + +sanity_check_paths = { + "files": ["libgks.a", "libgks.%s" % SHLIB_EXT, "libgli.a", "libgus.%s" % SHLIB_EXT], + "dirs": ["demo", "tcl/lib"], +} + +moduleclass = "vis" From 26036c363629c49f707d8c7bb5938ca3d8d87a59 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 28 Apr 2023 10:15:42 +0200 Subject: [PATCH 2157/2365] adding easyconfigs: cutadapt-2.10-GCCcore-10.2.0.eb --- .../cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b8f8f0dc94 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modufied by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Tom Strempel +# Helmholtz-Centre for Environmental Research - UFZ + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '2.10' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '0.8.4', { + 'checksums': ['dcd8f5ef5da5564f514a990573a48a0c347ee1fdbb9b6374d31592819868f7ba'], + }), + ('dnaio', '0.4.2', { + 'checksums': ['fa55a45bfd5d9272409b714158fb3a7de5dceac1034a0af84502c7f503ee84f8'], + }), + (name, version, { + 'checksums': ['936b88374b5b393a954852a0fe317a85b798dd4faf5ec52cf3ef4f3c062c242a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From a83a4d308f87ad28b528ab87588697ad81777426 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Apr 2023 11:27:24 +0200 Subject: [PATCH 2158/2365] adding easyconfigs: bcbio-gff-0.7.0-foss-2020b.eb --- .../b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb new file mode 100644 index 0000000000..66fc839020 --- /dev/null +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb @@ -0,0 +1,42 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v0.6.7 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'bcbio-gff' +version = '0.7.0' + +homepage = 'https://github.com/chapmanb/bcbb/tree/master/gff' + +description = """ +Read and write Generic Feature Format (GFF) with Biopython integration. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['f7b3922ee274106f8716703f41f05a1795aa9d73e903f4e481995ed8f5f65d2d'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' +local_targets = ['GFFOutput.py', 'GFFParser.py'] + +sanity_check_paths = { + 'files': [local_bcbiogffroot + '/BCBio/GFF/%s' % x for x in local_targets], + 'dirs': [local_bcbiogffroot], +} + +options = {'modulename': 'BCBio.GFF'} + +moduleclass = 'bio' From e4a05b31a2884d5f109cdc9e096009694c692e94 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Fri, 28 Apr 2023 16:55:35 +0200 Subject: [PATCH 2159/2365] Fix ZLIB linking --- easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb index 7820338ddf..ca2a334a1a 100644 --- a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb @@ -24,7 +24,9 @@ dependencies = [ ] preconfigopts = 'cd src && ' +preconfigopts += 'sed -i -e "/ac_cv_c_zlib=.*with_zlib/s,},}/libz.so," configure && ' configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc ' +configopts += '--with-zlib=$EBROOTZLIB/lib --with-zlibinclude=$EBROOTZLIB/include ' configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib' prebuildopts = 'cd src &&' From c23c0da440a86ded9a3c31ff870d76ec4b92cfb3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 28 Apr 2023 16:13:10 +0100 Subject: [PATCH 2160/2365] specify source_urls inside exts_default_options to ensure correct name expansion for the archivedd packages --- .../Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb | 18 ++++++++---------- .../Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb | 17 ++++++++--------- 2 files changed, 16 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb index be3f28cdb2..0489f0e3fc 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb @@ -9,37 +9,35 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('spatstat.utils', '2.1-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.utils'], 'checksums': ['ed3569fea295b62396c49cdcfe476414b0b0f3e52044175532f316a402d3f8a1'], }), ('spatstat.data', '2.1-0', { 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], }), ('spatstat.geom', '2.0-1', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'], 'checksums': ['70ebfe115e733b2e6778baf6e2935861472154c0dd21f15a84ec2a61e0a3f6e4'], }), ('spatstat.sparse', '2.0-0', { 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], }), ('spatstat.core', '2.0-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'], 'checksums': ['fde9a91bd32b7a3c8b25e802a16d470dcc919c24da5715149e1d91eeec119ba7'], }), (name, version, { diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb index d71472a2d5..b8a228157b 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb @@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('spatstat.utils', '2.2-0', { @@ -31,14 +32,12 @@ exts_list = [ 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], }), ('spatstat.geom', '2.2-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'], 'checksums': ['70b063a7f317f531b2afb3afaedb047fce81b39ee481a4067962529d6069634c'], }), ('spatstat.sparse', '2.0-0', { 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], }), ('spatstat.core', '2.2-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'], 'checksums': ['0ecbc1ae688c8d4f41db3efa6253ac8db5c432ef714240d01a2b195950d65253'], }), ('Matrix', '1.3-4', { From 0d233aa21df73796a2f5c1a6669b008cc49c45b0 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 2 May 2023 13:15:41 +0100 Subject: [PATCH 2161/2365] add Doxygen build dependency to X11 --- easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb index d1a9f51ec0..c5a69cfdb8 100644 --- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.55.3'), ('Ninja', '1.10.1'), + ('Doxygen', '1.8.20'), ] dependencies = [ From e77b1985943f429f64074f8b214f7c71ee5844b0 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 5 May 2023 19:57:21 +0200 Subject: [PATCH 2162/2365] review updates --- .../AlphaPulldown-0.30.4-foss-2020b.eb | 20 +++--- .../cctbx-base-2020.8-foss-2020b.eb | 69 +++++++++++++++++++ 2 files changed, 77 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb index e0c1549fb9..c9fa9aa972 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ # required for installing dm-tree - ('Bazel', '3.7.2'), + # ('Bazel', '3.7.2'), ] dependencies = [ @@ -29,6 +29,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('TensorFlow', '2.4.1'), ('tqdm', '4.56.2'), + ('dm-tree', '0.1.5'), ] use_pip = True @@ -45,17 +46,17 @@ exts_list = [ }), ('dm-haiku', '0.0.4', { 'modulename': 'haiku', + 'patches': ['%(name)s-%(version)s_fix-deps.patch'], 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + 'checksums': [ + {'dm-haiku-0.0.4.tar.gz': 'e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'}, + {'dm-haiku-0.0.4_fix-deps.patch': '66400ed767d25e63c0c3b6a631bc6ea2496aaac6346563669199d9874cd1c549'}, + ], }), ('toolz', '0.11.1', { 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], }), - ('dm-tree', '0.1.6', { - 'modulename': 'tree', - 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], - }), ('importlib-resources', '5.12.0', { 'modulename': 'importlib_resources', 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', @@ -68,15 +69,12 @@ exts_list = [ 'sources': ['ml_collections-%(version)s.tar.gz'], 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], }), - ('tabulate', '0.8.9', { - 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], - }), (name, version, { 'patches': ['%(name)s-%(version)s_fix-deps.patch'], 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'checksums': [ {'alphapulldown-0.30.4.tar.gz': '7797500abaee2e92d28034dc97844bca8c8d7281817e29dc110220824e9d1b5b'}, - {'AlphaPulldown-0.30.4_fix-deps.patch': 'c31cd3fcb6688f77a9277ccb779e54bb862c84e1cac485b03a9f00d10eb9ffe6'}, + {'AlphaPulldown-0.30.4_fix-deps.patch': 'ddadf42da3ca95423004f6bb7db6ce85e6a338e993411286f3bdf859e72e860f'}, ], }), ] @@ -88,6 +86,4 @@ sanity_check_paths = { "dirs": ["lib/python%(pyshortver)s/site-packages/alphapulldown"], } -sanity_check_commands = [('python -c "import alphapulldown"')] - moduleclass = "data" diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb new file mode 100644 index 0000000000..b01de853ba --- /dev/null +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb @@ -0,0 +1,69 @@ +# author: Denis Kristak (Inuits) +easyblock = "PythonBundle" + +name = "cctbx-base" +version = "2020.8" +local_pyver = "3.8.6" + +# local_pyver_special is used to create the wheel filename +# it contains the first two digits of the python version (with no delimiter) +local_tmp = local_pyver.split('.') +local_tmp.pop() +# compose a string +local_pyver_special = ''.join(local_tmp) +local_tmp = None # cleanup + +homepage = "https://github.com/cctbx/cctbx_project" +description = """ +The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix +project. The goal of the Phenix project is to advance automation of macromolecular structure determination. +Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable +library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific +applications. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', local_pyver), + ('Boost', '1.74.0'), + ('HDF5', '1.10.7'), + ('libGLU', '9.0.1'), + ('LIBSVM', '3.25'), + ('LibTIFF', '4.1.0'), + ('matplotlib', '3.3.3'), + ('mrcfile', '1.3.0'), +] + +local_metadata = "%(installdir)s/lib/python%(pyshortver)s/site-packages/cctbx_base-%(version)s.dist-info/METADATA" + + +exts_list = [ + ('reportlab', '3.5.66', { + 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], + }), + (name, version, { + 'modulename': 'cctbx', + # remove deps (they fail during sanity check, even though they are installed) + 'postinstallcmds': ["echo '' > %s" % local_metadata], + 'sources': [{ + 'download_filename': 'cctbx_base-%s-0_py%sh167b89d-cp%s-cp%sm-manylinux2010_x86_64.whl' % ( + version, local_pyver_special, local_pyver_special, local_pyver_special + ), + 'filename': 'cctbx_base-%s-cp%s-cp%s-manylinux2010_x86_64.whl' % ( + version, local_pyver_special, local_pyver_special + ), + }], + 'checksums': ['5c7ac0710d9011072c678771876aa57ca3735986ed321d403f51989a7444e592'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + "files": ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], + "dirs": ['lib/python%(pyshortver)s/site-packages/cctbx_website'], +} + +moduleclass = "lib" From d2febe064369732c4765c98004c063637a01692e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 5 May 2023 20:04:37 +0200 Subject: [PATCH 2163/2365] review updates --- .../a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb index c9fa9aa972..4bcbb49ca8 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -10,11 +10,6 @@ interaction screens and high-throughput modelling of higher-order oligomers usin toolchain = {'name': 'foss', 'version': '2020b'} -builddependencies = [ - # required for installing dm-tree - # ('Bazel', '3.7.2'), -] - dependencies = [ ('Python', '3.8.6'), ("OpenMM", "7.5.0"), From 7bd57c1a2788da306de9bc7327452c1646f35d91 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 5 May 2023 20:29:25 +0200 Subject: [PATCH 2164/2365] fixing gh errors --- .../a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb | 6 +++--- .../c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb | 1 - 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb index 4bcbb49ca8..1354c1e2a6 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -15,7 +15,7 @@ dependencies = [ ("OpenMM", "7.5.0"), ("Kalign", "3.3.1"), ('PyYAML', '5.3.1'), - ("cctbx-base", "2022.8"), + ("cctbx-base", "2020.8"), ('jax', '0.2.19'), # also provides absl-py ('Biopython', '1.78'), ('h5py', '3.1.0'), @@ -46,7 +46,7 @@ exts_list = [ 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': [ {'dm-haiku-0.0.4.tar.gz': 'e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'}, - {'dm-haiku-0.0.4_fix-deps.patch': '66400ed767d25e63c0c3b6a631bc6ea2496aaac6346563669199d9874cd1c549'}, + {'dm-haiku-0.0.4_fix-deps.patch': 'c509e0aa049401f340234b0a5eba59c9e8af8eff94b9e92f0693aeadfa4c5aa8'}, ], }), ('toolz', '0.11.1', { @@ -69,7 +69,7 @@ exts_list = [ 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'checksums': [ {'alphapulldown-0.30.4.tar.gz': '7797500abaee2e92d28034dc97844bca8c8d7281817e29dc110220824e9d1b5b'}, - {'AlphaPulldown-0.30.4_fix-deps.patch': 'ddadf42da3ca95423004f6bb7db6ce85e6a338e993411286f3bdf859e72e860f'}, + {'AlphaPulldown-0.30.4_fix-deps.patch': 'fc5bf395cb36d02efa6d538df49749e722b2d2c257197e3dac83a81c9405c0c9'}, ], }), ] diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb index b01de853ba..edb2dd6046 100644 --- a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb @@ -11,7 +11,6 @@ local_tmp = local_pyver.split('.') local_tmp.pop() # compose a string local_pyver_special = ''.join(local_tmp) -local_tmp = None # cleanup homepage = "https://github.com/cctbx/cctbx_project" description = """ From 50d80ff8616b47acd6d2df96ef1286967fe21fb6 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 10 May 2023 18:36:30 +0200 Subject: [PATCH 2165/2365] add missing FastTreeMP binary for FastTree --- .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb index 11318dc50b..2d4bc28f2b 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb @@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s - files_to_copy = [(['FastTree'], 'bin')] +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + sanity_check_paths = { 'files': ['bin/FastTree'], 'dirs': [], From a8d52316a240fc72b41e6230e5e4cb925a21a757 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2023 21:44:33 +0200 Subject: [PATCH 2166/2365] minor code cleanup in easyconfigs for cctbx-base and AlphaPullDown --- .../AlphaPulldown-0.30.4-foss-2020b.eb | 20 ++++++------- .../cctbx-base-2020.8-foss-2020b.eb | 28 ++++++++----------- 2 files changed, 22 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb index 1354c1e2a6..05ab7469fa 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -1,10 +1,10 @@ # created by Denis Kristak (Inuits) -easyblock = "PythonBundle" +easyblock = 'PythonBundle' -name = "AlphaPulldown" -version = "0.30.4" +name = 'AlphaPulldown' +version = '0.30.4' -homepage = "https://github.com/KosinskiLab/AlphaPulldown" +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' description = """AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" @@ -12,10 +12,10 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), - ("OpenMM", "7.5.0"), - ("Kalign", "3.3.1"), + ('OpenMM', '7.5.0'), + ('Kalign', '3.3.1'), ('PyYAML', '5.3.1'), - ("cctbx-base", "2020.8"), + ('cctbx-base', '2020.8'), ('jax', '0.2.19'), # also provides absl-py ('Biopython', '1.78'), ('h5py', '3.1.0'), @@ -77,8 +77,8 @@ exts_list = [ sanity_pip_check = True sanity_check_paths = { - "files": ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], - "dirs": ["lib/python%(pyshortver)s/site-packages/alphapulldown"], + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], } -moduleclass = "data" +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb index edb2dd6046..afe41e8b97 100644 --- a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb @@ -1,18 +1,15 @@ # author: Denis Kristak (Inuits) -easyblock = "PythonBundle" +easyblock = 'PythonBundle' -name = "cctbx-base" -version = "2020.8" -local_pyver = "3.8.6" +name = 'cctbx-base' +version = '2020.8' # local_pyver_special is used to create the wheel filename # it contains the first two digits of the python version (with no delimiter) -local_tmp = local_pyver.split('.') -local_tmp.pop() -# compose a string -local_pyver_special = ''.join(local_tmp) +local_pyver = '3.8.6' +local_pyver_special = ''.join(local_pyver.split('.')[:2]) -homepage = "https://github.com/cctbx/cctbx_project" +homepage = 'https://github.com/cctbx/cctbx_project' description = """ The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix project. The goal of the Phenix project is to advance automation of macromolecular structure determination. @@ -36,15 +33,11 @@ dependencies = [ local_metadata = "%(installdir)s/lib/python%(pyshortver)s/site-packages/cctbx_base-%(version)s.dist-info/METADATA" - exts_list = [ ('reportlab', '3.5.66', { 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], }), (name, version, { - 'modulename': 'cctbx', - # remove deps (they fail during sanity check, even though they are installed) - 'postinstallcmds': ["echo '' > %s" % local_metadata], 'sources': [{ 'download_filename': 'cctbx_base-%s-0_py%sh167b89d-cp%s-cp%sm-manylinux2010_x86_64.whl' % ( version, local_pyver_special, local_pyver_special, local_pyver_special @@ -54,6 +47,9 @@ exts_list = [ ), }], 'checksums': ['5c7ac0710d9011072c678771876aa57ca3735986ed321d403f51989a7444e592'], + # remove deps (they fail during sanity check, even though they are installed) + 'postinstallcmds': ["echo '' > %s" % local_metadata], + 'modulename': 'cctbx', }), ] @@ -61,8 +57,8 @@ use_pip = True sanity_pip_check = True sanity_check_paths = { - "files": ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], - "dirs": ['lib/python%(pyshortver)s/site-packages/cctbx_website'], + 'files': ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cctbx_website'], } -moduleclass = "lib" +moduleclass = 'lib' From ea6116e005817ff53ad707fa937e78d478fa5739 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 May 2023 11:27:12 +0200 Subject: [PATCH 2167/2365] consistently use make 4.3 as build dependency for recent OpenBLAS versions --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index c98d769985..48333ab642 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -31,6 +31,10 @@ checksums = [ '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', ] +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' From 54e572c4385ecd17ecdb85bc981386bff5050baa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 May 2023 11:21:06 +0200 Subject: [PATCH 2168/2365] enhance sanity check for recent LibTIFF easyconfigs --- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb index c2e41230be..30ebb82f4d 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -37,11 +37,14 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += '--disable-webp --disable-libdeflate ' +configopts += "--disable-webp --disable-libdeflate " sanity_check_paths = { - 'files': ['bin/tiffinfo'], + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], 'dirs': [], } +sanity_check_commands = ["tiffinfo -h"] + moduleclass = 'lib' From ee7f99abcdfdb56b84635fc3fbffbba162abce1b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 30 May 2023 14:08:50 +0200 Subject: [PATCH 2169/2365] adding easyconfigs: Demystify-0.0.17-foss-2020b.eb --- .../Demystify/Demystify-0.0.17-foss-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb new file mode 100644 index 0000000000..7e1167c2ac --- /dev/null +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Demystify' +version = '0.0.17' + +homepage = 'https://github.com/stacs-cp/demystify' +description = """ +Demystify is a tool which allows puzzles to be expressed in a high-level +constraint programming language and uses MUSes to automatically produce +descriptions of steps in the puzzle solving.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93779a131aa78f7de0dffdbe8e89124836b5eb6d0e9b4bc385821845a4628f52'] + +dependencies = [ + ('Python', '3.8.6'), + ('PySAT', '0.1.7.dev1'), + ('SciPy-bundle', '2020.11'), + ('Z3', '4.8.10', '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 45e29bdb8abe7c2261ac840f3eab3a7be21e798b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 2 Jun 2023 10:39:31 +0200 Subject: [PATCH 2170/2365] adding CUDA toolchains --- .../AlphaPulldown-0.30.4-fosscuda-2020b.eb | 84 +++++++++++++++++++ .../cctbx-base-2020.8-fosscuda-2020b.eb | 68 +++++++++++++++ 2 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..fe9b546828 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb @@ -0,0 +1,84 @@ +# created by Denis Kristak (Inuits) +easyblock = "PythonBundle" + +name = "AlphaPulldown" +version = "0.30.4" + +homepage = "https://github.com/KosinskiLab/AlphaPulldown" +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ("OpenMM", "7.5.0"), + ("Kalign", "3.3.1"), + ('PyYAML', '5.3.1'), + ("cctbx-base", "2020.8"), + ('jax', '0.2.19'), # also provides absl-py + ('Biopython', '1.78'), + ('h5py', '3.1.0'), + ('IPython', '7.18.1'), + ('JupyterLab', '2.2.8'), + ('matplotlib', '3.3.3'), + ('TensorFlow', '2.4.1'), + ('tqdm', '4.56.2'), + ('dm-tree', '0.1.5'), +] + +use_pip = True + +exts_list = [ + ('py3Dmol', '2.0.1.post1', { + 'modulename': 'py3Dmol', + 'checksums': ['add70ecf8f647970925eb8c1043c5c1343813fa49e613b77f0628e522c4148ac'], + }), + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'patches': ['%(name)s-%(version)s_fix-deps.patch'], + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': [ + {'dm-haiku-0.0.4.tar.gz': 'e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'}, + {'dm-haiku-0.0.4_fix-deps.patch': 'c509e0aa049401f340234b0a5eba59c9e8af8eff94b9e92f0693aeadfa4c5aa8'}, + ], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('importlib-resources', '5.12.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_fix-deps.patch'], + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': [ + {'alphapulldown-0.30.4.tar.gz': '7797500abaee2e92d28034dc97844bca8c8d7281817e29dc110220824e9d1b5b'}, + {'AlphaPulldown-0.30.4_fix-deps.patch': 'fc5bf395cb36d02efa6d538df49749e722b2d2c257197e3dac83a81c9405c0c9'}, + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + "files": ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + "dirs": ["lib/python%(pyshortver)s/site-packages/alphapulldown"], +} + +moduleclass = "data" diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb new file mode 100644 index 0000000000..b695ed8ce2 --- /dev/null +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb @@ -0,0 +1,68 @@ +# author: Denis Kristak (Inuits) +easyblock = "PythonBundle" + +name = "cctbx-base" +version = "2020.8" +local_pyver = "3.8.6" + +# local_pyver_special is used to create the wheel filename +# it contains the first two digits of the python version (with no delimiter) +local_tmp = local_pyver.split('.') +local_tmp.pop() +# compose a string +local_pyver_special = ''.join(local_tmp) + +homepage = "https://github.com/cctbx/cctbx_project" +description = """ +The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix +project. The goal of the Phenix project is to advance automation of macromolecular structure determination. +Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable +library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific +applications. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', local_pyver), + ('Boost', '1.74.0'), + ('HDF5', '1.10.7'), + ('libGLU', '9.0.1'), + ('LIBSVM', '3.25'), + ('LibTIFF', '4.1.0'), + ('matplotlib', '3.3.3'), + ('mrcfile', '1.3.0'), +] + +local_metadata = "%(installdir)s/lib/python%(pyshortver)s/site-packages/cctbx_base-%(version)s.dist-info/METADATA" + + +exts_list = [ + ('reportlab', '3.5.66', { + 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], + }), + (name, version, { + 'modulename': 'cctbx', + # remove deps (they fail during sanity check, even though they are installed) + 'postinstallcmds': ["echo '' > %s" % local_metadata], + 'sources': [{ + 'download_filename': 'cctbx_base-%s-0_py%sh167b89d-cp%s-cp%sm-manylinux2010_x86_64.whl' % ( + version, local_pyver_special, local_pyver_special, local_pyver_special + ), + 'filename': 'cctbx_base-%s-cp%s-cp%s-manylinux2010_x86_64.whl' % ( + version, local_pyver_special, local_pyver_special + ), + }], + 'checksums': ['5c7ac0710d9011072c678771876aa57ca3735986ed321d403f51989a7444e592'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + "files": ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], + "dirs": ['lib/python%(pyshortver)s/site-packages/cctbx_website'], +} + +moduleclass = "lib" From 553075f952b19b1603cd3b6679d339fd164de9fa Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 4 Jun 2023 15:43:07 +0200 Subject: [PATCH 2171/2365] Update json-fortran toolchains to reflect creation of fortran modules --- .../json-fortran-8.3.0-GCC-10.2.0.eb | 34 +++++++++++++++++++ .../json-fortran-8.3.0-iccifort-2020.4.304.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..fdd554d13d --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb @@ -0,0 +1,34 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.20.1'), +] + +configopts = [ + '-DUSE_GNU_INSTALL_CONVENTION=TRUE', +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..074e64ca5c --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb @@ -0,0 +1,34 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.20.1'), +] + +configopts = [ + '-DUSE_GNU_INSTALL_CONVENTION=TRUE', +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 96a8b97257daaeccb719bff2adffc2b54bed1e4d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Jun 2023 11:48:40 +0200 Subject: [PATCH 2172/2365] fix version string of Z3 in Demystify v0.0.17 --- .../easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb index 7e1167c2ac..ee305c91e2 100644 --- a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -19,7 +19,7 @@ dependencies = [ ('Python', '3.8.6'), ('PySAT', '0.1.7.dev1'), ('SciPy-bundle', '2020.11'), - ('Z3', '4.8.10', '-Python-%(pyver)s'), + ('Z3', '4.8.10'), ] use_pip = True From 2b7fd510b5149c5de9ffd6d15ab0936ca95bef74 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Jun 2023 11:49:29 +0200 Subject: [PATCH 2173/2365] set download_dep_fail in Demystify v0.0.17 --- easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb index ee305c91e2..356c7a33d8 100644 --- a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -23,6 +23,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True moduleclass = 'math' From f1db92b23512b07381962458cc7a20ec713d5ee0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 21 Jun 2023 14:56:48 +0200 Subject: [PATCH 2174/2365] Revert faulty sanity check command --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb index 30ebb82f4d..f5661b0938 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -45,6 +45,4 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["tiffinfo -h"] - moduleclass = 'lib' From 7a0cff8d7d066b13db8b50049efd72a59fb7539b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 21:49:56 +0200 Subject: [PATCH 2175/2365] fix homepage + source URL for popt v1.16 --- easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb index 5d58b1b1a3..b455329798 100644 --- a/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb @@ -1,19 +1,18 @@ easyblock = 'ConfigureMake' name = 'popt' -version = "1.16" +version = '1.16' -homepage = "http://freecode.com/projects/popt" +homepage = 'https://github.com/rpm-software-management/popt' description = """Popt is a C library for parsing command line parameters.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'optarch': False} -source_urls = ['https://src.fedoraproject.org/repo/pkgs/popt/popt-1.16.tar.gz/3743beefa3dd6247a73f8f7a32c14c33/'] +source_urls = ['https://ftp.osuosl.org/pub/rpm/popt/releases/historical/'] sources = [SOURCE_TAR_GZ] - checksums = ['e728ed296fe9f069a0e005003c3d6b2dde3d9cad453422a10d6558616d304cc8'] -toolchainopts = {'optarch': False} sanity_check_paths = { 'files': ['include/popt.h', ('lib/libpopt.a', 'lib64/libpopt.a'), From cb056bff2e11235a35f0069d82a4ab551a8680a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 21:51:31 +0200 Subject: [PATCH 2176/2365] sync EIGENSOFT 7.2.1 using foss/2020b with more recent EIGENSOFT easyconfigs --- .../e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb | 22 +++++++++++-------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb index 6199519bcc..09a1107118 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics # 6.1.4 modified by: # Adam Huffman # The Francis Crick Institute @@ -15,21 +15,25 @@ name = 'EIGENSOFT' version = '7.2.1' homepage = 'https://www.hsph.harvard.edu/alkes-price/software/' -description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. -2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal -components analysis to explicitly model ancestry differences between cases and controls along continuous axes of -variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral -populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. +2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal +components analysis to explicitly model ancestry differences between cases and controls along continuous axes of +variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral +populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/DReichLab/EIG/archive'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_Fix_makefile_openblas.patch'] +patches = [ + '%(name)s-%(version)s_Fix_makefile_openblas.patch', + ('%(name)s-%(version)s_restore-ploteig.patch', 0), +] checksums = [ 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz 'e49e3754f2326210114fe5a731a77c7ffd240c8a9134eb8e8e1517bfe06c71e1', # EIGENSOFT-7.2.1_Fix_makefile_openblas.patch + '8a7a0273ae4d0d3ec0c9927facd41a1a43b8540725af3bd06e007cd86afaf9e0', # EIGENSOFT-7.2.1_restore-ploteig.patch ] dependencies = [ @@ -44,10 +48,10 @@ buildopts = ' && make install' files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] -fix_perl_shebang_for = ['bin/*.perl'] +fix_perl_shebang_for = ['bin/*.perl', 'bin/ploteig'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL", "ploteig"]], 'dirs': [] } From b07ab1be175f199abb675717f0d409097a6303b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 22:06:31 +0200 Subject: [PATCH 2177/2365] explicitely specify -DPython3_INCLUDE_DIRS and -DPython3_LIBRARIES in ecFlow configure command Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 25947a6df2..ad372170aa 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -33,6 +33,8 @@ dependencies = [ configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DPython3_INCLUDE_DIRS=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPython3_LIBRARIES=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From bb3c00fcbc2dbc688df4ef5e53ad49417c3c6000 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 22:06:52 +0200 Subject: [PATCH 2178/2365] avoid hardcoding Python version, use %(pyshortver)s template instead Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index ad372170aa..877a0a096e 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -42,7 +42,7 @@ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_commands = ['ecflow_client --help'] sanity_check_paths = { 'files': ['bin/ecflow_client', 'bin/ecflow_server'], - 'dirs': ['lib/python3.8/site-packages/ecflow', 'share/ecflow/etc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/ecflow', 'share/ecflow/etc'], } moduleclass = "vis" From 215bd17c7a22f6c6e1e1f318b5c4b95c1237ec7e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 09:29:07 +0200 Subject: [PATCH 2179/2365] use SHLIB_EXT constant in libSBML easyconfig --- easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb index ea2d22663c..bbf22c8faf 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb @@ -43,7 +43,6 @@ checksums = [ '52b3274ce1fdfb329bc53feb67b9862833a1240539eca2f137fcdca00800e34e', # libsbml-fix_perl_auto_case.patch ] - builddependencies = [ ('CMake', '3.18.4'), ('make', '4.3'), @@ -66,11 +65,10 @@ configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF ' configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' configure_cmd += '../libSBML-%(version)s-Source/' - runtest = 'check' sanity_check_paths = { - 'files': ['lib64/libsbml.so', 'lib64/perl5/vendor_perl/LibSBML.pm'], + 'files': ['lib64/libsbml.%s' % SHLIB_EXT, 'lib64/perl5/vendor_perl/LibSBML.pm'], 'dirs': ['lib64', 'include', 'share'] } @@ -78,5 +76,4 @@ modextrapaths = { 'PERL5LIB': 'lib64/perl5/vendor_perl/', } - moduleclass = 'bio' From 8c4a2fd8ead49ea5599643b83e9c9789f1bc39c1 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 22 Jun 2023 09:48:33 +0100 Subject: [PATCH 2180/2365] Update easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 877a0a096e..2238d74273 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -33,6 +33,7 @@ dependencies = [ configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " configopts += "-DPython3_INCLUDE_DIRS=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPython3_LIBRARIES=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' From 9e84650217c2059e61334b8b559dc0f347c8628d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 12:02:53 +0200 Subject: [PATCH 2181/2365] add sanity check command for jq 1.5 --- easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb index 139e674e29..926327a17f 100644 --- a/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["jq --help"] + moduleclass = 'tools' From 8add571d66fa9bbcbae8e9aa94d83cc48ec431c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 12:06:14 +0200 Subject: [PATCH 2182/2365] add sanity check commands for Mesquite 2.3.0 --- .../easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb index 5121180a91..d28f9928ee 100644 --- a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb @@ -23,4 +23,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "msqquality -h", + "msqshape -h", +] + moduleclass = 'math' From b810481737825538a36d4adcac6ffa171233a640 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Thu, 22 Jun 2023 14:53:33 +0200 Subject: [PATCH 2183/2365] fix typo in segemehl-0.3.4-iccifort-2020.4.304.eb Co-authored-by: Alexander Grund --- .../s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb index 7a0308a476..1dba3da238 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb @@ -7,7 +7,7 @@ homepage = 'https://www.bioinf.uni-leipzig.de/Software/segemehl/' description = """segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able - to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.""" From 9ddc9027cabd7d046e2283a52cd890a8f01929f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 17:27:26 +0200 Subject: [PATCH 2184/2365] retain useful comment regarding disabling 'vectorize' toolchain option --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb index 38e19f85b0..c39a721d0c 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb @@ -13,6 +13,9 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2020b'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. toolchainopts = {'cstd': 'c++14', 'vectorize': False} source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] From f2b5f117f1f4f05fb785818fd77a7e2f496bb962 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 23 Jun 2023 11:16:17 +0100 Subject: [PATCH 2185/2365] add sanity check commands Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 2238d74273..eea4370632 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -40,10 +40,14 @@ prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -sanity_check_commands = ['ecflow_client --help'] sanity_check_paths = { 'files': ['bin/ecflow_client', 'bin/ecflow_server'], 'dirs': ['lib/python%(pyshortver)s/site-packages/ecflow', 'share/ecflow/etc'], } +sanity_check_commands = [ + "ecflow_client --help", + "python -c 'import ecflow'", +] + moduleclass = "vis" From 4f14114ed61edc32f43cf0e7f31559bd6fef5346 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 23 Jun 2023 11:34:23 +0100 Subject: [PATCH 2186/2365] update homepage --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index eea4370632..9d74ea2b9e 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -5,7 +5,7 @@ easyblock = "CMakeMake" name = 'ecFlow' version = '5.7.0' -homepage = "https://confluence.ecmwf.int/display/ECFLOW/ecflow+home" +homepage = "https://ecflow.readthedocs.io/en/latest/index.html" description = """ecFlow is a client/server workflow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides reasonable tolerance for hardware and From 4c851826e4d02335f00128ae63b9953c718b3a3f Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 23 Jun 2023 12:09:25 +0100 Subject: [PATCH 2187/2365] fix boost linking --- .../e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 9d74ea2b9e..66a241be8a 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -31,11 +31,15 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " -configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " -configopts += "-DPython3_INCLUDE_DIRS=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPython3_LIBRARIES=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts = " ".join([ + "-DBOOST_ROOT=$EBROOTBOOST", + "-DENABLE_STATIC_BOOST_LIBS=OFF", + "-DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib/libboost_python38.so", + "-DPython3_ROOT_DIR=$EBROOTPYTHON", + "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python", + "-DPython3_INCLUDE_DIRS=$EBROOTPYTHON/include/python%(pyshortver)s", + "-DPython3_LIBRARIES=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s" % SHLIB_EXT, +]) prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 5e38546384f4b52341fc52b9a11b0f12c0d616f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Jun 2023 13:27:04 +0200 Subject: [PATCH 2188/2365] remove excess trailing whitespace --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 66a241be8a..d4ce0c41bf 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -31,7 +31,7 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -configopts = " ".join([ +configopts = " ".join([ "-DBOOST_ROOT=$EBROOTBOOST", "-DENABLE_STATIC_BOOST_LIBS=OFF", "-DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib/libboost_python38.so", From d4c711574bbc24ef985770b4bf49acbe52a334a8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 23 Jun 2023 20:51:50 +0100 Subject: [PATCH 2189/2365] remove out of date comment --- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb | 3 --- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb | 3 --- 2 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb index 794ce9c825..2d5442b132 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb @@ -14,9 +14,6 @@ source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/ sources = [SOURCELOWER_TAR_GZ] checksums = ['195d5593772fc483f63f08794d79e4bab30c2ec58e6ce4b0fb6bcc0e0c48f31d'] -# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, -# other for new source tarball downloaded from GitHub - builddependencies = [('CMake', '3.18.4')] separate_build_dir = True diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb index 332c5869a4..1637aac0c6 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb @@ -14,9 +14,6 @@ source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/ sources = [SOURCELOWER_TAR_GZ] checksums = ['195d5593772fc483f63f08794d79e4bab30c2ec58e6ce4b0fb6bcc0e0c48f31d'] -# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, -# other for new source tarball downloaded from GitHub - builddependencies = [('CMake', '3.18.4')] separate_build_dir = True From f2ba0552a4b0f9edab857786a9dc7de5bf180f37 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 23 Jun 2023 20:56:25 +0100 Subject: [PATCH 2190/2365] update homepage for SUNDIALS 5.x and 6.x --- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb | 2 +- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb index 51543acdb7..29b35cb830 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '5.7.0' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb index ccf4e47963..52675e145f 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '5.7.0' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb index 5c283e4de3..76e6c5a3a9 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '5.7.0' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" From 768f84055a435338a0e82222c068ffca4d963717 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 29 Jun 2023 10:25:26 +0200 Subject: [PATCH 2191/2365] Update easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb b/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb index 92c0827777..1bce2a99d5 100644 --- a/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb +++ b/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb @@ -12,8 +12,8 @@ data.""" toolchain = {'name': 'intel', 'version': '2020b'} -# download sources from http://aim.tkgristmill.com/download/download.html (requires login) -# to run in professional mode, add required license files to the main AIMAll directory +download_instructions = """Download sources from http://aim.tkgristmill.com/download/download.html (requires login). +To run in professional mode, add required license files to the main AIMAll directory.""" sources = [ {'filename': 'aimall_%s_linux_64bit.tar.gz' % version.replace('.', '_'), 'extract_cmd': 'tar -xzf %s --strip-components=1'}, From 44cabf4f17fa44a367fddfaa50dac2d58c311076 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 30 Jun 2023 13:33:19 +0100 Subject: [PATCH 2192/2365] use upstream patch for symmbol compatibility in XZ 5.2.5 --- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index 2ba344e0ac..a76867949b 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -21,13 +21,13 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5_fix-symbols.patch', 'xz-5.2.5-cve-2022-1271.patch', ] checksums = [ - '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch - '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch + {'xz-5.2.5.tar.bz2': '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df'}, + {'xz-5.2.5_fix-symbols.patch': 'ce80545e7bd88466fd9561a8abb9da87e62ebc71a1531c909a492fa2844da6d0'}, + {'xz-5.2.5-cve-2022-1271.patch': '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec'}, ] builddependencies = [ From d1d10cc0b71c1080caf3632d115fb20ed6302959 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 30 Jun 2023 14:11:49 +0100 Subject: [PATCH 2193/2365] add system Autotools as a builddependency --- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index a76867949b..ab86b893cc 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -33,6 +33,8 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.21', '', SYSTEM), + # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency + ('Autotools','20220317', '', SYSTEM), ('binutils', '2.35'), ] From 31451147114f49489406747d969e69458e180bc3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 30 Jun 2023 14:33:48 +0100 Subject: [PATCH 2194/2365] add missing space --- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index ab86b893cc..633fc22773 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -34,7 +34,7 @@ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.21', '', SYSTEM), # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency - ('Autotools','20220317', '', SYSTEM), + ('Autotools', '20220317', '', SYSTEM), ('binutils', '2.35'), ] From 759eadaddf4502def1a7ecd32a2d5612f2e6414f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jul 2023 20:01:26 +0200 Subject: [PATCH 2195/2365] remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs --- easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb index 020ed48f66..ab70796cf4 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb @@ -50,6 +50,4 @@ configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' # Set C++ standard to C++17 for better stability configopts += ' -DCMAKE_CXX_STANDARD=17' -configopts += " -Dgallium-drivers=swrast" - moduleclass = 'data' From 2f6ef81dba4a5d05fe7dfbec08dd45daa002d637 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Jul 2023 11:00:14 +0200 Subject: [PATCH 2196/2365] Remove superflous dependencies from Horovod --- .../h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb | 1 - .../h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb index 7335bc5ac2..5a3037fc26 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ ('CMake', '3.18.4'), - ('flatbuffers', '1.12.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb index 450a4626c5..838513f4e8 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ ('CMake', '3.18.4'), - ('flatbuffers', '1.12.0'), ] dependencies = [ ('Python', '3.8.6'), From 3c07fee989ff430c85c0b0b6432041f6fa8d1b80 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Jul 2023 13:31:32 +0200 Subject: [PATCH 2197/2365] adding easyconfigs: Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.11.0.eb, Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.12.1.eb, Horovod-0.28.1-foss-2021b-CUDA-11.5.2-PyTorch-1.12.1.eb, Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb, Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.1.eb, Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb, Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb --- ...vod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 0000000000..3d2eb91b26 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.9.0' +versionsuffix = '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('PyTorch', local_pt_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 9492ba66ec3104f657f4e23ef8a3579e38225c73 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 7 Jul 2023 23:35:01 +0200 Subject: [PATCH 2198/2365] adding easyconfigs: Z3-4.10.2-GCCcore-11.3.0-Python-3.10.4.eb, Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb, Z3-4.8.11-GCCcore-10.3.0-Python-3.9.5.eb, Z3-4.8.12-GCCcore-11.2.0-Python-3.9.6.eb, Z3-4.8.16-GCCcore-11.3.0-Python-3.10.4.eb, Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb --- .../Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb new file mode 100644 index 0000000000..ab0584e8a8 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.8.10' +versionsuffix = '-Python-%(pyver)s' +_z3_solver_version = '%s.0' % version + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3_solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('GMP', '6.2.0'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py &&""" +_enable_gmp = "sed -i 's/^GMP=.*/GMP=True/' core/scripts/mk_util.py &&" + +exts_list = [ + ('z3-solver', _z3_solver_version, { + 'modulename': 'z3', + 'checksums': ['cd022a66524685bdd8b265027bd22f24c35f8db29a4287d005e0005757ffdc21'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + "cd %%(installdir)s && ln -s %s/include include" % _z3_site_path, + "cd %%(installdir)s/lib && ln -s ../%s/lib/libz3.so libz3.so" % _z3_site_path, +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From e14446e77c7678d743fe068ebdde4ba1eda79112 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 11 Jul 2023 17:19:15 +0200 Subject: [PATCH 2199/2365] use Z3 with Python bindings in Demystify v0.0.17 --- .../easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb index 356c7a33d8..3a7d86ba8d 100644 --- a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -19,7 +19,7 @@ dependencies = [ ('Python', '3.8.6'), ('PySAT', '0.1.7.dev1'), ('SciPy-bundle', '2020.11'), - ('Z3', '4.8.10'), + ('Z3', '4.8.10', '-Python-%(pyver)s'), ] use_pip = True From fccf4a49dccbe0f8da97e0a7f89a4678e0aef70f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 26 Jul 2023 14:19:21 +0100 Subject: [PATCH 2200/2365] fix flags and options in ScaLAPACK 2.1.0 --- .../s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb | 5 +---- 3 files changed, 3 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb index 1a51184125..adf6c43a9c 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,9 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb index 2fba79399b..e39f1c4ac2 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,9 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLAPACK/lib/liblapack.a" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb index 33b69ea09a..6d01acd1ff 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'iimpi', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,9 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], From 4a3c955a0c8a5c75fbe3982f3784d3a36950130d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 26 Jul 2023 14:55:18 +0100 Subject: [PATCH 2201/2365] revert how MPI is configured due to failure --- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb | 4 +++- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb | 4 +++- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb | 4 +++- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb index adf6c43a9c..6b0e672b3b 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2020b'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,6 +32,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb index e39f1c4ac2..e21675f74c 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2020b'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,6 +32,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLAPACK/lib/liblapack.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb index 6d01acd1ff..a0eb663ad6 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'iimpi', 'version': '2020b'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,6 +32,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], From 6e3231c702969ab07a801617bc59e87aadbf5b89 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 26 Jul 2023 15:31:57 +0100 Subject: [PATCH 2202/2365] undo changes to iimpi version --- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb index a0eb663ad6..33b69ea09a 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'iimpi', 'version': '2020b'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -34,6 +34,7 @@ configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' configopts += '-DCMAKE_C_COMPILER=mpicc ' configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], From 97353c013b0812f130eb9b1040ed020d488cf59a Mon Sep 17 00:00:00 2001 From: rocky_build Date: Mon, 31 Jul 2023 16:22:02 -0400 Subject: [PATCH 2203/2365] {bio}[foss/2020b] PartitionFinder v2.1.1 + PyTables v3.5.2 new source url --- ...onFinder-2.1.1-foss-2020b-Python-2.7.18.eb | 48 +++++++++++++++++++ ...PyTables-3.5.2-foss-2020b-Python-2.7.18.eb | 2 +- 2 files changed, 49 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PartitionFinder/PartitionFinder-2.1.1-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/p/PartitionFinder/PartitionFinder-2.1.1-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/PartitionFinder/PartitionFinder-2.1.1-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..71d28c2fc1 --- /dev/null +++ b/easybuild/easyconfigs/p/PartitionFinder/PartitionFinder-2.1.1-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,48 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'PartitionFinder' +version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.robertlanfear.com/partitionfinder' +description = """PartitionFinder 2 is a Python program for simultaneously +choosing partitioning schemes and models of molecular evolution for phylogenetic +analyses of DNA, protein, and morphological data. You can PartitionFinder 2 +before running a phylogenetic analysis, in order to decide how to divide up +your sequence data into separate blocks before analysis, and to simultaneously +perform model selection on each of those blocks.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'brettc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ccf3718996ee6ca496909b4b97d2b075028e0543eba3bc47a8c14b689c84e061'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', versionsuffix), + ('scikit-learn', '0.20.4', versionsuffix), + ('PyTables', '3.5.2', versionsuffix), +] + +postinstallcmds = ["cd %(installdir)s && chmod a+x PartitionFinder*"] +fix_python_shebang_for = ["*.py"] + +sanity_check_paths = { + 'files': ['%(name)sMorphology.py', '%(name)sProtein.py', '%(name)s.py'], + 'dirs': ['partfinder'], +} + +sanity_check_commands = [ + '%(name)s.py -p %(parallel)s %(installdir)s/examples/nucleotide/test.phy', + '%(name)sProtein.py -p %(parallel)s %(installdir)s/examples/aminoacid/test.phy', + '%(name)sMorphology.py -p %(parallel)s %(installdir)s/examples/morphology/test.phy --raxml', +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb index ce4f3ad63b..23f3a638cb 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb @@ -17,7 +17,7 @@ description = """PyTables is a package for managing hierarchical datasets and de toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = ['https://github.com/PyTables/PyTables/archive/'] +source_urls = ['https://github.com/PyTables/PyTables/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s-fix-libs.patch'] checksums = [ From 002f5839d7ba5a3301b8f17391071feab05cd6c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Aug 2023 21:55:24 +0200 Subject: [PATCH 2204/2365] fix installation of Python bindings for Arrow 0.17.1 by adding `--no-build-isolation` to `pip install` command --- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb | 4 +++- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 4 +++- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 4 +++- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb index e348b0044c..e4a039c796 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -44,7 +44,8 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -57,6 +58,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 8f577b4f44..941c31686a 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -47,7 +47,8 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -60,6 +61,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index 101f92aa06..0551ea8b33 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -44,7 +44,8 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -57,6 +58,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] From 46fb084a4c397635800478d0f28ac86ccabe0213 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 12:35:19 +0200 Subject: [PATCH 2205/2365] Fix spelling of BOOL values in CMake configopts CMake defines options as uppercase: > True if the constant is 1, ON, YES, TRUE, Y, or a non-zero number > False if the constant is 0, OFF, NO, FALSE, N, IGNORE, NOTFOUND, the empty string, or ends in the suffix -NOTFOUND Although it (now?) says "Named boolean constants are case-insensitive." this may not have always been the case. So make all values for `-DBUILD_SHARED_LIBS` ON/OFF to be consistent. --- easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb | 2 +- .../easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb index 958caa83e6..c4ec8d0dba 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('CMake', '3.18.4'), ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb index 148464f5a7..40c8715239 100644 --- a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(versi sources = [SOURCELOWER_TAR_GZ] checksums = ['5d1abd3dc3286167caf0c326ef14838ac8360aa1e912bd7bd6d212259fbff1ac'] -configopts = ['-DBUILD_SHARED_LIBS=on'] +configopts = '-DBUILD_SHARED_LIBS=ON' builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb index 38ed055e46..b7e6e5f85e 100644 --- a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(versi sources = [SOURCELOWER_TAR_GZ] checksums = ['5d1abd3dc3286167caf0c326ef14838ac8360aa1e912bd7bd6d212259fbff1ac'] -configopts = ['-DBUILD_SHARED_LIBS=on'] +configopts = '-DBUILD_SHARED_LIBS=ON' builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb index 28be3ea21d..7b350bf610 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=true'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], From 6ce7a50fb247eb86ddb88af27e0632379de737c3 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Wed, 23 Aug 2023 17:53:19 +0200 Subject: [PATCH 2206/2365] Remove EGL vendor dir prepend due to move to EasyBlock --- easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb index a2dbdd6eb6..2c63a42feb 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb @@ -67,7 +67,4 @@ configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" # This helps in certain X forwarding situations (e.g. XQuartz) postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] -# Tells libglvnd where to find EGL libraries -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} - moduleclass = 'vis' From da7656338f61b0d801167b518facb9db3a7cc737 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Sep 2023 09:50:22 +0200 Subject: [PATCH 2207/2365] strip out hardcoded -march=native used by RapidJSON 1.1.0 --- .../easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb index 0fd88903d3..c59421ba5d 100644 --- a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb @@ -22,6 +22,8 @@ builddependencies = [ ('CMake', '3.18.4'), ] +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " sanity_check_paths = { 'files': ['lib/pkgconfig/%(name)s.pc'], From f761fb31a9391c3376737ac4fb04f29254187fe3 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 6 Sep 2023 10:58:21 +0200 Subject: [PATCH 2208/2365] Disable detection of Dbus broker for at-spi2-core --- .../a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb index d065df3ef5..c157f92352 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb @@ -29,6 +29,8 @@ dependencies = [ ('X11', '20201008'), ] +# Hard disable Dbus broker detection +preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { From 53904181ae02539aae4ca6bf3f5992c6bda7da75 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 6 Sep 2023 11:28:07 +0200 Subject: [PATCH 2209/2365] Fix flake8 --- .../a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb index c157f92352..18f70fd3f8 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ dependencies = [ ] # Hard disable Dbus broker detection -preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" +preconfigopts = "sed -i s/'dbus_broker.found()'/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { From dcb91a6ddfdc0d6a23efe88c675fda0a180e8a68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2023 18:24:10 +0200 Subject: [PATCH 2210/2365] fix moduleclass for gdbm --- easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb index b28c2fd68d..9072dc51ea 100644 --- a/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb @@ -28,4 +28,4 @@ sanity_check_paths = { 'dirs': ['share/man'] } -moduleclass = "lib" +moduleclass = 'lib' From b6289167899b7c767b17d84ec48d61e09b893766 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Sep 2023 12:27:09 +0200 Subject: [PATCH 2211/2365] add patch for MPFR 4.1.0 to fix failing tsprintf test with glibc >= 2.37 --- easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb index 07cac7df6c..bedc68d8e8 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'] +patches = ['MPFR-4.1.0_patch-fix-tsprintf-test.patch'] +checksums = [ + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '51bdcb5ba5365f0a3b4be3ddf2af4c08ce05dfcd02478ad11e75f4fea40503eb'}, +] builddependencies = [ ('binutils', '2.35'), From 35a483f646650b3e09b7625a4cbf8f5e606cfd7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Sep 2023 12:32:31 +0200 Subject: [PATCH 2212/2365] fix patch for MFPR 4.1.0 to fix broken tsprint test on glibc >= 2.37 --- easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb index bedc68d8e8..b43fbb0dc5 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = ['MPFR-4.1.0_patch-fix-tsprintf-test.patch'] checksums = [ {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, - {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '51bdcb5ba5365f0a3b4be3ddf2af4c08ce05dfcd02478ad11e75f4fea40503eb'}, + {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '039fad7a79ec4a9fd9ce77c9a73d9278187b8430087bc1afec18883df40321ae'}, ] builddependencies = [ From 1b1240ad883d00b4f63a3adffd7383c1fdd9a79b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Sep 2023 15:41:38 +0200 Subject: [PATCH 2213/2365] backport lchown patch to PMIx 3.1.x + 3.2.x --- easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb index efe2a2d3ed..fa9cd00470 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb @@ -23,7 +23,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['88934195174455df478b996313095df25b51d0caf5a5cce01b22f0ccdc6c5cf7'] +patches = ['PMIx-3.1.x_lchown.patch'] +checksums = [ + {'pmix-3.1.5.tar.bz2': '88934195174455df478b996313095df25b51d0caf5a5cce01b22f0ccdc6c5cf7'}, + {'PMIx-3.1.x_lchown.patch': '9a4d5e3cb0e619f2e9ac2ffad0b8cb2b22f5c67973080724c79519fb34d55776'}, +] builddependencies = [('binutils', '2.35')] From 0ff613532881104225334db85580f650562f8c62 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 15 Sep 2023 16:18:38 +0100 Subject: [PATCH 2214/2365] adding easyconfigs: NBO-7.0.10-GCC-10.2.0.eb, NBO-7.0.10-GCC-9.3.0.eb, NBO-7.0.10-GCC-10.3.0.eb, NBO-7.0.10-GCC-11.2.0.eb, NBO-7.0.10-GCC-11.3.0.eb, NBO-7.0.10-GCC-12.2.0.eb and patches: NBO-7.0.10_make.patch --- .../n/NBO/NBO-7.0.10-GCC-10.2.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb new file mode 100644 index 0000000000..fc8d53fb04 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb @@ -0,0 +1,54 @@ +# this recipe is configured for use with Gaussian G16, revision A03 or later + +easyblock = 'MakeCp' + +name = 'NBO' +version = '7.0.10' + +homepage = 'http://nbo.chem.wisc.edu/' +description = """ The Natural Bond Orbital (NBO) program is a discovery tool +for chemical insights from complex wavefunctions. """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers + +# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +sources = ['nbo%(version)s-src.tar.gz'] +patches = [ + 'NBO-%(version)s_make.patch', +] +checksums = [ + {'nbo7.0.10-src.tar.gz': 'a60d1f4d4592ec386b5378841d9fba75918c48b50de08d8de0a50db42bc96da1'}, + {'NBO-7.0.10_make.patch': 'c37f5a9980c56198f9610611b0fbda8ad65c961ec19b163d602dc3330fced145'}, +] + +dependencies = [ + ('OpenBLAS', '0.3.12'), +] + +local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers + +buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' +buildopts += 'BLASLIB="$LDFLAGS $LIBBLAS" ' +buildopts += 'INT=%s ' % local_intlength + +parallel = 1 + +files_to_copy = ['bin', 'dox', 'man', 'tests'] + +postinstallcmds = [ + 'sed -i -e "s|setenv GAUNBO.*|setenv GAUNBO g16nbo|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv BINDIR.*|setenv BINDIR %(installdir)s/bin|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv INT.*|setenv INT %s|" %%(installdir)s/bin/gaunbo{6,7}' % local_intlength, + 'cp %(builddir)s/nbo7/gennbo %(builddir)s/nbo7/gennbo.sh %(installdir)s/bin', + 'sed -i -e "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo', + 'sed -i "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo.sh', +] + +sanity_check_paths = { + 'files': ['bin/%s.%s.exe' % (x, local_intlength) for x in ('gennbo', 'g09nbo', 'g16nbo', 'nbo7')], + 'dirs': [], +} + +moduleclass = 'chem' From 47e90ed07191efb5b5b33ec2cca64c98223beb7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Sep 2023 15:13:03 +0200 Subject: [PATCH 2215/2365] fix permission issues when copying xvfb-run script in Xvfb easyconfigs --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb index 5341032753..43d07a3d4e 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb @@ -95,7 +95,9 @@ components = [ }), ] -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] sanity_check_paths = { 'files': ['bin/Xvfb', 'bin/xvfb-run'], From 19317c3fa41e669fa04fe22dad0e137ec88a970d Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 19 Sep 2023 17:43:21 +0100 Subject: [PATCH 2216/2365] Some suggested cleanup done, used gfbf toolchain where possible --- easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb index fc8d53fb04..c09432b5ec 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb @@ -30,7 +30,6 @@ dependencies = [ local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' -buildopts += 'BLASLIB="$LDFLAGS $LIBBLAS" ' buildopts += 'INT=%s ' % local_intlength parallel = 1 From ed8b695fc662fa6aa08476f2d78ab1099c70355a Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 20 Sep 2023 15:10:13 +0100 Subject: [PATCH 2217/2365] Installa instructions added, test report uploaded --- easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb index c09432b5ec..2ae4e5ed5c 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb @@ -12,8 +12,10 @@ for chemical insights from complex wavefunctions. """ toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers -# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx -# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +download_instructions = """ +NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +""" sources = ['nbo%(version)s-src.tar.gz'] patches = [ 'NBO-%(version)s_make.patch', From 7ea7229d70ce5e43924eb391f77d660f8b26024e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Sep 2023 12:09:17 +0200 Subject: [PATCH 2218/2365] fix source URL for segemehl 0.3.4 --- easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb | 2 +- .../s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb index f6c29cfd24..80454f74e0 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb @@ -14,7 +14,7 @@ description = """segemehl is a software to map short sequencer reads to referenc toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] +source_urls = ['http://legacy.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb index 1dba3da238..e9ae1cd887 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb @@ -14,7 +14,7 @@ description = """segemehl is a software to map short sequencer reads to referenc toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] +source_urls = ['http://legacy.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] From e4d4993d3386fae725b3e3f98b1f9f4af0c1c7bb Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 28 Sep 2023 14:56:30 +0200 Subject: [PATCH 2219/2365] avoid hardcoded paths for pillow --- easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 7bdf247647..6c8f256ce9 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -28,6 +28,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb index 38e7492daf..f925080a09 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -26,6 +26,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True From 24cfa8eb1fe11cec01ed2e420685d87a579341a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 16:22:19 +0200 Subject: [PATCH 2220/2365] adding easyconfigs: imutils-0.5.4-fosscuda-2020b.eb --- .../i/imutils/imutils-0.5.4-fosscuda-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..0c948731f6 --- /dev/null +++ b/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'imutils' +version = '0.5.4' + +homepage = 'https://github.com/jrosebr1/imutils' +description = """A series of convenience functions to make basic image processing operations such as translation, +rotation, resizing, skeletonization, and displaying Matplotlib images easier with OpenCV and Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['03827a9fca8b5c540305c0844a62591cf35a0caec199cb0f2f0a4a0fb15d8f24'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('OpenCV', '4.5.1', '-contrib'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'vis' From 06be63bb3de1c0864496a4e440d46a1e65cd1de4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Oct 2023 08:48:39 +0200 Subject: [PATCH 2221/2365] use Java/1.8 wrapper for SNAP-ESA and SNAP-ESA-python --- ...0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb new file mode 100644 index 0000000000..d68dbe513e --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'SNAP-ESA-python' +version = '8.0' +local_javasuffix = '-Java-%(javaver)s' +versionsuffix = local_javasuffix + '-Python-%(pyver)s' + +homepage = 'https://step.esa.int/main/toolboxes/snap/' +description = "Python interface to the Sentinel Application Platform (SNAP) API" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Java', '1.8', '', SYSTEM), + ('SNAP-ESA', version, local_javasuffix, SYSTEM), + ('Python', '2.7.18'), +] + +local_pysite = 'lib/python%(pyshortver)s/site-packages' +local_pyinstalldir = '%%(installdir)s/%s' % local_pysite + +postinstallcmds = [ + # Install snappy from SNAP-ESA + # snappy-conf is buggy and it hangs after doing the installation of snappy, + # start snappy-conf in a new SID and kill all processes of its PGID + # whenever it prints the final line starting with "or copy" + "mkdir -p %s" % local_pyinstalldir, + ('LOG="$(mktemp -d)/snappy-conf.log"; mkfifo $LOG; trap "rm -f $LOG" EXIT;' + 'setsid snappy-conf $EBROOTPYTHON/bin/python %s 2>&1 > $LOG & CONFPID=$!;' + 'while read line; do echo "$line"; [ -z "${line##or copy*}" ] && kill -- -$CONFPID; done < $LOG;') + % local_pyinstalldir, +] + +sanity_check_paths = { + 'files': [], + 'dirs': [local_pysite], +} + +sanity_check_commands = ["python -c 'import snappy'"] + +modextrapaths = {'PYTHONPATH': [local_pysite]} + +local_javaopts = " -Dsnap.pythonExecutable=python" +local_javaopts += " -Dsnap.pythonModuleDir=%s" % local_pyinstalldir + +modluafooter = 'setenv("JAVA_TOOL_OPTIONS", os.getenv("JAVA_TOOL_OPTIONS").."%s")' % local_javaopts + +moduleclass = 'geo' From 66a7eeb9df064355ad6c1b16ba2e4ff369e251ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 17 Oct 2023 13:31:13 +0200 Subject: [PATCH 2222/2365] Disable threadedmpi with gompi for recent SCOTCH --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb index 82ed7faf68..ce355224a7 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb @@ -11,6 +11,7 @@ toolchainopts = {'pic': True} source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] +threadedmpi = False builddependencies = [ ('Bison', '3.7.1'), From 6bc6ed7eafea9d44296df3cbcd8307ff7517810d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Oct 2023 15:31:53 +0200 Subject: [PATCH 2223/2365] take into account that $JAVA_TOOL_OPTIONS may not be defined + add modtclfooter equivalent to modluafooter --- ...-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb index d68dbe513e..410cd5034d 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb @@ -43,6 +43,10 @@ modextrapaths = {'PYTHONPATH': [local_pysite]} local_javaopts = " -Dsnap.pythonExecutable=python" local_javaopts += " -Dsnap.pythonModuleDir=%s" % local_pyinstalldir -modluafooter = 'setenv("JAVA_TOOL_OPTIONS", os.getenv("JAVA_TOOL_OPTIONS").."%s")' % local_javaopts +# update $JAVA_TOOL_OPTIONS when module is loaded, use empty string as default value if $JAVA_TOOL_OPTIONS is not set +modluafooter = 'setenv("JAVA_TOOL_OPTIONS", (os.getenv("JAVA_TOOL_OPTIONS") or "") .. "%s")' % local_javaopts +# likewise, but when using Tcl as module syntax +local_tcl_JAVA_TOOL_OPTIONS = '[expr {[info exists ::env(JAVA_TOOL_OPTIONS)] ? $::env(JAVA_TOOL_OPTIONS) : ""}]' +modtclfooter = 'setenv JAVA_TOOL_OPTIONS [concat %s "%s"]' % (local_tcl_JAVA_TOOL_OPTIONS, local_javaopts) moduleclass = 'geo' From c4d45b91a1431833a80033a7114795ff296e6b31 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 20 Oct 2023 11:21:37 +0200 Subject: [PATCH 2224/2365] fix pybind11 incompatibility with some CUDA versions and add Catch2 dependency for tests --- .../easyconfigs/c/Catch2/Catch2-2.13.9.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/Catch2/Catch2-2.13.9.eb diff --git a/easybuild/easyconfigs/c/Catch2/Catch2-2.13.9.eb b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.9.eb new file mode 100644 index 0000000000..23d28166d6 --- /dev/null +++ b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.9.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Catch2' +version = '2.13.9' + +homepage = 'https://github.com/catchorg/Catch2' +description = """A modern, C++-native, header-only, + test framework for unit-tests, TDD and BDD + - using C++11, C++14, C++17 and later +""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/catchorg/Catch2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['06dbc7620e3b96c2b69d57bf337028bf245a211b3cddb843835bfe258f427a52'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('GCCcore', '10.2.0'), # required to a access CMake when using hierarchical module naming scheme + ('binutils', '2.35', '', ('GCCcore', '10.2.0')), # to make CMake compiler health check pass on old systems + ('CMake', '3.18.4', '', ('GCCcore', '10.2.0')), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/catch2', 'lib64/cmake'], +} + +moduleclass = 'lib' From 5715ba07370fe4de34da3718369eeddef385c8f5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 23 Oct 2023 10:51:17 +0200 Subject: [PATCH 2225/2365] Remove executable flag from Easyconfigs This permission flag seems to have been set accidentally. --- easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb | 0 easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb | 0 .../easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb | 0 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb | 0 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb | 0 .../easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb | 0 .../s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb | 0 .../s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb | 0 easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb | 0 9 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb mode change 100755 => 100644 easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb mode change 100755 => 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb mode change 100755 => 100644 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb mode change 100755 => 100644 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb mode change 100755 => 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb mode change 100755 => 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb mode change 100755 => 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb mode change 100755 => 100644 easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/datamash/datamash-1.5-GCCcore-10.2.0.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb old mode 100755 new mode 100644 From 18774c6ceec227de1d4ee0ad7b87cf048efb1f25 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Mon, 23 Oct 2023 19:06:19 +0200 Subject: [PATCH 2226/2365] remove source_urls from exts_default_options since default value is used in Nipype-1.6.0-foss-2020b.eb --- easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb index b4ace4a205..ce60ce71e3 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('traits', '6.2.0', { 'checksums': ['16fa1518b0778fd53bf0547e6a562b1787bf68c8f6b7995a13bd1902529fdb0c'], From a0509eab78c3bfeb82ee9a2cfd2b29f3d0929972 Mon Sep 17 00:00:00 2001 From: xina Date: Wed, 25 Oct 2023 13:53:59 +0200 Subject: [PATCH 2227/2365] generalize wget using sysroot template --- easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb index b553d12489..5dd1424e3c 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] From 8c0baf1c4f41c9e047e5c6b17810243b4340d7c1 Mon Sep 17 00:00:00 2001 From: xina Date: Thu, 26 Oct 2023 15:28:54 +0200 Subject: [PATCH 2228/2365] fix style for long lines --- easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb index 5dd1424e3c..a32a03e427 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb @@ -32,7 +32,10 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] From 884ddb32d9ddeb2fcdfb828d82c7fd80bd69bfda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 Oct 2023 14:28:25 +0100 Subject: [PATCH 2229/2365] add sanity check commands for recent GDB versions --- easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb index ce54295778..0300093f74 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' From e940ffee6e63a2bf62355f5e6901f1baff87ea4f Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 30 Oct 2023 10:36:46 +0100 Subject: [PATCH 2230/2365] Only set flag --enable-asmjit when installing on x86_64 --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb index da1d6cc277..dd7b783721 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -35,7 +35,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb index efbec7485f..10d4af1198 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used From eeb835d570dbf623df76192a42503de58df2cdcc Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 30 Oct 2023 16:01:43 +0100 Subject: [PATCH 2231/2365] remove flag since it is auto-enabled since version 2.8 --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb | 1 + easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb index dd7b783721..73cd893be2 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -36,6 +36,7 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' if ARCH == 'x86_64': + # the flag is not supported on aarch64 configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb index 10d4af1198..dc86085993 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -34,6 +34,7 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' if ARCH == 'x86_64': + # the flag is not supported on aarch64 configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' From 864863fb9664b0262d9e4f46154dbd3f85f4ad3d Mon Sep 17 00:00:00 2001 From: Xavier Delaruelle Date: Fri, 3 Nov 2023 21:06:15 +0100 Subject: [PATCH 2232/2365] Fix some typos found in software descriptions There are some typos in the docs/version-specific/supported-software.md document reported by codespell tool [1]. Most often these issues comes from the upstream description of the software, which has usually been corrected since the creation of the easyconfig file. This commit fixes the typo issues in software description for non-archived easyconfig files. [1] https://github.com/codespell-project/codespell --- .../easyconfigs/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb | 2 +- easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb | 2 +- .../easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb | 2 +- easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb index 6e85259214..5c7ed9eed8 100644 --- a/easybuild/easyconfigs/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb @@ -6,7 +6,7 @@ version = '0.1.20' versionsuffix = '-R-%(rver)s' homepage = 'https://cole-trapnell-lab.github.io/garnett' -description = """Garnett is a software package that faciliates automated cell type classification from single-cell +description = """Garnett is a software package that facilitates automated cell type classification from single-cell expression data.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb b/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb index be07346800..4225f3c60e 100644 --- a/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/meshtool/meshtool-16-GCC-10.2.0.eb @@ -4,7 +4,7 @@ name = 'meshtool' version = '16' homepage = 'https://bitbucket.org/aneic/meshtool' -description = """Meshtool is a comand-line tool written in C++. It is designed to apply various manipulations to +description = """Meshtool is a command-line tool written in C++. It is designed to apply various manipulations to volumetric meshes.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb index 1aa8772b2a..ad208054f1 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.4.8' homepage = 'https://molmod.github.io/molmod/' -description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." +description = "MolMod is a Python library with many components that are useful to write molecular modeling programs." toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb index 70260a39f7..007548886b 100644 --- a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb @@ -6,7 +6,7 @@ versionsuffix = '-R-%(rver)s' homepage = 'http://qualimap.bioinfo.cipf.es/' description = """Qualimap 2 is a platform-independent application written in Java and R that provides both - a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of + a Graphical User Interface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb index b2e44cb235..9b46ca4cac 100644 --- a/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb @@ -5,7 +5,7 @@ version = '1.2.4' homepage = 'http://tclap.sourceforge.net/' description = """TCLAP is a small, flexible library that provides a simple interface for defining and accessing -command line arguments. It was intially inspired by the user friendly CLAP libary.""" +command line arguments. It was initially inspired by the user friendly CLAP library.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} From ab7d2fb7e85a0542b568109150e9dd926a81fc1f Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 13 Nov 2023 14:38:59 +0100 Subject: [PATCH 2233/2365] Make Pillow easyconfigs aware of sysroot --- .../easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 7 +++++++ 2 files changed, 14 insertions(+) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 6c8f256ce9..2195b83f13 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -28,8 +28,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb index f925080a09..c304bb9fc6 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -26,8 +26,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True From 46d1ef3c2e07a0c9a27a8cba111b3211a8fe83c6 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 13 Nov 2023 15:57:14 +0100 Subject: [PATCH 2234/2365] Fix typo --- easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 2195b83f13..34563e55ac 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb index c304bb9fc6..bc254d1f99 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " From d6eed10c656b7b612c2c38f8304061089da04b36 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 14 Nov 2023 13:11:07 +0100 Subject: [PATCH 2235/2365] fix possible error/crash in NCCL on x86 due to cpuid --- .../n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb index 81fa9b3dfa..3c825519ba 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -16,10 +16,14 @@ dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -patches = ['NCCL-2.8.3_fix-isend-irecv.patch'] +patches = [ + 'NCCL-2.8.3_fix-isend-irecv.patch', + 'NCCL-2.16.2_fix-cpuid.patch', +] checksums = [ - '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6', # v2.8.3-1.tar.gz - '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92', # NCCL-2.8.3_fix-isend-irecv.patch + {'v2.8.3-1.tar.gz': '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6'}, + {'NCCL-2.8.3_fix-isend-irecv.patch': '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, ] moduleclass = 'lib' From c595a67ae28710e8b611edc532c751ac7bb93c9a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 16 Nov 2023 14:44:04 +0100 Subject: [PATCH 2236/2365] adding easyconfigs: xxHash-0.8.1-GCCcore-10.2.0.eb --- .../x/xxHash/xxHash-0.8.1-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d659f1192d --- /dev/null +++ b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'xxHash' +version = '0.8.1' + +homepage = 'https://cyan4973.github.io/xxHash' +description = "xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/Cyan4973/xxHash/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3bb6b7d6f30c591dd65aaaff1c8b7a5b94d81687998ca9400082c739a690436c'] + +builddependencies = [ + ('binutils', '2.35'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/xxhsum', 'include/xxh3.h', 'include/xxhash.h', + 'lib/libxxhash.a', 'lib/libxxhash.%s' % SHLIB_EXT, 'lib/pkgconfig/libxxhash.pc'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["xxhsum --help"] + +moduleclass = 'tools' From 573f5702d4ac407f81c445abb9e9e90944e85e91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Nov 2023 12:15:55 +0100 Subject: [PATCH 2237/2365] enhance easyconfigs for gnuplot 5.4.x to make sure that Lua dependency is always used --- .../easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb index cd32053b88..afa4c64d21 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb @@ -44,6 +44,9 @@ dependencies = [ preconfigopts = 'autoreconf && ' +# make sure that right Lua library is used (bypassing pkg-config) +preconfigopts += 'export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' + configopts = '--with-qt=qt5 --without-latex ' sanity_check_paths = { From bcfa7548d16100e8cd527915352eb02b2baaefb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Nov 2023 15:34:13 +0100 Subject: [PATCH 2238/2365] patch Pillow's setup.py rather than hardcoding system paths in $CPATH and $LIBRARY_PATH --- .../easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 9 +++++---- .../easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 34563e55ac..40bd77d8b9 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -29,10 +29,11 @@ dependencies = [ download_dep_fail = True -# If we have a sysroot, make sure it is picked up -# (should not affect non-sysroot as the template is empty in this scenario) -preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb index bc254d1f99..f3df005a93 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -27,10 +27,11 @@ dependencies = [ download_dep_fail = True -# If we have a sysroot, make sure it is picked up -# (should not affect non-sysroot as the template is empty in this scenario) -preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " From 5110abc697dd1c7862c8a657e85c1211308ef787 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 21 Nov 2023 16:46:55 +0100 Subject: [PATCH 2239/2365] clean up easyconfigs that explicitly set `use_pip`, `sanity_pip_check` and `download_dep_fail` --- .../a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb | 4 ---- .../a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb | 4 ---- .../a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb | 4 ---- .../a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb | 4 ---- easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb | 3 --- easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb | 3 --- easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb | 3 --- easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb | 3 --- easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb | 3 --- easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb | 3 --- easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb | 3 --- easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb | 3 --- easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb | 3 --- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 5 ----- .../a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb | 5 ----- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb | 5 ----- .../a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb | 5 ----- .../a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 5 ----- .../AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb | 5 ----- .../AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb | 5 ----- .../a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb | 4 ---- .../a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb | 4 ---- easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb | 5 ----- .../easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb | 4 ---- .../a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb | 4 ---- .../a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb | 4 ---- .../a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb | 4 ---- .../easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb | 4 ---- .../easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb | 4 ---- .../easyconfigs/a/apex/apex-20210420-fosscuda-2020b.eb | 5 ----- .../a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb | 5 ----- .../artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 3 --- .../easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb | 4 ---- .../easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb | 4 ---- .../easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb | 4 ---- easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb | 4 ---- easybuild/easyconfigs/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb | 4 ---- easybuild/easyconfigs/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb | 4 ---- .../b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb | 3 --- .../b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb | 4 ---- .../easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb | 4 ---- .../b/Biopython/Biopython-1.78-fosscuda-2020b.eb | 4 ---- .../easyconfigs/b/Biopython/Biopython-1.78-intel-2020b.eb | 4 ---- .../easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb | 4 ---- .../easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb | 4 ---- .../b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb | 4 ---- easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb | 5 ----- easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb | 4 ---- .../easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb | 4 ---- easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb | 4 ---- .../easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb | 4 ---- .../easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb | 4 ---- easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 4 ---- easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb | 4 ---- easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb | 4 ---- .../CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb | 5 ----- .../easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb | 3 --- .../c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb | 3 --- .../c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb | 6 ------ .../CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 5 ----- .../c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb | 5 ----- easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb | 4 ---- easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb | 4 ---- .../c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb | 3 --- .../c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb | 3 --- .../easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb | 3 --- .../c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb | 3 --- .../c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb | 5 ----- easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb | 4 ---- .../easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb | 6 ------ .../easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb | 6 ------ .../c/carputils/carputils-20210513-foss-2020b.eb | 4 ---- .../c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb | 3 --- .../c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb | 4 ---- .../cell2location-0.05-alpha-fosscuda-2020b.eb | 7 ------- .../easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb | 4 ---- .../c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 3 --- .../c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb | 4 ---- .../easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb | 3 --- .../easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb | 3 --- easybuild/easyconfigs/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb | 3 --- .../easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb | 3 --- .../easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb | 3 --- .../DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb | 5 ----- .../d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb | 5 ----- easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb | 4 ---- .../easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb | 4 ---- easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb | 4 ---- .../easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb | 4 ---- .../d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb | 4 ---- .../d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb | 4 ---- easybuild/easyconfigs/d/dill/dill-0.3.3-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb | 2 -- .../easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb | 5 ----- .../d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb | 3 --- .../easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 3 --- easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb | 4 ---- easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb | 5 ----- .../e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb | 4 ---- easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb | 4 ---- .../e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb | 4 ---- .../e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb | 4 ---- .../easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb | 5 ----- .../e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb | 3 --- easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb | 3 --- easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb | 4 ---- .../easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb | 4 ---- easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb | 4 ---- easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb | 4 ---- .../easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb | 3 --- easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb | 5 ----- .../easyconfigs/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb | 5 ----- .../flatbuffers-python-1.12-GCCcore-10.2.0.eb | 4 ---- .../f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb | 3 --- .../easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb | 5 ----- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb | 4 ---- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb | 4 ---- .../g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb | 4 ---- .../g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb | 4 ---- .../g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb | 4 ---- .../g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb | 4 ---- easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb | 4 ---- .../easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb | 5 ----- easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb | 3 --- .../easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb | 3 --- .../easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb | 3 --- .../easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb | 5 ----- .../easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb | 3 --- .../easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb | 5 ----- .../g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb | 3 --- .../g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb | 5 ----- .../g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb | 3 --- .../g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb | 3 --- .../g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb | 3 --- easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb | 4 ---- easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb | 4 ---- .../easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb | 4 ---- .../g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb | 4 ---- .../easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb | 4 ---- easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb | 3 --- easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb | 5 ----- .../Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb | 3 --- .../Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb | 3 --- .../Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb | 3 --- .../Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb | 3 --- .../Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb | 3 --- .../Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb | 3 --- .../h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb | 3 --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb | 4 ---- easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb | 4 ---- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb | 4 ---- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb | 4 ---- .../h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb | 4 ---- .../h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb | 4 ---- .../h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb | 4 ---- .../h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb | 4 ---- .../IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 2 -- .../easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb | 4 ---- .../i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb | 3 --- .../easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb | 4 ---- .../easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb | 4 ---- .../imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb | 5 ----- .../easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb | 5 ----- .../easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb | 3 --- .../j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb | 4 ---- .../j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb | 3 --- easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 7 ------- easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 7 ------- easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb | 4 ---- .../easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb | 5 ----- easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb | 4 ---- .../k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb | 4 ---- .../easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb | 4 ---- easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb | 3 --- easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb | 3 --- easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb | 3 --- .../easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb | 3 --- .../l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb | 3 --- .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb | 3 --- .../l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb | 3 --- .../l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 3 --- easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb | 4 ---- easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb | 4 ---- .../MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 4 ---- .../m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb | 3 --- easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb | 3 --- .../easyconfigs/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb | 3 --- easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb | 3 --- easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb | 4 ---- .../easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb | 4 ---- .../easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb | 4 ---- .../m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb | 4 ---- .../m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb | 4 ---- .../Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb | 4 ---- .../easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb | 4 ---- easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb | 5 ----- .../easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb | 5 ----- .../m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb | 4 ---- .../matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 4 ---- .../matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb | 3 --- .../m/matplotlib/matplotlib-3.3.3-foss-2020b.eb | 3 --- .../m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb | 3 --- .../m/matplotlib/matplotlib-3.3.3-intel-2020b.eb | 3 --- .../m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb | 3 --- .../m/matplotlib/matplotlib-3.5.1-foss-2020b.eb | 4 ---- .../m/matplotlib/matplotlib-3.5.1-intel-2020b.eb | 4 ---- easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb | 4 ---- easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 4 ---- .../easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb | 4 ---- .../m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb | 4 ---- .../m/mkl-service/mkl-service-2.3.0-intel-2020b.eb | 5 ----- easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb | 4 ---- .../easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb | 4 ---- .../easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb | 4 ---- .../easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb | 5 ----- .../easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb | 5 ----- .../easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb | 4 ---- .../easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb | 4 ---- .../easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb | 4 ---- .../easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb | 4 ---- .../easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb | 4 ---- .../nanomax-analysis-utils-0.4.3-foss-2020b.eb | 4 ---- .../nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb | 4 ---- .../n/neptune-client/neptune-client-0.10.5-foss-2020b.eb | 4 ---- .../n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb | 3 --- .../netcdf4-python-1.5.5.1-fosscuda-2020b.eb | 3 --- .../n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb | 3 --- .../easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb | 4 ---- .../easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb | 4 ---- .../easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb | 4 ---- .../easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb | 4 ---- .../easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb | 4 ---- .../easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb | 3 --- .../easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb | 3 --- easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb | 3 --- .../easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb | 3 --- easybuild/easyconfigs/n/numba/numba-0.52.0-intel-2020b.eb | 3 --- easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb | 3 --- .../easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb | 3 --- .../o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb | 4 ---- .../OpenStackClient-5.5.0-GCCcore-10.2.0.eb | 2 -- .../o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb | 5 ----- .../o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb | 4 ---- .../o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb | 4 ---- .../o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb | 4 ---- .../o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb | 3 --- .../easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb | 4 ---- .../p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb | 5 ----- .../p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb | 4 ---- .../easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 3 --- .../easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 3 --- easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb | 4 ---- easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb | 4 ---- .../easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb | 3 --- .../easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb | 3 --- .../p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb | 3 --- easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb | 5 ----- .../easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb | 4 ---- .../easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb | 3 --- easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb | 3 --- easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 1 - easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb | 5 ----- easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb | 5 ----- .../easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb | 3 --- .../p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb | 3 --- .../p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb | 3 --- .../p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb | 5 ----- easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb | 3 --- .../easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 3 --- .../easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb | 3 --- .../easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb | 5 ----- .../p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb | 5 ----- .../easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb | 4 ---- .../easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb | 4 ---- .../easyconfigs/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb | 3 --- .../p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb | 2 -- .../easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb | 3 --- .../easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb | 4 ---- .../p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb | 4 ---- .../easyconfigs/p/PyTables/PyTables-3.6.1-foss-2020b.eb | 4 ---- .../p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb | 4 ---- .../easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020b.eb | 4 ---- .../PyTorch-Geometric-1.6.3-foss-2020b.eb | 4 ---- .../PyTorch-Geometric-1.6.3-fosscuda-2020b.eb | 4 ---- ...PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb | 4 ---- .../PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb | 3 --- .../p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb | 4 ---- .../easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb | 3 --- .../p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb | 5 ----- easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb | 5 ----- .../p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb | 4 ---- .../easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 3 --- .../easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb | 3 --- .../p/pandapower/pandapower-2.7.0-foss-2020b.eb | 4 ---- .../easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb | 3 --- .../parallel-fastq-dump-0.6.7-gompi-2020b.eb | 5 ----- .../easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb | 5 ----- .../easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb | 5 ----- .../p/photontorch/photontorch-0.4.1-foss-2020b.eb | 3 --- .../p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb | 3 --- .../p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb | 4 ---- .../p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb | 4 ---- .../protobuf-python-3.14.0-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb | 3 --- .../p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb | 3 --- .../p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb | 5 ----- easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb | 4 ---- .../easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb | 4 ---- easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb | 4 ---- .../easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb | 4 ---- .../pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb | 5 ----- .../p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb | 5 ----- .../p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb | 5 ----- .../easyconfigs/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb | 4 ---- .../easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb | 4 ---- .../p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb | 5 ----- .../easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb | 5 ----- easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb | 4 ---- .../easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb | 4 ---- .../easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb | 4 ---- easybuild/easyconfigs/p/pymca/pymca-5.6.3-foss-2020b.eb | 3 --- .../easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb | 3 --- .../easyconfigs/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb | 5 ----- .../p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb | 4 ---- .../p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb | 4 ---- .../p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb | 4 ---- .../p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb | 4 ---- .../p/pysamstats/pysamstats-1.1.2-foss-2020b.eb | 5 ----- .../easyconfigs/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb | 4 ---- .../easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb | 6 ------ .../pytest-benchmark-3.4.1-GCCcore-10.2.0.eb | 4 ---- .../p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb | 3 --- .../p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb | 3 --- .../python-Levenshtein-0.12.1-foss-2020b.eb | 5 ----- .../p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb | 4 ---- .../p/python-igraph/python-igraph-0.9.0-foss-2020b.eb | 4 ---- .../p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb | 4 ---- .../p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb | 4 ---- .../p/python-parasail/python-parasail-1.2.4-foss-2020b.eb | 4 ---- .../python-parasail-1.2.4-fosscuda-2020b.eb | 4 ---- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 3 --- .../q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb | 5 ----- easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb | 5 ----- easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb | 4 ---- .../q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb | 3 --- .../easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb | 4 ---- easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb | 4 ---- .../easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb | 4 ---- .../easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb | 4 ---- .../r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb | 3 --- .../easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb | 3 --- .../easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb | 4 ---- .../easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb | 4 ---- .../s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb | 5 ----- easybuild/easyconfigs/s/SEPP/SEPP-4.4.0-foss-2020b.eb | 4 ---- .../SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb | 5 ----- .../SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb | 3 --- .../s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb | 3 --- .../s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb | 3 --- .../s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb | 4 ---- .../s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb | 4 ---- .../easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb | 4 ---- .../easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb | 4 ---- .../easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb | 4 ---- .../easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb | 4 ---- .../s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb | 4 ---- .../s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb | 3 --- .../easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb | 4 ---- .../s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb | 4 ---- .../easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb | 4 ---- easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb | 2 -- .../easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 2 -- .../Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb | 4 ---- easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb | 4 ---- .../s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb | 5 ----- .../s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb | 3 --- .../s/scikit-build/scikit-build-0.11.1-foss-2020b.eb | 3 --- .../s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb | 3 --- .../s/scikit-build/scikit-build-0.11.1-intel-2020b.eb | 3 --- .../s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb | 3 --- .../s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb | 3 --- .../s/scikit-image/scikit-image-0.18.1-foss-2020b.eb | 3 --- .../s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb | 3 --- .../s/scikit-image/scikit-image-0.18.1-intel-2020b.eb | 3 --- .../s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb | 3 --- .../scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb | 4 ---- .../s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb | 4 ---- .../s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb | 4 ---- .../s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb | 4 ---- .../s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb | 4 ---- easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb | 3 --- easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb | 3 --- .../s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb | 4 ---- .../easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb | 3 --- .../s/spglib-python/spglib-python-1.16.0-foss-2020b.eb | 5 ----- .../s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb | 5 ----- .../s/spglib-python/spglib-python-1.16.0-intel-2020b.eb | 5 ----- .../s/statsmodels/statsmodels-0.12.1-foss-2020b.eb | 3 --- .../s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb | 4 ---- .../s/statsmodels/statsmodels-0.12.1-intel-2020b.eb | 3 --- easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb | 4 ---- .../easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb | 3 --- .../easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb | 3 --- .../easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb | 3 --- easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb | 5 ----- easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb | 5 ----- easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb | 4 ---- easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 3 --- .../t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb | 4 ---- easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb | 3 --- .../t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 3 --- .../t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 4 ---- .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 3 --- .../t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 3 --- .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 3 --- .../easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb | 4 ---- .../t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb | 4 ---- .../easyconfigs/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb | 4 ---- easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb | 4 ---- easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb | 4 ---- .../tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb | 5 ----- .../tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb | 5 ----- .../tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb | 5 ----- .../tensorflow-probability-0.12.1-foss-2020b.eb | 4 ---- .../tensorflow-probability-0.12.1-fosscuda-2020b.eb | 4 ---- .../torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb | 4 ---- .../torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb | 4 ---- .../torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb | 4 ---- .../torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb | 4 ---- .../torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb | 4 ---- easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb | 4 ---- .../typing-extensions-3.7.4.3-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb | 3 --- .../u/umap-learn/umap-learn-0.4.6-foss-2020b.eb | 5 ----- .../u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb | 5 ----- .../u/umap-learn/umap-learn-0.5.3-foss-2020b.eb | 4 ---- easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb | 4 ---- easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb | 4 ---- .../easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb | 3 --- .../easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb | 4 ---- .../x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb | 5 ----- easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-intel-2020b.eb | 5 ----- easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb | 5 ----- .../easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb | 5 ----- .../easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb | 5 ----- easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb | 5 ----- easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb | 4 ---- .../z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb | 4 ---- easybuild/easyconfigs/z/zarr/zarr-2.8.1-foss-2020b.eb | 4 ---- 466 files changed, 1806 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb index aadacfddca..8c7793c01b 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb @@ -25,10 +25,6 @@ dependencies = [ ('kim-api', '2.2.1'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb index bf5397af7f..9df173cbc5 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb @@ -25,10 +25,6 @@ dependencies = [ ('kim-api', '2.2.1'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - # required because we're building Python packages using Intel compilers on top of Python built with GCC check_ldshared = True diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb index 53c3b5c829..a11acd1dc2 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb @@ -25,10 +25,6 @@ dependencies = [ ('kim-api', '2.2.1'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb index 76029e0a09..46212bd615 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb @@ -25,10 +25,6 @@ dependencies = [ ('kim-api', '2.2.1'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - # required because we're building Python packages using Intel compilers on top of Python built with GCC check_ldshared = True diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb index 5f6282b086..061976b5e3 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-foss-2020b.eb @@ -21,9 +21,6 @@ dependencies = [ ('spglib-python', '1.16.0'), # optional ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('ase', version, { 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb index 743f7822aa..cff9594840 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-fosscuda-2020b.eb @@ -21,9 +21,6 @@ dependencies = [ ('spglib-python', '1.16.0'), # optional ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('ase', version, { 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb index 9fd13e7e5b..28f70c828d 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020b.eb @@ -21,9 +21,6 @@ dependencies = [ ('spglib-python', '1.16.0'), # optional ] -use_pip = True -sanity_pip_check = True - # required because we're building Python packages (MarkupSafe, # ase-ext) using Intel compilers on top of Python built with GCC. check_ldshared = True diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb index 6376980043..341a4a53ba 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-foss-2020b.eb @@ -21,9 +21,6 @@ dependencies = [ ('spglib-python', '1.16.0'), # optional ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('ase', version, { 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb index f128fd8021..60e79afad3 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-fosscuda-2020b.eb @@ -21,9 +21,6 @@ dependencies = [ ('spglib-python', '1.16.0'), # optional ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('ase', version, { 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb index 56fba957d6..485206e49a 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.21.1-intel-2020b.eb @@ -21,9 +21,6 @@ dependencies = [ ('spglib-python', '1.16.0'), # optional ] -use_pip = True -sanity_pip_check = True - # required because we're building Python packages (MarkupSafe, # ase-ext) using Intel compilers on top of Python built with GCC. check_ldshared = True diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb index 87ef103fc6..aee9f6b2eb 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb @@ -21,9 +21,6 @@ dependencies = [ ('spglib-python', '1.16.0'), # optional ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('pytest-mock', '3.6.1', { 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb index 1754c068f5..3321ef3e8d 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb @@ -21,9 +21,6 @@ dependencies = [ ('spglib-python', '1.16.0'), # optional ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('pytest-mock', '3.6.1', { 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb index e1212c2381..2338c47460 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb @@ -21,9 +21,6 @@ dependencies = [ ('spglib-python', '1.16.0'), # optional ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('pytest-mock', '3.6.1', { 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index fa55dd0f5a..f6ee200cfd 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -88,12 +88,9 @@ components = [ '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch ], 'start_dir': 'alphafold-%(version)s', - 'use_pip': True, }), ] -use_pip = True - exts_list = [ ('PDBFixer', '1.7', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], @@ -169,8 +166,6 @@ sanity_check_commands = [ "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] -sanity_pip_check = True - modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb index 4d23d09d29..75db88dd0b 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb @@ -88,12 +88,9 @@ components = [ '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch ], 'start_dir': 'alphafold-%(version)s', - 'use_pip': True, }), ] -use_pip = True - exts_list = [ ('PDBFixer', '1.7', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], @@ -169,8 +166,6 @@ sanity_check_commands = [ "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] -sanity_pip_check = True - modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb index 8806522d26..66824433a6 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb @@ -90,12 +90,9 @@ components = [ '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch ], 'start_dir': 'alphafold-%(version)s', - 'use_pip': True, }), ] -use_pip = True - exts_list = [ ('PDBFixer', '1.7', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], @@ -171,8 +168,6 @@ sanity_check_commands = [ "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] -sanity_pip_check = True - modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb index 5c6a924e87..39b1a7c019 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb @@ -90,12 +90,9 @@ components = [ '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch ], 'start_dir': 'alphafold-%(version)s', - 'use_pip': True, }), ] -use_pip = True - exts_list = [ ('PDBFixer', '1.7', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], @@ -168,8 +165,6 @@ sanity_check_commands = [ "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] -sanity_pip_check = True - modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index 1cff76362a..d90fa11e46 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -94,12 +94,9 @@ components = [ '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', - 'use_pip': True, }), ] -use_pip = True - exts_list = [ ('PDBFixer', '1.7', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], @@ -172,8 +169,6 @@ sanity_check_commands = [ "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] -sanity_pip_check = True - modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb index c9603b16d6..8f4a0548ff 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb @@ -95,12 +95,9 @@ components = [ '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', - 'use_pip': True, }), ] -use_pip = True - exts_list = [ ('PDBFixer', '1.7', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], @@ -173,8 +170,6 @@ sanity_check_commands = [ "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] -sanity_pip_check = True - modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb index 2dcc49bc3a..7ecc3335ca 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -95,12 +95,9 @@ components = [ '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', - 'use_pip': True, }), ] -use_pip = True - exts_list = [ ('PDBFixer', '1.7', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], @@ -173,8 +170,6 @@ sanity_check_commands = [ "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] -sanity_pip_check = True - modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb index 05ab7469fa..6135637a22 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -27,8 +27,6 @@ dependencies = [ ('dm-tree', '0.1.5'), ] -use_pip = True - exts_list = [ ('py3Dmol', '2.0.1.post1', { 'modulename': 'py3Dmol', @@ -74,8 +72,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb index fe9b546828..3cdf5fa98f 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb @@ -27,8 +27,6 @@ dependencies = [ ('dm-tree', '0.1.5'), ] -use_pip = True - exts_list = [ ('py3Dmol', '2.0.1.post1', { 'modulename': 'py3Dmol', @@ -74,8 +72,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { "files": ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], "dirs": ["lib/python%(pyshortver)s/site-packages/alphapulldown"], diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb index e2262d8d25..41b7744f93 100644 --- a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb @@ -20,9 +20,4 @@ dependencies = [ ('typing-extensions', '3.7.4.3'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb index d37a02530c..537b89a6a6 100644 --- a/easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ ('h5py', '3.1.0'), ] -use_pip = True - exts_list = [ ('natsort', '7.1.1', { 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], @@ -35,6 +33,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb index 5ed303535e..d913618d8b 100644 --- a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb @@ -34,8 +34,4 @@ dependencies = [ ('imageio', '2.9.0'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb index 58040804ad..50fd79899c 100644 --- a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb @@ -32,8 +32,4 @@ dependencies = [ ('imageio', '2.9.0'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb index 24cc2f9f1f..86f067f3ce 100644 --- a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb @@ -32,8 +32,4 @@ dependencies = [ ('imageio', '2.9.0'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb index db39bb21b3..cf6d8de85b 100644 --- a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -44,8 +44,6 @@ components = [ }), ] -use_pip = True - exts_list = [ ('helperlibs', '0.2.1', { 'checksums': ['4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732'], @@ -97,6 +95,4 @@ sanity_check_commands = [ "antismash --version", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb index 57cfc9ef19..c69a7b6bb5 100644 --- a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb @@ -43,8 +43,6 @@ components = [ }), ] -use_pip = True - exts_list = [ ('helperlibs', '0.2.1', { 'checksums': ['4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732'], @@ -79,6 +77,4 @@ sanity_check_commands = [ "antismash --version", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/apex/apex-20210420-fosscuda-2020b.eb b/easybuild/easyconfigs/a/apex/apex-20210420-fosscuda-2020b.eb index 9507c3802d..d4aefdb6d5 100644 --- a/easybuild/easyconfigs/a/apex/apex-20210420-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/apex/apex-20210420-fosscuda-2020b.eb @@ -21,13 +21,8 @@ dependencies = [ ('PyTorch', '1.7.1'), ] -download_dep_fail = True -use_pip = True - installopts = "--no-cache-dir --global-option='--cpp_ext' --global-option='--cuda_ext' --global-option='--pyprof'" -sanity_pip_check = True - sanity_check_commands = ["python -c 'from apex import amp'"] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb index 06b4ffb6c8..7b486d4f4a 100644 --- a/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb @@ -18,11 +18,6 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -download_dep_fail = True -use_pip = True - sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 80e2cc8068..f473322e5c 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -43,9 +43,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('clint', '0.5.1', { 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb index 879b5774c3..ab2fbb4268 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb @@ -15,10 +15,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True - -sanity_pip_check = True - exts_list = [ ('pyerfa', '1.7.3', { 'modulename': 'erfa', diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb index 878eb8ce9f..08411ca88a 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb @@ -15,10 +15,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True - -sanity_pip_check = True - exts_list = [ ('pyerfa', '1.7.3', { 'modulename': 'erfa', diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb index 8479d0024e..903e0674b3 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb @@ -15,10 +15,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True - -sanity_pip_check = True - exts_list = [ ('pyerfa', '1.7.3', { 'modulename': 'erfa', diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb index 48d0a53aeb..84d5b402f5 100644 --- a/easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb @@ -28,10 +28,6 @@ dependencies = [ ('MetaEuk', '4'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - postinstallcmds = [ 'mkdir -p %(installdir)s/bin %(installdir)s/doc', 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb index b88e140a4d..2c8f327027 100644 --- a/easybuild/easyconfigs/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb @@ -28,10 +28,6 @@ dependencies = [ ('MetaEuk', '4'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - postinstallcmds = [ 'mkdir -p %(installdir)s/bin %(installdir)s/doc', 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb index 07b410d350..0a751183af 100644 --- a/easybuild/easyconfigs/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb @@ -28,10 +28,6 @@ dependencies = [ ('MetaEuk', '4'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - postinstallcmds = [ 'mkdir -p %(installdir)s/bin %(installdir)s/doc', 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb index 7d8438a884..05cf100235 100644 --- a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb @@ -16,9 +16,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('soupsieve', '2.2.1', { 'checksums': ['052774848f448cf19c7e959adf5566904d525f33a3f8b6ba6f6f8f26ec7de0cc'], diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb index a593b6c844..870a0d3e85 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb @@ -22,10 +22,6 @@ dependencies = [ ('SciPy-bundle', '2020.11', versionsuffix), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - # Run only tests that don't require internet connection runtest = 'python setup.py test --offline' diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb index e3d678f0ed..9b3f063cb1 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-foss-2020b.eb @@ -21,10 +21,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - # Run only tests that don't require internet connection runtest = 'python setup.py test --offline' diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-fosscuda-2020b.eb index 41f07d6177..7d0f43fd2f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-fosscuda-2020b.eb @@ -21,10 +21,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - # Run only tests that don't require internet connection runtest = 'python setup.py test --offline' diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020b.eb index b06996d99b..15fb03b774 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020b.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020b.eb @@ -21,10 +21,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - # Run only tests that don't require internet connection runtest = 'python setup.py test --offline' diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb index b677ee8f20..04ce4f3028 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb @@ -22,8 +22,6 @@ dependencies = [ ('CuPy', '8.5.0'), ] -use_pip = True - exts_list = [ ('python-editor', '1.0.4', { 'modulename': 'editor', @@ -101,8 +99,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/bonito'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb index 59554e81a1..f2b748f8d3 100644 --- a/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb @@ -26,8 +26,6 @@ dependencies = [ ('ont-fast5-api', '3.3.0'), ] -use_pip = True - # strip out too strict version requirements for dependencies local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && " # fix requirements for stuff we include as a proper dependency @@ -110,8 +108,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/bonito'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb index b08a96811d..382bedd030 100644 --- a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb @@ -25,10 +25,6 @@ dependencies = [ ('Python', '3.8.6'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - options = {'modulename': 'brotli'} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb index 66fc839020..3ca36911d1 100644 --- a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb @@ -25,10 +25,6 @@ dependencies = [ ('Biopython', '1.78'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' local_targets = ['GFFOutput.py', 'GFFParser.py'] diff --git a/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb b/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb index f9ba69782d..a3f3693c43 100644 --- a/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/b/bcolz/bcolz-1.2.1-foss-2020b.eb @@ -28,9 +28,6 @@ dependencies = [ ('PyTables', '3.6.1'), ] -download_dep_fail = True -use_pip = True - preinstallopts = "BLOSC_DIR=$EBROOTBLOSC" sanity_check_paths = { @@ -40,6 +37,4 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import bcolz; bcolz.test()'"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb index 59ace9b78d..2fa54376e2 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('typing-extensions', '3.7.4.3'), ] -use_pip = True - exts_list = [ ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], @@ -34,6 +32,4 @@ sanity_check_paths = { sanity_check_commands = ["bokeh --help"] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb index 8e06a02627..b51d9f9d43 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('typing-extensions', '3.7.4.3'), ] -use_pip = True - exts_list = [ ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], @@ -34,6 +32,4 @@ sanity_check_paths = { sanity_check_commands = ["bokeh --help"] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb index d3c12b132a..706ee596f5 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('typing-extensions', '3.7.4.3'), ] -use_pip = True - exts_list = [ ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], @@ -34,6 +32,4 @@ sanity_check_paths = { sanity_check_commands = ["bokeh --help"] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb index 513e9f6b2f..f96cc03618 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('typing-extensions', '3.7.4.3'), ] -use_pip = True - exts_list = [ ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], @@ -34,6 +32,4 @@ sanity_check_paths = { sanity_check_commands = ["bokeh --help"] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb index a2429cf4d0..67f22a6705 100644 --- a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb @@ -18,10 +18,6 @@ osdependencies = [('libdb-dev', 'libdb-devel')] builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - # Need to unset LIBS or pip install crashes. preinstallopts = 'unset LIBS && ' diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb index 9a080037a6..262fe6aad5 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb @@ -24,8 +24,4 @@ dependencies = [ ('Raysect', '0.7.1') ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb index f80768c259..2b683aad14 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -24,8 +24,4 @@ dependencies = [ ('Raysect', '0.7.1') ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb index e87a4eff59..8ba151985f 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb @@ -24,8 +24,4 @@ dependencies = [ ('Raysect', '0.7.1') ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb index 95c8e30c60..376242695f 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb @@ -24,8 +24,4 @@ dependencies = [ ('Raysect', '0.7.1') ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb index aaec5e3760..4638c0d32a 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb @@ -27,9 +27,6 @@ dependencies = [ ('pybedtools', '0.8.2', versionsuffix), ] -download_dep_fail = True -use_pip = True - options = {'modulename': 'circ2'} sanity_check_paths = { @@ -39,6 +36,4 @@ sanity_check_paths = { sanity_check_commands = ["CIRCexplorer2 denovo --help"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb index a52d587933..4bba2206c3 100644 --- a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb @@ -21,8 +21,6 @@ dependencies = [ ('python-Levenshtein', '0.12.1'), ] -use_pip = True - exts_list = [ ('mappy', '2.17', { 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], @@ -47,6 +45,5 @@ sanity_check_commands = [ 'cd %(builddir)s/CIRIlong/%(name)s-%(version)s && make test', 'CIRI-long --help', ] -sanity_pip_check = True moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb index 4afe9aa817..b8f169bcc8 100644 --- a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb @@ -40,9 +40,6 @@ exts_list = [ }), ] -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/cnvkit.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb index e8a5cb71f3..c5d5cf7a6d 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb @@ -31,10 +31,6 @@ dependencies = [ ('scikit-learn', '0.20.4', versionsuffix), ] -download_dep_fail = True - -use_pip = True - sanity_check_paths = { 'files': ['bin/concoct'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], @@ -42,6 +38,4 @@ sanity_check_paths = { sanity_check_commands = ["concoct --help"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb index e815134c6e..743acb941e 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -35,9 +35,6 @@ dependencies = [ ('Seaborn', '0.9.1', '-Python-%(pyver)s'), ] -download_dep_fail = True -use_pip = True - # strip out too strict version requirements for dependencies preinstallopts = "sed -i 's/,<=[0-9]*//g' setup.py && sed -i 's/==/>=/g' setup.py && " @@ -55,8 +52,6 @@ sanity_check_commands = [ local_test_cmd, ] -sanity_pip_check = True - options = {'modulename': name} modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb index e1a264c229..4659d76481 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb @@ -34,9 +34,6 @@ dependencies = [ ('Seaborn', '0.11.1'), ] -download_dep_fail = True -use_pip = True - # strip out too strict version requirements for dependencies preinstallopts = "sed -i 's/,<=[0-9]*//g' setup.py && sed -i 's/==/>=/g' setup.py && " @@ -54,8 +51,6 @@ sanity_check_commands = [ local_test_cmd, ] -sanity_pip_check = True - options = {'modulename': name} modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} diff --git a/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb index c3feca2d8a..6aa0a88629 100644 --- a/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb @@ -24,10 +24,6 @@ source_urls = ['https://github.com/csb-toolbox/CSB/releases/download/R-%(version sources = [SOURCELOWER_TAR_GZ] checksums = ['3f05924acaca6673f94fc430965eabfe59a0c9b2cbdda8c1cb50a43ffe83f254'] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - dependencies = [ ('Python', '3.8.6'), ('matplotlib', '3.3.3'), diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb index be6d64350b..2192fdc7fa 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb @@ -26,10 +26,6 @@ dependencies = [ ('GSL', '2.6'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb index 4ce73ac7ec..cb726e86e4 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb @@ -25,9 +25,6 @@ dependencies = [ ('PyYAML', '5.3.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('OWSLib', '0.24.1', { 'checksums': ['4973c2ba65ec850a3fcc1fb94cefe5ed2fed83aaf2a5e2135c78810ad2a8f0e1'], diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb index 2301189a3a..2135a8f521 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb @@ -25,9 +25,6 @@ dependencies = [ ('PyYAML', '5.3.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('OWSLib', '0.24.1', { 'checksums': ['4973c2ba65ec850a3fcc1fb94cefe5ed2fed83aaf2a5e2135c78810ad2a8f0e1'], diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb index b86e1d18a3..200d507153 100644 --- a/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb @@ -19,9 +19,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -sanity_pip_check = True -use_pip = True - exts_list = [ ('natsort', '7.1.1', { 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb index 47616f4265..007fb40d94 100644 --- a/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb @@ -19,9 +19,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -sanity_pip_check = True -use_pip = True - exts_list = [ ('natsort', '7.1.1', { 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb index 3930c1d64b..04f2236821 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb @@ -41,9 +41,6 @@ dependencies = [ ('DendroPy', '4.5.2', versionsuffix), ] -download_dep_fail = True -use_pip = True - # also install CheckM databases, see https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm postinstallcmds = [ "cp -a %(builddir)s/data %(installdir)s", @@ -58,6 +55,4 @@ sanity_check_paths = { sanity_check_commands = ["checkm test %(builddir)s/checkm_test_results"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb index dddce517cb..adec31e36e 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ ('cuTENSOR', '1.2.2.5', '-CUDA-%(cudaver)s', SYSTEM), ] -use_pip = True - exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} postinstallcmds = [ # req for sanity check on build nodes without libcuda.so. @@ -39,6 +37,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb index 7c9a95c040..8aa80047a4 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb @@ -36,12 +36,6 @@ builddependencies = [('binutils', '2.35')] # This results in not beeing able to choose Cython version in multi_dep. dependencies = [('Python', '3.8.6')] -download_dep_fail = True - -use_pip = True - -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb index 08933e6092..b747ba9017 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb @@ -36,12 +36,6 @@ builddependencies = [('binutils', '2.35')] # This results in not beeing able to choose Cython version in multi_dep. dependencies = [('Python', '3.8.6')] -download_dep_fail = True - -use_pip = True - -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/c/carputils/carputils-20210513-foss-2020b.eb b/easybuild/easyconfigs/c/carputils/carputils-20210513-foss-2020b.eb index ee94dbf3d2..82b0ce4901 100644 --- a/easybuild/easyconfigs/c/carputils/carputils-20210513-foss-2020b.eb +++ b/easybuild/easyconfigs/c/carputils/carputils-20210513-foss-2020b.eb @@ -19,8 +19,6 @@ dependencies = [ ('meshalyzer', '2.2'), ] -use_pip = True - # version restrictions are too strict, so strip them out local_carputils_preinstallopts = "sed -i 's/[=><]=[0-9].*//g' requirements.py3.txt && " # inject proper version, to prevent installing carputils with 0.0.0 as version... @@ -67,8 +65,6 @@ sanity_check_paths = { sanity_check_commands = ["carphelp --help"] -sanity_pip_check = True - modextravars = {'CARPUTILS_SETTINGS': '%(installdir)s/settings.yaml'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb index afe41e8b97..66f537471f 100644 --- a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb @@ -53,9 +53,6 @@ exts_list = [ }), ] -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], 'dirs': ['lib/python%(pyshortver)s/site-packages/cctbx_website'], diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb index b695ed8ce2..ecf4c4cf84 100644 --- a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb @@ -36,7 +36,6 @@ dependencies = [ local_metadata = "%(installdir)s/lib/python%(pyshortver)s/site-packages/cctbx_base-%(version)s.dist-info/METADATA" - exts_list = [ ('reportlab', '3.5.66', { 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], @@ -57,9 +56,6 @@ exts_list = [ }), ] -use_pip = True -sanity_pip_check = True - sanity_check_paths = { "files": ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], "dirs": ['lib/python%(pyshortver)s/site-packages/cctbx_website'], diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 9a0eeba162..5150980005 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -43,12 +43,7 @@ dependencies = [ preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " -use_pip = True - exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, } exts_list = [ @@ -124,8 +119,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/loompy', 'bin/scanpy'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb index 9d69f0f5eb..152f380e38 100644 --- a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb @@ -21,10 +21,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - sanity_check_paths = { 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index 2a47fefb4a..a7307e3a97 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -26,9 +26,6 @@ dependencies = [ ('Seaborn', '0.11.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('colorlover', '0.3.0', { 'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb index 26af108903..ee0f8d906f 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb @@ -27,8 +27,6 @@ builddependencies = [ dependencies = [('Python', '2.7.18')] -use_pip = True - exts_list = [ ('bz2file', '0.98', { 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], @@ -51,6 +49,4 @@ sanity_check_commands = [ "python -c 'import cutadapt.seqio'", # requires xopen ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb index b8f8f0dc94..754f14bd46 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb @@ -26,9 +26,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('xopen', '0.8.4', { 'checksums': ['dcd8f5ef5da5564f514a990573a48a0c347ee1fdbb9b6374d31592819868f7ba'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb index 31fce71f99..df95ca0d5d 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb @@ -28,9 +28,6 @@ dependencies = [ ('python-isal', '0.11.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('xopen', '1.1.0', { 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], diff --git a/easybuild/easyconfigs/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb index a510be9b2b..bd4bec9dbd 100644 --- a/easybuild/easyconfigs/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb @@ -18,9 +18,6 @@ dependencies = [ ('pytest-xdist', '2.1.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('funcy', '1.15', { 'checksums': ['65b746fed572b392d886810a98d56939c6e0d545abb750527a717c21ced21008'], diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb index e06ee84b7f..43b7b86327 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -59,9 +59,6 @@ exts_list = [ }), ] -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/drop'], 'dirs': [], diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb index 8091ae5611..d5ca4b706d 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb @@ -56,9 +56,6 @@ exts_list = [ }), ] -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/drop'], 'dirs': [], diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb index 8dd1572be9..96dff919eb 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb @@ -27,9 +27,6 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '2.7.18')] -download_dep_fail = True -use_pip = True - fix_python_shebang_for = ['bin/*.py'] sanity_check_paths = { @@ -39,6 +36,4 @@ sanity_check_paths = { sanity_check_commands = ["sumtrees.py --help"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb index a7a6526bca..fee0868898 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb @@ -26,9 +26,6 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -download_dep_fail = True -use_pip = True - fix_python_shebang_for = ['bin/*.py'] sanity_check_paths = { @@ -38,6 +35,4 @@ sanity_check_paths = { sanity_check_commands = ["sumtrees.py --help"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb index c1d37aafe9..37cfcc5fb3 100644 --- a/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('bokeh', '2.2.3'), ] -use_pip = True - exts_list = [ ('fsspec', '0.8.7', { 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], @@ -70,6 +68,4 @@ sanity_check_paths = { sanity_check_commands = ["dask-scheduler --help"] -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb index 530ef90ea3..8ed1c35da2 100644 --- a/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-fosscuda-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('bokeh', '2.2.3'), ] -use_pip = True - exts_list = [ ('fsspec', '0.8.7', { 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], @@ -68,6 +66,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb index 1436265c5c..ecf8a22c9e 100644 --- a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('bokeh', '2.2.3'), ] -use_pip = True - exts_list = [ ('fsspec', '0.8.7', { 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], @@ -70,6 +68,4 @@ sanity_check_paths = { sanity_check_commands = ["dask-scheduler --help"] -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb index b012d3c660..929025fe26 100644 --- a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('bokeh', '2.2.3'), ] -use_pip = True - exts_list = [ ('fsspec', '0.8.7', { 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], @@ -68,6 +66,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb index 4d594c3759..e38a7cd686 100644 --- a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb @@ -19,10 +19,6 @@ dependencies = [ ('NiBabel', '3.2.1'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/dicom2nifti'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb index 20fcaa7cfc..3ec515d54f 100644 --- a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb @@ -19,10 +19,6 @@ dependencies = [ ('NiBabel', '3.2.1'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/dicom2nifti'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.3-GCCcore-10.2.0.eb index 4f1d3426ae..ab34d50b7f 100644 --- a/easybuild/easyconfigs/d/dill/dill-0.3.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/dill/dill-0.3.3-GCCcore-10.2.0.eb @@ -22,8 +22,4 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb index aa3a70ea80..d8dcf64851 100644 --- a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb @@ -34,8 +34,6 @@ dependencies = [ # Bundled upb sets -Werror, failing on any warning. Disable for harmless warnings buildopts = "--copt='-Wno-error=stringop-truncation'" -sanity_pip_check = True - options = {'modulename': 'reverb'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb index 2ec06598b3..e444b966c7 100644 --- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb @@ -19,11 +19,6 @@ builddependencies = [ ] dependencies = [('Python', '3.8.6')] -download_dep_fail = True - -use_pip = True -sanity_pip_check = True - options = {'modulename': 'tree'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb index b6aae99f16..46586020a2 100644 --- a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -22,9 +22,6 @@ dependencies = [ ('CMake', '3.18.4'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('portalocker', '2.3.2', { 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index 52e3809d42..a30e864c23 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -27,9 +27,6 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('fenics-ufl', '2019.1.0', { 'modulename': 'ufl', diff --git a/easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb b/easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb index b9da3e2f02..15711a15f0 100644 --- a/easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb @@ -20,8 +20,6 @@ dependencies = [ start_dir = 'src/addon/ESMPy' -download_dep_fail = True - # ESMPy's setup.py script doesn't support using "pip install" use_pip = False @@ -29,6 +27,4 @@ buildopts = "--ESMFMKFILE=$EBROOTESMF/lib/esmf.mk" options = {'modulename': 'ESMF'} -sanity_pip_check = True - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb index f4d0c02af9..cb9b36ddf6 100644 --- a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb @@ -19,9 +19,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True - options = {'modulename': 'ete3'} sanity_check_paths = { @@ -29,6 +26,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb index 30df322fee..ad377b08e6 100644 --- a/easybuild/easyconfigs/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb @@ -19,10 +19,6 @@ dependencies = [ ('ecCodes', '2.20.0'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - options = {'modulename': 'eccodes'} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb index e79e34bf1e..d28d60e6be 100644 --- a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb @@ -15,8 +15,4 @@ dependencies = [ ('Python', '3.8.6'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb index 8ebfa69235..02a167deba 100644 --- a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb @@ -36,10 +36,6 @@ dependencies = [ # strip out (too) strict version requirements for dependencies preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " -use_pip = True -sanity_pip_check = True -download_dep_fail = True - sanity_check_paths = { 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb index 536eecf003..6cf33db466 100644 --- a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb @@ -36,10 +36,6 @@ dependencies = [ # strip out (too) strict version requirements for dependencies preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " -use_pip = True -sanity_pip_check = True -download_dep_fail = True - sanity_check_paths = { 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb index f9d8338984..ff0614928b 100644 --- a/easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb @@ -21,9 +21,4 @@ dependencies = [ ('Python', '3.8.6'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb index 1e133b2aea..aa26265cbd 100644 --- a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb @@ -18,8 +18,4 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb index 03490cd20d..262981fa95 100644 --- a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb @@ -20,9 +20,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -sanity_pip_check = True -use_pip = True - exts_list = [ ('picmistandard', '0.0.14', { 'checksums': ['8f83b25b281fc0309a0c4f75c7605afd5fa0ef4df3b3ac115069478c119bc8c3'], diff --git a/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb index 25617e478e..d1e7b38c75 100644 --- a/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb @@ -18,9 +18,6 @@ dependencies = [ ('BeautifulSoup', '4.9.3'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('graphviz', '0.17', { 'source_tmpl': '%(name)s-%(version)s.zip', diff --git a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb index 4ddcccb74e..37d3a4ba76 100644 --- a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb @@ -19,8 +19,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb index 7126f817a8..12a34b0c60 100644 --- a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb @@ -19,8 +19,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb index fd9e2798fc..187b08065d 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb @@ -20,8 +20,6 @@ dependencies = [ ('Shapely', '1.8a1'), ] -use_pip = True - exts_list = [ ('cligj', '0.7.2', { 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], @@ -44,6 +42,4 @@ sanity_check_paths = { sanity_check_commands = ["fio --help"] -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb index 4deaf15039..dbc0d641f9 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb @@ -20,8 +20,6 @@ dependencies = [ ('Shapely', '1.8a1'), ] -use_pip = True - exts_list = [ ('cligj', '0.7.2', { 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], @@ -44,6 +42,4 @@ sanity_check_paths = { sanity_check_commands = ["fio --help"] -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb index 923379d86b..ea736672a8 100644 --- a/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb @@ -18,9 +18,6 @@ dependencies = [ builddependencies = [('binutils', '2.35')] -use_pip = True -sanity_pip_check = True - exts_list = [ ('itsdangerous', '1.1.0', { 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb index 6ab5c77652..611a9d32df 100644 --- a/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-GCC-10.2.0.eb @@ -15,9 +15,6 @@ checksums = ['070f9fbee28eef8e8f87aaecc048053f50a8102a3715e71b16c9c46819a4e07c'] dependencies = [('Python', '3.8.6')] -download_dep_fail = True -use_pip = True - if ARCH == "aarch64": preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' @@ -28,6 +25,4 @@ sanity_check_paths = { sanity_check_commands = ['%(namelower)s --help'] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb index 8a10044a12..9d58a9667a 100644 --- a/easybuild/easyconfigs/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb @@ -15,9 +15,6 @@ checksums = ['070f9fbee28eef8e8f87aaecc048053f50a8102a3715e71b16c9c46819a4e07c'] dependencies = [('Python', '3.8.6')] -download_dep_fail = True -use_pip = True - sanity_check_paths = { 'files': ['bin/flye'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], @@ -25,6 +22,4 @@ sanity_check_paths = { sanity_check_commands = ['%(namelower)s --help'] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb index 7d9f73d559..50c8a63725 100644 --- a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb @@ -17,10 +17,6 @@ dependencies = [ ('Python', '3.8.6'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - preinstallopts = 'VERSION=%(version)s ' options = {'modulename': 'flatbuffers'} diff --git a/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb index 877385766c..fd3f68b440 100644 --- a/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb @@ -28,9 +28,6 @@ dependencies = [ ('tbb', '2020.3'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('rowan', '1.3.0.post1', { 'source_urls': ['https://pypi.python.org/packages/source/r/rowan'], diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb index 18701693a4..a21d0dfe33 100644 --- a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb @@ -24,9 +24,6 @@ dependencies = [ ('pydot', '1.4.2'), ] -download_dep_fail = True -use_pip = True - preinstallopts = "sed -i 's/==[0-9]*.[0-9]*.[0-9]*//g' requirements.txt && " # wget was here only to download some src files which we download via sources preinstallopts += "sed -i 's/wget//g' requirements.txt && " @@ -47,6 +44,4 @@ sanity_check_commands = [ "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb index 6758eb6089..d7eb16cc6f 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb @@ -35,10 +35,6 @@ dependencies = [ prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' preinstallopts = prebuildopts -download_dep_fail = True -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', '-runscript', '-setup', '-upfplot']], diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb index 0714f4060f..2c7b81fa3b 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -35,10 +35,6 @@ dependencies = [ prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' preinstallopts = prebuildopts -download_dep_fail = True -use_pip = True -sanity_pip_check = True - # required because we're building a Python package using Intel compilers on top of Python built with GCC. check_ldshared = True diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb index 7c88872300..4ac79a96d8 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb @@ -35,10 +35,6 @@ dependencies = [ prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' preinstallopts = prebuildopts -download_dep_fail = True -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', '-runscript', '-setup', '-upfplot']], diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb index 978ddc9ef5..40a999e312 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb @@ -34,10 +34,6 @@ dependencies = [ prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' preinstallopts = prebuildopts -download_dep_fail = True -use_pip = True -sanity_pip_check = True - # required because we're building a Python package using Intel compilers on top of Python built with GCC. check_ldshared = True diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb index 465fd9c9b0..6ee58a76a5 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb @@ -36,10 +36,6 @@ dependencies = [ prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' preinstallopts = prebuildopts -download_dep_fail = True -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', '-runscript', '-setup', '-upfplot']], diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb index 5688561947..c551cb07f2 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -36,10 +36,6 @@ dependencies = [ prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' preinstallopts = prebuildopts -download_dep_fail = True -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', '-runscript', '-setup', '-upfplot']], diff --git a/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb index 0ac934a041..6ce4b95009 100644 --- a/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb @@ -14,8 +14,6 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True - exts_list = [ ('paramz', '0.9.5', { 'checksums': ['0917211c0f083f344e7f1bc997e0d713dbc147b6380bc19f606119394f820b9a'], @@ -30,6 +28,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb index 1fe9874788..0bed20eb35 100644 --- a/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb @@ -16,9 +16,4 @@ dependencies = [ ('PyTorch', '1.7.1'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb index 5e4aad028e..9bdccacd92 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb @@ -69,9 +69,6 @@ exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_urls': [PYPI_SOURCE], - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True, } exts_list = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb index 706f52ed24..b4dd34b1bf 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb @@ -70,9 +70,6 @@ exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_urls': [PYPI_SOURCE], - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True, } exts_list = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb index abde5c2363..03155a5055 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb @@ -70,9 +70,6 @@ exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_urls': [PYPI_SOURCE], - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True, } exts_list = [ diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb index 5f2ae47346..f54f1f06fb 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb @@ -28,9 +28,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -download_dep_fail = True -use_pip = True - options = {'modulename': 'gtdbtk'} sanity_check_paths = { @@ -38,6 +35,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb index d40e1ff699..752b7e13b1 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb @@ -28,8 +28,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -download_dep_fail = True -use_pip = True options = {'modulename': 'gtdbtk'} @@ -38,6 +36,5 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_pip_check = True moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb index 4d81bd500b..7630d98dcb 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb @@ -28,9 +28,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -download_dep_fail = True -use_pip = True - options = {'modulename': 'gtdbtk'} sanity_check_paths = { @@ -38,6 +35,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 280fb4af01..9d5d923af6 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -54,9 +54,6 @@ skipsteps = ['test'] exts_defaultclass = 'PythonPackage' exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, - 'sanity_pip_check': True, } local_genomeworks_preinstallopts = "sed -i 's/[=~]=/>=/g' requirements.txt && " diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb index 2eabe89e52..4212fd0def 100644 --- a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb @@ -25,15 +25,10 @@ dependencies = [ ('matplotlib', '3.3.3') ] -download_dep_fail = True -use_pip = True - options = {'modulename': False} fix_python_shebang_for = ['bin/*.py'] -sanity_pip_check = True - sanity_check_commands = ["get_organelle_from_reads.py -h"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb index 85b9fc305f..08b6924204 100644 --- a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb @@ -15,9 +15,6 @@ dependencies = [ ('git', '2.28.0', '-nodocs'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('smmap', '4.0.0', { 'checksums': ['7e65386bd122d45405ddf795637b7f7d2b532e7e401d46bbe3fb49b9986d5182'], diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb index 65e2cb1163..1713346d42 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb @@ -19,9 +19,6 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('click', '8.0.3', { 'checksums': ['410e932b050f5eed773c4cda94de75971c89cdb3155a72a0831139a79e5ecb5b'], diff --git a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb index 10bf3fc560..19471a207a 100644 --- a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb @@ -17,9 +17,6 @@ dependencies = [ ('libyaml', '0.2.5'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('cryptography', '2.8', { 'checksums': ['3cda1f0ed8747339bbdf71b9f38ca74c7b592f24f65cdb3ab3765e4b02871651'], diff --git a/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb index 3492441af2..e18b6b9c19 100644 --- a/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-foss-2020b.eb @@ -14,8 +14,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # for numpy, pandas ] -use_pip = True - exts_list = [ ('smart_open', '4.1.2', { 'checksums': ['4bbb6233364fc1173cc0af6b7a56ed76fce32509514f1978a995a5835f3177f1'], @@ -25,6 +23,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb index 20eab35edc..b66e79c460 100644 --- a/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb +++ b/easybuild/easyconfigs/g/gensim/gensim-3.8.3-intel-2020b.eb @@ -14,8 +14,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # for numpy, pandas ] -use_pip = True - exts_list = [ ('smart_open', '4.1.2', { 'checksums': ['4bbb6233364fc1173cc0af6b7a56ed76fce32509514f1978a995a5835f3177f1'], @@ -25,6 +23,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb index 3c5929e842..e41f1355ea 100644 --- a/easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb @@ -18,8 +18,6 @@ builddependencies = [ dependencies = [('Python', '3.8.6')] -use_pip = True - exts_list = [ ('geographiclib', '1.50', { 'checksums': ['12bd46ee7ec25b291ea139b17aa991e7ef373e21abd053949b75c0e9ca55c632'], @@ -29,6 +27,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb index 6291abd1fc..4c5ca952c1 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb @@ -18,8 +18,4 @@ dependencies = [ ('MPC', '1.2.1'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb index 3d95fae8ad..6d5a48514a 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb @@ -18,8 +18,4 @@ dependencies = [ ('MPC', '1.2.1'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb index aa1e4ba5b7..050847af16 100644 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb @@ -12,8 +12,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True - exts_list = [ ('blessings', '1.7', { 'checksums': ['98e5854d805f50a5b58ac2333411b0482516a8210f23f43308baeb58d77c157d'], @@ -34,6 +32,4 @@ sanity_check_paths = { sanity_check_commands = ["gpustat --help"] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb index 7753fb4bfa..1f8bfba881 100644 --- a/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb @@ -62,9 +62,6 @@ files_to_copy = [ exts_defaultclass = 'PythonPackage' exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, - 'sanity_pip_check': True, 'source_urls': [PYPI_SOURCE], } exts_list = [ diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb index 0c2f4b1d60..31bc978aab 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb @@ -24,9 +24,6 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -download_dep_fail = True - sanity_check_paths = { 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'], @@ -34,8 +31,6 @@ sanity_check_paths = { sanity_check_commands = ['%(namelower)s-count --help'] -sanity_pip_check = True - options = {'modulename': '%(name)s'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb index de3f87c495..609faa926b 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb @@ -20,9 +20,6 @@ dependencies = [ ('TensorFlow', local_tf_version), ] -use_pip = True -sanity_pip_check = True - preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb index 5a3037fc26..32757cca2c 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb @@ -20,9 +20,6 @@ dependencies = [ ('PyTorch', local_pt_version), ] -use_pip = True -sanity_pip_check = True - preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb index 838513f4e8..b4c2e230ac 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -20,9 +20,6 @@ dependencies = [ ('PyTorch', local_pt_version), ] -use_pip = True -sanity_pip_check = True - preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb index 1382aa8245..5f3f66b801 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -21,9 +21,6 @@ dependencies = [ ('TensorFlow', local_tf_version), ] -use_pip = True -sanity_pip_check = True - preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb index ad341bc26e..08775cbcd4 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -21,9 +21,6 @@ dependencies = [ ('TensorFlow', local_tf_version), ] -use_pip = True -sanity_pip_check = True - preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb index 3d2eb91b26..dd6af99bcc 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -20,9 +20,6 @@ dependencies = [ ('PyTorch', local_pt_version), ] -use_pip = True -sanity_pip_check = True - preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' diff --git a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb index e78c32c265..efecbc6544 100644 --- a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb @@ -24,9 +24,6 @@ dependencies = [ ('Spark', '3.1.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('cloudpickle', '1.6.0', { 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb index 3d23598929..88ca816ac3 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb @@ -22,10 +22,6 @@ dependencies = [ ('HDF5', '1.10.7'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 # without this environment variable, pip will fetch the minimum numpy version h5py supports during intall, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb index 2ccf55fe6a..d1de160e97 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb @@ -22,10 +22,6 @@ dependencies = [ ('HDF5', '1.10.7'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 # without this environment variable, pip will fetch the minimum numpy version h5py supports during install, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb index ab4a302e17..63aebd44bf 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb @@ -22,10 +22,6 @@ dependencies = [ ('HDF5', '1.10.7'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 # without this environment variable, pip will fetch the minimum numpy version h5py supports during install, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb index f8dce1b3d7..cbf5fd8210 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb @@ -22,10 +22,6 @@ dependencies = [ ('HDF5', '1.10.7'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 # without this environment variable, pip will fetch the minimum numpy version h5py supports during install, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb index b02cdc7690..26c09f0d05 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb @@ -17,8 +17,4 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb index 4779ef3e22..c03620d197 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb @@ -18,8 +18,4 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb index 6b59173187..f433d5203d 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb @@ -17,8 +17,4 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb index cf62caebaa..e6d7a93bd7 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb @@ -17,8 +17,4 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb index e96de73689..0fb450ad45 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb @@ -20,8 +20,6 @@ dependencies = [ ('ZeroMQ', '4.3.3'), ] -use_pip = True - exts_list = [ ('ipython_genutils', '0.2.0', { 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], @@ -142,6 +140,4 @@ sanity_check_commands = [ "NOSE_EXCLUDE='system_interrupt' iptest", ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 48e8d55811..aab9ec0426 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -39,8 +39,6 @@ dependencies = [ ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, } exts_defaultclass = 'PythonPackage' exts_list = [ diff --git a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb index 2b39682fdb..c801e2d60d 100644 --- a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb @@ -21,8 +21,6 @@ dependencies = [ ('coverage', '5.5'), ] -use_pip = True - exts_list = [ ('pytest-runner', '5.3.0', { 'modulename': 'ptr', @@ -36,8 +34,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/idemux'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index acd6766b2c..9b0fed9db7 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -50,9 +50,6 @@ dependencies = [ ('h5py', '3.1.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('bitshuffle', '0.3.5', { 'sources': ['%(version)s.tar.gz'], diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb index 51d59be8f6..90b1d5b148 100644 --- a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb @@ -18,8 +18,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb index 2213be1626..e9a4559326 100644 --- a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb @@ -18,8 +18,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb index c13fa13ed4..f777a7fe46 100644 --- a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb @@ -17,11 +17,6 @@ dependencies = [ ('scikit-learn', '0.23.2'), ] -use_pip = True -download_dep_fail = True - options = {'modulename': 'imblearn'} -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb index 0c948731f6..db3b0b207b 100644 --- a/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb @@ -18,9 +18,4 @@ dependencies = [ ('OpenCV', '4.5.1', '-contrib'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb index 1e5a19bc40..1c05b20306 100644 --- a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb @@ -21,8 +21,6 @@ dependencies = [ ('pyfaidx', '0.5.9.5'), ] -use_pip = True - exts_list = [ ('argcomplete', '1.12.3', { 'checksums': ['2c7dbffd8c045ea534921e63b0be6fe65e88599990d8dc408ac8c542b72a5445'], @@ -62,6 +60,5 @@ sanity_check_commands = [ "isocirc -t 1 read_toy.fa chr16_toy.fa chr16_toy.gtf chr16_circRNA_toy.bed output" ), ] -sanity_pip_check = True moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb index 36fecff59c..fbd9f14c94 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -22,8 +22,6 @@ dependencies = [ osdependencies = [OS_PKG_OPENSSL_DEV] -use_pip = True - exts_list = [ ('certipy', '0.1.3', { 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], @@ -110,8 +108,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], } -sanity_pip_check = True - sanity_check_commands = ['jupyterhub --help'] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb index 1f63a8e302..a0d9aaa592 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb @@ -18,9 +18,6 @@ dependencies = [ ('IPython', '7.18.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('json5', '0.9.5', { 'checksums': ['703cfee540790576b56a92e1c6aaa6c4b0d98971dc358ead83812aa4d06bdb96'], diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index e583b752f4..bc3e0480ec 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -32,8 +32,6 @@ local_tf_builddir = '%(builddir)s/' + local_tf_dir local_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir -use_pip = True - # running the tests with lots of cores results in test failures because not enough threads can be started, # so limit to a reasonable number of cores to use at maximum maxparallel = 5 @@ -43,9 +41,6 @@ default_component_specs = { 'sources': [SOURCE_TAR_GZ], 'source_urls': [PYPI_SOURCE], 'start_dir': '%(name)s-%(version)s', - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, } components = [ @@ -106,6 +101,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index 039ed9bd0d..ba868854c6 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -34,16 +34,11 @@ local_tf_builddir = '%(builddir)s/' + local_tf_dir local_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir -use_pip = True - default_easyblock = 'PythonPackage' default_component_specs = { 'sources': [SOURCE_TAR_GZ], 'source_urls': [PYPI_SOURCE], 'start_dir': '%(name)s-%(version)s', - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, } components = [ @@ -120,6 +115,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb b/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb index f5feb4ef74..f408b376c5 100644 --- a/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb +++ b/easybuild/easyconfigs/j/joypy/joypy-0.2.4-intel-2020b.eb @@ -20,8 +20,4 @@ dependencies = [ ('matplotlib', '3.3.3',), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb index d5a6b4d2ec..c065d25b93 100644 --- a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb @@ -17,9 +17,4 @@ builddependencies = [ dependencies = [('Python', '3.8.6')] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb index 2f81c7cf31..756c1e7c80 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb @@ -17,8 +17,6 @@ dependencies = [ ('TensorFlow', '2.4.1'), # provides h5py 2.1.0 ] -use_pip = True - exts_list = [ ('Keras_Applications', '1.0.8', { 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], @@ -31,6 +29,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb index f8e15be695..ec8929b7b5 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -19,8 +19,6 @@ dependencies = [ ('TensorFlow', local_tf_version), # provides h5py 2.1.0 ] -use_pip = True - exts_list = [ ('Keras_Applications', '1.0.8', { 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], @@ -33,6 +31,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb index 06a6be6a59..4fc733084c 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb @@ -17,8 +17,6 @@ dependencies = [ ('TensorFlow', '2.4.1'), # provides h5py 2.1.0 ] -use_pip = True - exts_list = [ ('Keras_Applications', '1.0.8', { 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], @@ -31,6 +29,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb index 3e11982630..4d2634b42d 100644 --- a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-foss-2020b.eb @@ -14,9 +14,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('asteval', '0.9.23', { 'checksums': ['f5096a924b1d2f147e70327245d95fc8f534dbe94277b6828ce2a8c049d3a438'], diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb index 2c4a3881dd..60cd617730 100644 --- a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.2-intel-2020b.eb @@ -14,9 +14,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('asteval', '0.9.23', { 'checksums': ['f5096a924b1d2f147e70327245d95fc8f534dbe94277b6828ce2a8c049d3a438'], diff --git a/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb b/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb index bae0931936..a290fefcd6 100644 --- a/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb @@ -21,8 +21,6 @@ dependencies = [ ('networkx', '2.5'), ] -use_pip = True - exts_list = [ ('amply', '0.1.4', { 'checksums': ['cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38'], @@ -52,7 +50,6 @@ postinstallcmds = [ ' -executable -type f -exec chmod +x {} \\;', ] -sanity_pip_check = True sanity_check_paths = { 'files': ['bin/LncLOOM'], 'dirs': ['lib/python%(pyshortver)s/site-packages/LncLOOMv2'], diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb index 6df451ff57..459b91dad0 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb @@ -25,9 +25,6 @@ dependencies = [ ('python-igraph', '0.9.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('ddt', '1.4.2', { 'checksums': ['64a67366a2715e636b88694cc6075cc02db292f01098b8e385397c894d395378'], diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb index 8aad4bf9f1..ae2f5af19b 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb @@ -25,9 +25,6 @@ dependencies = [ ('python-igraph', '0.9.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('ddt', '1.4.2', { 'checksums': ['64a67366a2715e636b88694cc6075cc02db292f01098b8e385397c894d395378'], diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index 2a82e9c481..542cfc7bf1 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -25,9 +25,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, - 'sanity_pip_check': True, } exts_list = [ (name, version, { diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb index 2458724db7..1955082621 100644 --- a/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb @@ -15,9 +15,6 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -sanity_pip_check = True -use_pip = True - exts_list = [ ('wrapt', '1.12.1', { 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index 1a6ef6836a..cca7752cf8 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -42,9 +42,6 @@ components = [ 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], 'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'], 'start_dir': '%(name)s-%(version)s', - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True, }), ] diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb index 64f5e58792..75c2751715 100644 --- a/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.6-intel-2020b.eb @@ -15,8 +15,6 @@ dependencies = [ ('numba', '0.52.0'), ] -use_pip = True - exts_list = [ ('numpy_groupies', '0.9.13', { 'checksums': ['7b17b291322353f07c51598512d077e3731da0a048cfa8f738f3460d1ef0658d'], @@ -33,6 +31,4 @@ sanity_check_paths = { sanity_check_commands = ["loompy --help"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb index dbd3721ba1..da0865afaa 100644 --- a/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb @@ -19,8 +19,4 @@ dependencies = [ ('libxslt', '1.1.34'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb index f9fc548a6e..b2753431c9 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -18,8 +18,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True - exts_list = [ ('matlabengine', _engine_version, { 'modulename': 'matlab.engine', @@ -27,8 +25,6 @@ exts_list = [ }), ] -sanity_pip_check = True - # Test that connection with MATLAB can be established successfully sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb index 62cbd2a419..31d808c243 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb @@ -21,9 +21,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('GridDataFormats', '0.5.0', { 'modulename': 'gridData', diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb index a9fa73da54..61672a415b 100644 --- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb @@ -17,7 +17,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -use_pip = True exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], @@ -38,6 +37,4 @@ exts_list = [ # a massive number of extra dependencies. See # https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml -sanity_pip_check = True - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb index 8a14999b77..a14e188d5d 100644 --- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb @@ -17,7 +17,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -use_pip = True exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], @@ -38,6 +37,4 @@ exts_list = [ # a massive number of extra dependencies. See # https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml -sanity_pip_check = True - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb index 0b9e574190..f4d415e26b 100644 --- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb @@ -17,7 +17,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -use_pip = True exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], @@ -38,6 +37,4 @@ exts_list = [ # a massive number of extra dependencies. See # https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml -sanity_pip_check = True - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb index d4c483239b..8c91fddf7e 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb @@ -11,10 +11,6 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} sources = [SOURCE_TAR_GZ] checksums = ['8195c8c1400ceb53496064314c6736719c6f25e7479cd24c77be3d9361cddc27'] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - builddependencies = [('binutils', '2.35')] multi_deps = {'Python': ['3.8.6', '2.7.18']} diff --git a/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb index 07a664b8e8..94295f1343 100644 --- a/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb @@ -21,8 +21,4 @@ dependencies = [ ('SimpleITK', '2.1.0'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb index e5bb3979d8..3767368ae1 100644 --- a/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb @@ -21,8 +21,4 @@ dependencies = [ ('SimpleITK', '2.1.0'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb index f71e6ef6e2..1c51b68308 100644 --- a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb @@ -20,8 +20,6 @@ dependencies = [ ('Seaborn', '0.11.1'), ] -use_pip = True - exts_list = [ ('progressbar33', '2.4', { 'modulename': 'progressbar', @@ -52,6 +50,4 @@ sanity_check_commands = [ "megalodon -h", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb index 0561598001..c60f26b61a 100644 --- a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb @@ -20,8 +20,6 @@ dependencies = [ ('Seaborn', '0.11.1'), ] -use_pip = True - exts_list = [ ('progressbar33', '2.4', { 'modulename': 'progressbar', @@ -52,6 +50,4 @@ sanity_check_commands = [ "megalodon -h", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb index d930cd3469..995a851ffc 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb @@ -22,10 +22,6 @@ dependencies = [ ('Python', '3.8.6') ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - sanity_check_commands = ["hg --help"] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb index 660814b8cc..213225dfb5 100644 --- a/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb @@ -20,10 +20,6 @@ dependencies = [ ('Ninja', '1.10.1'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - options = {'modulename': 'mesonbuild'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb index fa7173c514..1b08034e2a 100644 --- a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb @@ -24,8 +24,4 @@ dependencies = [ preinstallopts = 'export TORCH_CUDA_ARCH_LIST="%(cuda_cc_semicolon_sep)s" && ' -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb index ef76f02541..1f38d2c832 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb @@ -29,8 +29,6 @@ dependencies = [ ('networkx', '2.5'), ] -use_pip = True - exts_list = [ ('colormath', '3.0.0', { 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], @@ -68,6 +66,4 @@ sanity_check_paths = { sanity_check_commands = ["multiqc --help"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb index 4d89465bea..6a5d45cbf2 100644 --- a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-foss-2020b.eb @@ -12,9 +12,6 @@ toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] checksums = ['393ebc85413bd1b573909736caeadd9d7757f41cceb7bd29f3b30f5107237cba'] -download_dep_fail = True -use_pip = True - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -29,8 +26,6 @@ dependencies = [ # configparser is part of stdlib in Python 3 preinstallopts = "sed -i 's/.*configparser.*//g' setup.py && " -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/myokit'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb index 44daa4b563..3a55db7a48 100644 --- a/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb @@ -12,9 +12,6 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] checksums = ['393ebc85413bd1b573909736caeadd9d7757f41cceb7bd29f3b30f5107237cba'] -download_dep_fail = True -use_pip = True - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -29,8 +26,6 @@ dependencies = [ # configparser is part of stdlib in Python 3 preinstallopts = "sed -i 's/.*configparser.*//g' setup.py && " -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/myokit'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb index e59fa99490..acf2310cd7 100644 --- a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb @@ -30,8 +30,4 @@ dependencies = [ ('RcppGSL', '0.3.8', versionsuffix), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb index 0cbbd4ffc6..03648a4381 100644 --- a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -18,8 +18,4 @@ dependencies = [ ('IPython', '7.18.1'), # has traitlets ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb index 39d7dd5cf4..171f790a64 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb @@ -23,9 +23,6 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb index 4a49f2dc22..17d226d026 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb @@ -23,9 +23,6 @@ dependencies = [ ('Pillow', '8.0.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb index 06ed98ff90..e8f714c5d4 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb @@ -23,9 +23,6 @@ dependencies = [ ('Pillow', '8.0.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb index a79ad30577..403fa88da2 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb @@ -23,9 +23,6 @@ dependencies = [ ('Pillow', '8.0.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb index 845af2bf73..0ae55de9ae 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb @@ -23,9 +23,6 @@ dependencies = [ ('Pillow', '8.0.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb index 7069e0d149..9f7fcdae7c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb @@ -24,14 +24,10 @@ dependencies = [ ('Qhull', '2020.2') ] -use_pip = True -sanity_pip_check = True - # avoid that matplotlib downloads and builds its own copies of freetype and qhull _fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " _fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template > mplsetup.cfg && " - _include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " exts_list = [ diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb index 0c81a702dd..2ef0b7945f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb @@ -24,14 +24,10 @@ dependencies = [ ('Qhull', '2020.2') ] -use_pip = True -sanity_pip_check = True - # avoid that matplotlib downloads and builds its own copies of freetype and qhull _fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " _fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template > mplsetup.cfg && " - _include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " exts_list = [ diff --git a/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb b/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb index 3193eac6e2..4e70c7b7c0 100644 --- a/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb +++ b/easybuild/easyconfigs/m/maze/maze-20170124-foss-2020b.eb @@ -29,10 +29,6 @@ dependencies = [ preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ -use_pip = True -download_dep_fail = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/maze_server', 'bin/extract_reference_slices'], 'dirs': ['lib/python%(pyshortver)s/site-packages/templates'], diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index a6ccdd5505..5fe1f8f7b4 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -39,8 +39,6 @@ dependencies = [ ('BCFtools', '1.11'), ] -use_pip = True - exts_list = [ # required for ont-fast5-api ('progressbar33', '2.4', { @@ -81,8 +79,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb index e03e3bf731..31c671af27 100644 --- a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb @@ -20,8 +20,4 @@ dependencies = [ ('Keras', '2.4.3'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb index 7bca8c2f08..413db008b1 100644 --- a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb @@ -20,8 +20,4 @@ dependencies = [ ('Keras', '2.4.3'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb b/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb index 4c23f71ea9..66be6f2401 100644 --- a/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb @@ -21,11 +21,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # for numpy ] -download_dep_fail = True -use_pip = True - options = {'modulename': 'mkl'} -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb index ad208054f1..a0a74c8a50 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -19,10 +19,6 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" runtest += "python setup.py build_ext -i; pytest -ra" diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb index 60b2d1678d..f1dfa5cec5 100644 --- a/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb @@ -29,10 +29,6 @@ dependencies = [ ('Python', '3.8.6'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - runtest = 'python -c "import mpmath; mpmath.runtests();"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb index 7219684d61..0cbc428952 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb @@ -16,10 +16,6 @@ provide basic MRC file I/O functions. """ toolchain = {'name': 'foss', 'version': '2020b'} -use_pip = True -sanity_pip_check = True -download_dep_fail = True - sources = [SOURCELOWER_TAR_GZ] checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb index 0b2fdf52c7..679837b053 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb @@ -16,10 +16,6 @@ provide basic MRC file I/O functions. """ toolchain = {'name': 'fosscuda', 'version': '2020b'} -use_pip = True -sanity_pip_check = True -download_dep_fail = True - sources = [SOURCELOWER_TAR_GZ] checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] diff --git a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb index f6ff4874bc..e540bfa733 100644 --- a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb @@ -26,9 +26,6 @@ dependencies = [ ('joypy', '0.2.4'), ] -download_dep_fail = True -use_pip = True - # replace strict Seaborn & pauvre version requirement with minimal version requirements, preinstallopts = "sed -i 's/==0/>=0/g' setup.py && " @@ -39,6 +36,4 @@ sanity_check_paths = { sanity_check_commands = ["NanoComp --help"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb index d8059101c3..6a853d802c 100644 --- a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb @@ -29,9 +29,6 @@ dependencies = [ ('Kaleido', '0.1.0'), ] -download_dep_fail = True -use_pip = True - # replace strict Seaborn & pauvre version requirement with minimal version requirements preinstallopts = "sed -i 's/==0/>=0/g' setup.py && " @@ -42,6 +39,4 @@ sanity_check_paths = { sanity_check_commands = ["NanoPlot --help"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb index 5ee1fef6ce..c17c0e3c95 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ ('pydicom', '2.1.2'), ] -use_pip = True - exts_list = [ ('bz2file', '0.98', { 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], @@ -41,6 +39,4 @@ sanity_check_commands = [ "parrec2nii --help", ] -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb index cf9d4e9046..77723e4527 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ ('pydicom', '2.1.2'), ] -use_pip = True - exts_list = [ ('bz2file', '0.98', { 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], @@ -41,6 +39,4 @@ sanity_check_commands = [ "parrec2nii --help", ] -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb index 0dacbc3487..7b1e5a4bac 100644 --- a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb @@ -17,10 +17,6 @@ dependencies = [ ('scikit-learn', '0.23.2'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb index 896f9805cf..44e8e2cf53 100644 --- a/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.15.0-intel-2020b.eb @@ -22,8 +22,4 @@ dependencies = [ ('nanomath', '1.2.0'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb index 86a33153d9..b516e1b8e3 100644 --- a/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.0-intel-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True - exts_list = [ ('Python-Deprecated', '1.1.0', { 'modulename': 'deprecated', @@ -28,6 +26,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb index 4affa74280..c4a0d9b383 100644 --- a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb @@ -20,8 +20,4 @@ checksums = ['887874f9ab8ba42b31e47a51503aa85be7b215073151415d38b231f748072a42'] options = {'modulename': 'nmutils'} -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb index 738e464088..ebd8ab21d6 100644 --- a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb @@ -20,8 +20,4 @@ checksums = ['887874f9ab8ba42b31e47a51503aa85be7b215073151415d38b231f748072a42'] options = {'modulename': 'nmutils'} -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb index e48419cb64..b872b8da2f 100644 --- a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb +++ b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ ('PyYAML', '5.3.1'), ] -use_pip = True - exts_list = [ ('monotonic', '1.6', { 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], @@ -63,6 +61,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb index 58f903e181..7721fd2c2e 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb @@ -16,9 +16,6 @@ dependencies = [ ('cURL', '7.72.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('cftime', '1.4.1', { 'checksums': ['7c55540bc164746c3c4f86a07c9c7b9ed4dfb0b0d988348ec63cec065c58766d'], diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb index 4970fc6590..1ecd816cd0 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb @@ -18,9 +18,6 @@ dependencies = [ ('cURL', '7.72.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('cftime', '1.4.1', { 'checksums': ['7c55540bc164746c3c4f86a07c9c7b9ed4dfb0b0d988348ec63cec065c58766d'], diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb index 4877a91283..325f42d0fd 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb @@ -16,9 +16,6 @@ dependencies = [ ('cURL', '7.72.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('cftime', '1.2.0', { 'checksums': ['ff0a175edda260357ff7d24a32bbe0a8c72eafd5f6a404ce487127f9d01836db'], diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb index 4b5d73a3cd..e2e3222eb0 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-foss-2020b.eb @@ -17,8 +17,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb index b7466845d8..4d40433ae0 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-fosscuda-2020b.eb @@ -17,8 +17,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb index 49cf679c99..6f756c62f7 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-intel-2020b.eb @@ -17,8 +17,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb index d6967a10d7..5e991b35af 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb @@ -17,8 +17,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb index 8a5bed3a71..00fb9d1646 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb @@ -17,8 +17,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb index af8ddb251b..a00ea50fc2 100644 --- a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb @@ -32,9 +32,6 @@ dependencies = [ ('lxml', '4.6.2'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('linecache2', '1.0.0', { 'checksums': ['4b26ff4e7110db76eeb6f5a7b64a82623839d595c2038eeda662f2a2db78e97c'], diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb index e00878d774..dee8909b57 100644 --- a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb @@ -32,9 +32,6 @@ dependencies = [ ('lxml', '4.6.2'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('linecache2', '1.0.0', { 'checksums': ['4b26ff4e7110db76eeb6f5a7b64a82623839d595c2038eeda662f2a2db78e97c'], diff --git a/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb index 0f17be0040..7e8cf418ac 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.52.0-foss-2020b.eb @@ -19,9 +19,6 @@ dependencies = [ ('LLVM', '10.0.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('llvmlite', '0.35.0', { 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], diff --git a/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb index be5572c9dd..979731abbd 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.52.0-fosscuda-2020b.eb @@ -19,9 +19,6 @@ dependencies = [ ('LLVM', '10.0.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('llvmlite', '0.35.0', { 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], diff --git a/easybuild/easyconfigs/n/numba/numba-0.52.0-intel-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.52.0-intel-2020b.eb index b5137cf2da..a97a815853 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.52.0-intel-2020b.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.52.0-intel-2020b.eb @@ -19,9 +19,6 @@ dependencies = [ ('LLVM', '10.0.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('llvmlite', '0.35.0', { 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], diff --git a/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb index bd578f812f..ceb0717012 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2020b.eb @@ -19,9 +19,6 @@ dependencies = [ ('LLVM', '11.0.0'), ] -use_pip = True -sanity_pip_check = True - local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " diff --git a/easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb b/easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb index c8466673ed..1f5d36b949 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.53.1-fosscuda-2020b.eb @@ -19,9 +19,6 @@ dependencies = [ ('LLVM', '11.0.0'), ] -use_pip = True -sanity_pip_check = True - local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " diff --git a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb index 765db86558..5425817e36 100644 --- a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb @@ -23,10 +23,6 @@ dependencies = [ ('IPython', '7.18.1'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - preinstallopts = "sed -i \"s|get_python_lib()|get_python_lib(prefix='%(installdir)s')|g\" setup.py &&" fix_python_shebang_for = ['bin/obi'] diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb index b013362d2e..2b699a6f1b 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -17,7 +17,6 @@ dependencies = [ builddependencies = [('binutils', '2.35')] exts_default_options = { - 'use_pip': True, } exts_list = [ ('pbr', '5.6.0', { @@ -121,7 +120,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb index abe97dde5d..145640746b 100644 --- a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb @@ -23,9 +23,6 @@ dependencies = [ ('MMseqs2', '13-45111'), ] -download_dep_fail = True -use_pip = True - # see https://github.com/davidemms/OrthoFinder/pull/500 preinstallopts = 'sed -i "s/ExampleDataset/ExampleData/g" setup.py && ' @@ -39,6 +36,4 @@ sanity_check_paths = { sanity_check_commands = ["orthofinder --help"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb index 3c6475ccad..d1fdb60855 100644 --- a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb @@ -23,10 +23,6 @@ dependencies = [ ('MMseqs2', '13-45111'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - options = {'modulename': 'scripts_of'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb index a8d05c6400..fdc7fcadf1 100644 --- a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb @@ -14,8 +14,6 @@ dependencies = [ ('h5py', '3.1.0'), ] -use_pip = True - exts_list = [ ('progressbar33', '2.4', { 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], @@ -38,6 +36,4 @@ sanity_check_commands = [ "single_to_multi_fast5 --help", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb index b4a6b8321b..6d009fdf1b 100644 --- a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb @@ -14,8 +14,6 @@ dependencies = [ ('h5py', '3.1.0'), ] -use_pip = True - exts_list = [ ('progressbar33', '2.4', { 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], @@ -38,6 +36,4 @@ sanity_check_commands = [ "single_to_multi_fast5 --help", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb index 0ce06b699c..1401c9209b 100644 --- a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb @@ -16,9 +16,6 @@ dependencies = [ ('Pillow', '8.0.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('et_xmlfile', '1.1.0', { 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], diff --git a/easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb b/easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb index 966cf0a6e7..721821f7ae 100644 --- a/easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb @@ -17,8 +17,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb index 9c4aa141b7..0e831be23b 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb @@ -28,9 +28,6 @@ dependencies = [ ('freetype', '2.10.3') ] -use_pip = True -download_dep_fail = True - options = {'modulename': 'PIL'} sanity_check_paths = { @@ -38,6 +35,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], } -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb index a8a8a9dd9f..ff4e25b298 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb @@ -23,10 +23,6 @@ dependencies = [ ('freetype', '2.10.3') ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - options = {'modulename': 'PIL'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 6c8f256ce9..475823cded 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -27,11 +27,8 @@ dependencies = [ ('freetype', '2.10.3') ] -download_dep_fail = True # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " -use_pip = True -sanity_pip_check = True options = {'modulename': 'PIL'} diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb index f925080a09..6fe6fb0d41 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -25,11 +25,8 @@ dependencies = [ ('freetype', '2.10.3') ] -download_dep_fail = True # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " -use_pip = True -sanity_pip_check = True options = {'modulename': 'PIL'} diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb index 7e14731b26..af50932ddf 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb @@ -18,8 +18,4 @@ dependencies = [ options = {'modulename': 'pyamg'} -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb index c1cb9119b5..cc7ab66ab7 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb @@ -18,8 +18,4 @@ dependencies = [ options = {'modulename': 'pyamg'} -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb index 3a973ddf49..cbf8defe8d 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -19,9 +19,6 @@ local_preinstallopts = './configure.py --cuda-root="$EBROOTCUDA" --boost-inc-dir local_preinstallopts += '--boost-lib-dir="$EBROOTBOOST/lib" --no-use-shipped-boost ' local_preinstallopts += '--boost-python-libname=boost_python38 && ' -use_pip = True -sanity_pip_check = True - exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb index a4dcd75516..9658c9544e 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb @@ -24,9 +24,6 @@ dependencies = [ ] # PyGTK needs PyCairo installed by pip -use_pip = True -sanity_pip_check = True -download_dep_fail = True # remove pyproject.toml, which causes trouble (header files and .pc file are not installed) preinstallopts = "rm pyproject.toml && " diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index ee4425b49c..d4e87b9a1c 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -22,7 +22,6 @@ dependencies = [ ] exts_default_options = { - 'use_pip': True } exts_list = [ @@ -37,6 +36,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb b/easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb index 2104001428..b70b3f82df 100644 --- a/easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyFoam/PyFoam-2020.5-foss-2020b.eb @@ -16,9 +16,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # for numpy ] -download_dep_fail = True -use_pip = True - options = {'modulename': name} fix_python_shebang_for = ['bin/*.py'] @@ -30,6 +27,4 @@ sanity_check_paths = { sanity_check_commands = ["pyFoam%s.py --help" % x for x in ('Execute', 'Runner', 'Version')] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb index 34cef2e071..75e88368c3 100644 --- a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb @@ -19,8 +19,4 @@ dependencies = [ ('GEOS', '3.9.1'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb index 5114a27aba..21449c04d5 100644 --- a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb @@ -22,9 +22,6 @@ dependencies = [ ('xarray', '0.16.2'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('typing_extensions', '3.7.4.3', { 'checksums': ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'], diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb index fd9f3d7d32..890f1ea942 100644 --- a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb @@ -23,9 +23,6 @@ dependencies = [ ('xarray', '0.16.2'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('typing_extensions', '3.7.4.3', { 'checksums': ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'], diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb index c96cc51c18..017acd4449 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -27,7 +27,6 @@ dependencies = [ toolchain = {'name': 'foss', 'version': '2020b'} use_pip = False -sanity_pip_check = True exts_list = [ ('Pmw', '2.0.1', { diff --git a/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb index ea2eaeedee..154b8a0dcd 100644 --- a/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-foss-2020b.eb @@ -20,11 +20,6 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] checksums = ['d891038825869190bb6a8187aadc1957254907b7465c7aab83f07835607e41df'] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - sanity_check_commands = ["python -c 'from pyod.models.knn import KNN'"] moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb index f6d7667e03..90de91c1f8 100644 --- a/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyOD/PyOD-0.8.7-intel-2020b.eb @@ -20,11 +20,6 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] checksums = ['d891038825869190bb6a8187aadc1957254907b7465c7aab83f07835607e41df'] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - sanity_check_commands = ["python -c 'from pyod.models.knn import KNN'"] moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb index 3ea1d13273..2ea0722046 100644 --- a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb @@ -14,9 +14,6 @@ dependencies = [ ('pocl', '1.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb index 0f033662e7..94d57e6466 100644 --- a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb @@ -13,9 +13,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb index 8bf189b529..11e0d3d783 100644 --- a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb @@ -14,9 +14,6 @@ dependencies = [ ('pocl', '1.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb index 8d15298523..73977bc211 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb @@ -32,11 +32,6 @@ dependencies = [ ('Python', '3.8.6'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - options = {'modulename': 'OpenGL'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb index 4a89af3e9d..931260b56a 100644 --- a/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb @@ -43,7 +43,4 @@ exts_list = [ }), ] -use_pip = True -sanity_pip_check = True - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index 2fc24f0a12..b2fab8f4e4 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -36,7 +36,6 @@ components = [ 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], 'start_dir': 'sip-%s' % local_sipver, - 'use_pip': True, 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.5.0', { @@ -44,14 +43,12 @@ components = [ 'sources': [SOURCE_TAR_GZ], 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], 'start_dir': 'PyQt-builder-%(version)s', - 'use_pip': True, }), ('PyQt5_sip', '12.8.1', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], 'start_dir': 'PyQt5_sip-%(version)s', - 'use_pip': True, }), (name, version, { 'source_urls': [PYPI_SOURCE], diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb index 775d1c1a6e..307a924374 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb @@ -47,7 +47,6 @@ components = [ 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], 'start_dir': 'sip-%s' % local_sipver, - 'use_pip': True, 'options': {'modulename': 'PyQt5.sip'}, }), @@ -56,7 +55,6 @@ components = [ 'sources': [SOURCE_TAR_GZ], 'checksums': ['6ade47445b7d8c08eb96e91ebda5f8b3494b3e7a9da2be343b9d0704419cb5c7'], 'start_dir': 'PyQt-builder-%(version)s', - 'use_pip': True, }), ('PyQt5_sip', '12.9.0', { @@ -64,7 +62,6 @@ components = [ 'sources': [SOURCE_TAR_GZ], 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], 'start_dir': 'PyQt5_sip-%(version)s', - 'use_pip': True, }), (name, version, { diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb index b8ec4d2ff1..4e34ea0b66 100644 --- a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb @@ -21,9 +21,4 @@ dependencies = [ ('PyOpenGL', '3.1.5'), ] -use_pip = True -download_dep_fail = True - -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb index 2d988f4afb..5c40d2fe13 100644 --- a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb @@ -21,9 +21,4 @@ dependencies = [ ('PyOpenGL', '3.1.5'), ] -use_pip = True -download_dep_fail = True - -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb index bd934ce0e1..db8b6d538b 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb @@ -17,8 +17,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -use_pip = True - exts_list = [ ('colorama', '0.4.4', { 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], @@ -41,6 +39,4 @@ sanity_check_commands = [ "pyretisrun --help", ] -sanity_pip_check = True - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb index f157cad034..2b41d869f4 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb @@ -17,8 +17,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -use_pip = True - exts_list = [ ('colorama', '0.4.4', { 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], @@ -41,6 +39,4 @@ sanity_check_commands = [ "pyretisrun --help", ] -sanity_pip_check = True - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb b/easybuild/easyconfigs/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb index 6e7c393204..ad589671f9 100644 --- a/easybuild/easyconfigs/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb @@ -17,9 +17,6 @@ dependencies = [ ('py-aiger', '6.1.14'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('pypblib', '0.0.4', { 'checksums': ['71dd930bf177ca38d6eeb473702d05df07e11f20382db0c766465297eaf49062'], diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb index b2ad02c66b..956583ecc4 100644 --- a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -25,8 +25,6 @@ dependencies = [ ] use_pip = False -sanity_pip_check = True -download_dep_fail = True preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb index 766b4a7e03..cb5f68f439 100644 --- a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb @@ -14,9 +14,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ (name, version, { 'modulename': '%(namelower)s', diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb index fdc220d285..77d2e587e0 100644 --- a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb @@ -17,8 +17,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb index 23f3a638cb..6c632eb5c9 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb @@ -33,10 +33,6 @@ dependencies = [ ('Blosc', '1.21.0'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - local_bins = ['pt2to3', 'ptdump', 'ptrepack'] sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bins], diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2020b.eb index 31070d115f..2b26340937 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2020b.eb @@ -31,10 +31,6 @@ dependencies = [ ('Blosc', '1.21.0'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bins], diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb index 3213dd286e..590ad898b3 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb @@ -33,10 +33,6 @@ dependencies = [ ('Blosc', '1.21.0'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bins], diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020b.eb index d2a6ff233d..408f28c82c 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020b.eb @@ -31,10 +31,6 @@ dependencies = [ ('Blosc', '1.21.0'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bins], diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb index ac1c2f2460..26e003457d 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb @@ -20,8 +20,6 @@ dependencies = [ ('ASE', '3.20.1'), ] -use_pip = True - exts_list = [ ('googledrivedownloader', '0.4', { 'modulename': 'google_drive_downloader', @@ -51,6 +49,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb index f68754b35b..647000e5bb 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb @@ -20,8 +20,6 @@ dependencies = [ ('ASE', '3.20.1'), ] -use_pip = True - exts_list = [ ('googledrivedownloader', '0.4', { 'modulename': 'google_drive_downloader', @@ -51,6 +49,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb index c3de9720e6..2bbb7cf4f1 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -23,8 +23,6 @@ dependencies = [ ('YACS', '0.1.8'), ] -use_pip = True - exts_list = [ ('googledrivedownloader', '0.4', { 'modulename': 'google_drive_downloader', @@ -54,6 +52,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb index 28c09209b9..59975bdece 100644 --- a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb @@ -20,9 +20,6 @@ dependencies = [ ('torchvision', '0.8.2', versionsuffix), ] -sanity_pip_check = True -use_pip = True - exts_list = [ ('portalocker', '2.3.0', { 'checksums': ['4e913d807aa6598c320e8a50c50e2ee0602bc45240b485e3f8bc06f13060084c'], diff --git a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb index 5dda1d5325..e503721fc1 100644 --- a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb @@ -16,10 +16,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # for numpy ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - options = {'modulename': 'pywt'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb index 3035aed1cc..1430010d3f 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb @@ -17,10 +17,6 @@ multi_deps = {'Python': ['3.8.6', '2.7.18']} dependencies = [('libyaml', '0.2.5')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - options = {'modulename': 'yaml'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb index 1d62246901..14ede1b9c4 100644 --- a/easybuild/easyconfigs/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb @@ -19,8 +19,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True - exts_list = [ ('setuptools_scm', '6.0.1', { 'checksums': ['d1925a69cb07e9b29416a275b9fadb009a23c148ace905b2fb220649a6c18e92'], @@ -50,8 +48,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/pylint'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb index d6de3792fc..37d49a3312 100644 --- a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb @@ -30,9 +30,6 @@ exts_list = [ }), ] -use_pip = True -sanity_pip_check = True - sanity_check_commands = ['pyomo -h'] moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb index 7496740a8f..9877aa9b6f 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb @@ -31,9 +31,4 @@ dependencies = [ ('XZ', '5.2.5'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb index 099b411c19..f3859c5755 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb @@ -30,9 +30,4 @@ dependencies = [ ('XZ', '5.2.5'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb index cc0bc1b1e0..ce7a2d484c 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb @@ -32,8 +32,4 @@ dependencies = [ ('XZ', '5.2.5'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index 591c3feab6..05777350e9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -31,10 +31,7 @@ osdependencies = [OS_PKG_OPENSSL_DEV] install_pip = True exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, 'source_urls': [PYPI_SOURCE], - 'use_pip': True, } # order is important! diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 4662198909..bf47608722 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -38,13 +38,9 @@ osdependencies = [OS_PKG_OPENSSL_DEV] install_pip = True exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, 'source_urls': [PYPI_SOURCE], - 'use_pip': True, } - # order is important! # package versions updated 13 October 2020 exts_list = [ diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb index 733968e101..4d357e0549 100644 --- a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb +++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb @@ -27,9 +27,6 @@ dependencies = [ ('prokka', '1.14.5'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('sklearn', '0.0', { 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], diff --git a/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb index b7d9b8c920..2e56be59de 100644 --- a/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb @@ -22,8 +22,4 @@ dependencies = [ runtest = 'pytest' -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb index b84ba84bea..d691f5d633 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb @@ -27,9 +27,6 @@ dependencies = [ ('Kent_tools', '411'), ] -use_pip = True -sanity_pip_check = True - github_account = 'cov-lineages' exts_default_options = { 'source_urls': [GITHUB_SOURCE], diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb index c74bb75c50..062e88a43a 100644 --- a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb @@ -25,9 +25,6 @@ dependencies = [ ('SRA-Toolkit', '2.10.9'), ] -download_dep_fail = True -use_pip = True - sanity_check_paths = { "files": ["bin/parallel-fastq-dump"], "dirs": ["lib/python%(pyshortver)s/site-packages"], @@ -38,6 +35,4 @@ options = {'modulename': False} sanity_check_commands = ["parallel-fastq-dump --version"] -sanity_pip_check = True - moduleclass = "bio" diff --git a/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb b/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb index 7b5a085266..5cafc5395f 100644 --- a/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb +++ b/easybuild/easyconfigs/p/pauvre/pauvre-0.1924-intel-2020b.eb @@ -22,9 +22,6 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -download_dep_fail = True -use_pip = True - # fix incorrect requirement, correct name is 'scikit-learn' preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " @@ -35,6 +32,4 @@ sanity_check_paths = { sanity_check_commands = ["pauvre --help"] -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb index 3a1f3d0bc3..f1f1dd52ed 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb @@ -20,9 +20,6 @@ dependencies = [ ('spglib-python', '1.16.0'), ] -download_dep_fail = True -use_pip = True - sanity_check_paths = { 'files': ['bin/phonopy'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], @@ -30,6 +27,4 @@ sanity_check_paths = { sanity_check_commands = ["phonopy --help"] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb index 0a19fe634e..c0947588f3 100644 --- a/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb @@ -22,9 +22,6 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('torch-lfilter', '0.0.3', { 'source_tmpl': 'torch_lfilter-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb index 75ef1ef367..07a2db3b05 100644 --- a/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb @@ -22,9 +22,6 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('torch-lfilter', '0.0.3', { 'source_tmpl': 'torch_lfilter-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb index 854336b2eb..fa0adac445 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb @@ -19,8 +19,4 @@ dependencies = [ ('pkg-config', '0.29.2'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb index cd0c9c372f..bf91c7f773 100644 --- a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb @@ -14,8 +14,6 @@ builddependencies = [ dependencies = [('Python', '3.8.6')] -use_pip = True - exts_list = [ ('retrying', '1.3.3', { 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], @@ -25,6 +23,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb index 00f2bd3ae2..8b082eb66d 100644 --- a/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb @@ -23,10 +23,6 @@ dependencies = [ ('matplotlib', '2.2.5', versionsuffix), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - sanity_check_commands = ['pmx --help'] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb index 8d37e9a2d1..8d86d99895 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb @@ -19,10 +19,6 @@ dependencies = [ ('protobuf', version) ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - # Make sure protobuf is installed as a regular folder or it will not be found if # other google packages are installed in other site-packages folders sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb index 6cb55d2040..615cf62352 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb @@ -12,9 +12,6 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True -sanity_pip_check = True - exts_list = [ (name, version, { 'source_urls': ['https://github.com/giampaolo/psutil/archive'], diff --git a/easybuild/easyconfigs/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb index f292e1aa4b..748a3d36bd 100644 --- a/easybuild/easyconfigs/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb @@ -20,9 +20,6 @@ dependencies = [ ('DFA', '2.1.2'), # needed by py-aiger-dfa ] -use_pip = True -sanity_pip_check = True - # sortedcontainers<3.0.0,>=2.3.0 required, Python/3.8.6 contains sortedcontainers 2.2.2 exts_list = [ ('sortedcontainers', '2.3.0', { diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb index 3bca83e40e..cee4a5c5d5 100644 --- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb @@ -20,11 +20,6 @@ dependencies = [ ('cURL', '7.72.0'), ] -use_pip = True -download_dep_fail = True - options = {'modulename': name} -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb index 1a72ee67c6..59e60d255a 100644 --- a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb @@ -20,10 +20,6 @@ checksums = ['f39f56ff58868ab7f12d6fa5c7bf6b7d111b7fa687f3816c5d8d11cb75fa82f0'] options = {'modulename': 'pyFAI'} -use_pip = True -download_dep_fail = True -sanity_pip_check = True - modextravars = { 'PYFAI_OPENCL': '0', } diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb index c5766420e2..20969e97fe 100644 --- a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb @@ -20,10 +20,6 @@ checksums = ['f39f56ff58868ab7f12d6fa5c7bf6b7d111b7fa687f3816c5d8d11cb75fa82f0'] options = {'modulename': 'pyFAI'} -use_pip = True -download_dep_fail = True -sanity_pip_check = True - modextravars = { 'PYFAI_OPENCL': '0', } diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb index 09b5d4fc47..6b9656132e 100644 --- a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb @@ -18,8 +18,4 @@ dependencies = [ ('FFTW', '3.3.8'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb index bff68e6702..df834c210e 100644 --- a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb @@ -18,8 +18,4 @@ dependencies = [ ('FFTW', '3.3.8'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb index 37d55f3c11..b905ef059a 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb @@ -18,9 +18,4 @@ dependencies = [ ('Pysam', '0.16.0.1', versionsuffix), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb index c37bdeea0d..e5cfa19ed6 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb @@ -17,9 +17,4 @@ dependencies = [ ('Pysam', '0.16.0.1'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb index 33f837b9ad..e4a7c9273c 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb @@ -17,9 +17,4 @@ dependencies = [ ('Pysam', '0.16.0.1'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb index 7d182f0b70..f1415c207f 100644 --- a/easybuild/easyconfigs/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb @@ -21,8 +21,4 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb index 8476b86031..84abe7301d 100644 --- a/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb @@ -18,8 +18,4 @@ dependencies = [ ('Graphviz', '2.47.0', '-Java-11'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb index b4502d6142..f8220244a9 100644 --- a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb @@ -15,9 +15,6 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -download_dep_fail = True -use_pip = True - sanity_check_paths = { 'files': ['bin/faidx'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], @@ -25,6 +22,4 @@ sanity_check_paths = { sanity_check_commands = ["faidx --help"] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb index 184d742345..493eae6062 100644 --- a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb @@ -11,9 +11,6 @@ toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCE_TAR_GZ] checksums = ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'] -use_pip = True -download_dep_fail = True - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11') @@ -25,6 +22,4 @@ sanity_check_paths = { } sanity_check_commands = ['pyfasta extract --help'] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb index 8e5e9cc501..57877c1793 100644 --- a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb @@ -32,8 +32,6 @@ exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_urls': [PYPI_SOURCE], - 'download_dep_fail': True, - 'use_pip': True, } exts_list = [ @@ -51,6 +49,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/pygmo'], } -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb index d42c422ae7..a2dfa4a36a 100644 --- a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb @@ -18,8 +18,4 @@ dependencies = [ ('Graphviz', '2.47.0', '-Java-11'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb index 37ad133e5d..7db5b198f8 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb @@ -24,8 +24,6 @@ dependencies = [ ('plotly.py', '4.14.3'), ] -use_pip = True - exts_list = [ ('numpy', '1.20.1', { 'sources': ['numpy-%(version)s.zip'], @@ -59,6 +57,4 @@ sanity_check_paths = { sanity_check_commands = ["pmg --help"] -sanity_pip_check = True - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymca/pymca-5.6.3-foss-2020b.eb b/easybuild/easyconfigs/p/pymca/pymca-5.6.3-foss-2020b.eb index a36cfe17e6..6a075fe950 100644 --- a/easybuild/easyconfigs/p/pymca/pymca-5.6.3-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pymca/pymca-5.6.3-foss-2020b.eb @@ -18,9 +18,6 @@ dependencies = [ ('silx', '0.14.0'), ] -use_pip = True -sanity_pip_check = True - exts_default_options = { 'source_urls': [GITHUB_SOURCE], 'sources': ['v%(version)s.tar.gz'], diff --git a/easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb index 473c95d50e..1a48c1777a 100644 --- a/easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb @@ -14,9 +14,6 @@ dependencies = [ ('silx', '0.14.0'), ] -use_pip = True -sanity_pip_check = True - exts_default_options = { 'source_urls': [GITHUB_SOURCE], 'sources': ['v%(version)s.tar.gz'], diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb index 55cfb0d3a0..f55e87bc23 100644 --- a/easybuild/easyconfigs/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb @@ -20,9 +20,6 @@ dependencies = [ ('PROJ', '7.2.1'), ] -download_dep_fail = True -use_pip = True - preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " sanity_check_paths = { @@ -32,6 +29,4 @@ sanity_check_paths = { sanity_check_commands = ['pyproj --help'] -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb index 2e18fed82c..0c067c3cef 100644 --- a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb @@ -32,10 +32,6 @@ dependencies = [ ('ASE', _aseversion), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb index b6a80dcfb0..e1ea6ae4f9 100644 --- a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb @@ -32,10 +32,6 @@ dependencies = [ ('ASE', _aseversion), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb index 380ab5a451..b2908699a7 100644 --- a/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb @@ -17,10 +17,6 @@ dependencies = [ ('Python', '3.8.6'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - options = {'modulename': 'pyroapi'} sanity_check_commands = [ diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb index ec240437e2..5330fd6991 100644 --- a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -use_pip = True - exts_list = [ ('opt_einsum', '3.3.0', { 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], @@ -30,6 +28,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb index ee98447bea..159ddd871a 100644 --- a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb @@ -12,9 +12,6 @@ toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCE_TAR_GZ] checksums = ['6d8b41934fdc700552d689f473860c64525a88600460344d0cac2095424750c6'] -use_pip = True -download_dep_fail = True - # acceptance of pysam>0.16 preinstallopts = "sed -i -e 's/ (<0.16)//g' setup.py && " @@ -29,6 +26,4 @@ sanity_check_commands = [ "pysamstats --help", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb b/easybuild/easyconfigs/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb index 88589c72da..46b4726651 100644 --- a/easybuild/easyconfigs/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('rasterio', '1.2.3'), ] -use_pip = True - # the latest pypi version of pysheds is currently behind the github one at 0.2.7 exts_list = [ ('geojson', '2.5.0', { @@ -30,6 +28,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb index 96e075cd30..e6e16e8ebf 100644 --- a/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb @@ -24,8 +24,4 @@ dependencies = [ options = {'modulename': 'shapefile'} -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb index 6e7e7a5935..4193c40386 100644 --- a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb @@ -35,18 +35,12 @@ dependencies = [ ('spoa', '4.0.7'), ] -download_dep_fail = True - preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " # strip out cmake requirements, since we provide that as proper dependency preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " -use_pip = True - options = {'modulename': 'spoa'} -sanity_pip_check = True - sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb index fc22ef3468..8d24623363 100644 --- a/easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb @@ -14,8 +14,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True - exts_list = [ ('py-cpuinfo', '8.0.0', { 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], @@ -36,6 +34,4 @@ sanity_check_commands = [ "pytest-benchmark --help", ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb index cfd093a102..e965d4a4ed 100644 --- a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb @@ -35,9 +35,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('apipkg', '1.5', { 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb index 93631bf96c..1bb218d676 100644 --- a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb @@ -35,9 +35,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('apipkg', '1.5', { 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], diff --git a/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb index 9934a63e08..29ac9cd57f 100644 --- a/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb @@ -15,11 +15,6 @@ dependencies = [ ('Python', '3.8.6'), ] -download_dep_fail = True -use_pip = True - options = {'modulename': 'Levenshtein'} -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb index f5f38e7600..6c705174cf 100644 --- a/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb @@ -21,10 +21,6 @@ dependencies = [ ('lxml', '4.6.2'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - options = {'modulename': 'docx'} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb index 792aba8a30..8c9840297c 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb @@ -22,8 +22,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -use_pip = True - exts_list = [ ('texttable', '1.6.3', { 'checksums': ['ce0faf21aa77d806bbff22b107cc22cce68dc9438f97a2df32c93e9afa4ce436'], @@ -48,6 +46,4 @@ sanity_check_paths = { # cairo must be available for proper plotting support sanity_check_commands = ["python -c 'from igraph.drawing.utils import find_cairo; cairo = find_cairo(); cairo.Context'"] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb index 5b5c25791f..732eedd4b3 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb @@ -22,8 +22,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -use_pip = True - exts_list = [ ('texttable', '1.6.3', { 'checksums': ['ce0faf21aa77d806bbff22b107cc22cce68dc9438f97a2df32c93e9afa4ce436'], @@ -48,6 +46,4 @@ sanity_check_paths = { # cairo must be available for proper plotting support sanity_check_commands = ["python -c 'from igraph.drawing.utils import find_cairo; cairo = find_cairo(); cairo.Context'"] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb index a8d2cb81ce..6cd7de18a2 100644 --- a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb @@ -24,10 +24,6 @@ dependencies = [ ('ISA-L', '2.30.0'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' installopts = '--no-binary isal' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb index cd8f3bb5c6..d9e831998b 100644 --- a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb @@ -20,10 +20,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - # make sure setup.py finds the parasail library preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb index 0f02c50779..9357b64bd7 100644 --- a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb @@ -20,10 +20,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - # make sure setup.py finds the parasail library preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index dfb7a16b6b..a38c9f0d7e 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -15,9 +15,6 @@ dependencies = [ builddependencies = [('binutils', '2.35')] -use_pip = True -sanity_pip_check = True - exts_list = [ ('APScheduler', '3.9.1', { 'checksums': ['65e6574b6395498d371d045f2a8a7e4f7d50c6ad21ef7313d15b1c7cf20df1e3'], diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb index 81762184ba..a7093ce817 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb @@ -24,9 +24,6 @@ dependencies = [ ('Boost', '1.74.0'), ] -download_dep_fail = True -use_pip = True - install_target = 'install_full' postinstallcmds = ["cd %(installdir)s/bin && ln -s quast.py quast"] @@ -46,6 +43,4 @@ sanity_check_commands = [ "%(namelower)s -h", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb index d0057cb1ac..8122dd21f3 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb @@ -11,7 +11,6 @@ assemblies, thus is suitable for comparison.""" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True} - dependencies = [ ('Python', '3.8.6'), ('Perl', '5.32.0'), @@ -20,8 +19,6 @@ dependencies = [ ('Boost', '1.74.0'), ] -use_pip = True - exts_list = [ ('simplejson', '3.17.2', { 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], @@ -54,6 +51,4 @@ sanity_check_commands = [ "%(namelower)s -h", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb index 863392420b..08a161c2dc 100644 --- a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb @@ -19,8 +19,4 @@ dependencies = [ ('PyQt5', '5.15.1') ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb index 26585354a2..005a376969 100644 --- a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb @@ -22,8 +22,4 @@ dependencies = [ ('QtPy', '1.9.0'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb index fad68609dd..839b89e90d 100644 --- a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb +++ b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2020b.eb @@ -13,9 +13,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('inflection', '0.5.1', { 'checksums': ['1a29730d366e996aaacffb2f1f1cb9593dc38e2ddd30c91250c6dde09ea9b417'], diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb index 2c05582ea3..83fa2b808e 100644 --- a/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb @@ -13,8 +13,6 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True - exts_list = [ ('isodate', '0.6.0', { 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], @@ -24,6 +22,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb b/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb index fa1a05370a..a73312d431 100644 --- a/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RagTag/RagTag-2.0.1-foss-2020b.eb @@ -30,10 +30,6 @@ dependencies = [ ('unimap', '0.1'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/ragtag.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb b/easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb index d86d97d9b0..bc288c57d2 100644 --- a/easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/Ragout/Ragout-2.3-foss-2020b.eb @@ -24,10 +24,6 @@ dependencies = [ ('networkx', '2.5'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - sanity_check_commands = ['ragout --help'] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb index 53e51415d5..310bcb4f96 100644 --- a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb @@ -18,8 +18,4 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb index 0d104c5782..92c63adbd4 100644 --- a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb @@ -18,8 +18,4 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb index 9f2bd8d726..560b073c28 100644 --- a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb @@ -44,9 +44,6 @@ components = [ 'e3b4d6a8d612a909cb9b920a7770406955f093b2788f6d7bf6ccab5527eda86a', ], 'start_dir': 'rmats-turbo-%(version)s/rMATS_pipeline', - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True, 'options': {'modulename': 'rmatspipeline'}, }), ] diff --git a/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb b/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb index 841aded314..7f9b0f03b6 100644 --- a/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb @@ -20,9 +20,6 @@ dependencies = [ ('minimap2', '2.18'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ # This is not upstream version, but artic tweaked one, which is exactly required. ('Porechop', '0.3.2pre', { diff --git a/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb b/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb index 1589973f77..b2b28b73b4 100644 --- a/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rasterio/rasterio-1.2.3-foss-2020b.eb @@ -15,8 +15,6 @@ dependencies = [ ('GDAL', '3.2.1'), ] -use_pip = True - exts_list = [ ('affine', '2.3.0', { 'checksums': ['2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102'], @@ -59,6 +57,4 @@ sanity_check_commands = [ "rio --help", ] -sanity_pip_check = True - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb index ed589a49fb..220e5de607 100644 --- a/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb @@ -18,10 +18,6 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/scons', 'bin/sconsign'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb index 6d851b6b51..5ae762f6bf 100644 --- a/easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb @@ -15,9 +15,6 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -download_dep_fail = True -use_pip = True - sanity_check_paths = { 'files': ['bin/scons', 'bin/sconsign'], 'dirs': [], @@ -25,8 +22,6 @@ sanity_check_paths = { sanity_check_commands = ["scons --help"] -sanity_pip_check = True - # no Python module to import during sanity check options = {'modulename': False} diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.4.0-foss-2020b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.4.0-foss-2020b.eb index 7e693b99a6..8566bc73f6 100644 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.4.0-foss-2020b.eb @@ -23,10 +23,6 @@ dependencies = [ fix_python_shebang_for = ['bin/*.py'] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - local_bin_files = [ 'run_abundance.py', 'run_sepp.py', 'run_tipp.py', 'run_tipp_tool.py', 'run_upp.py', 'split_sequences.py' diff --git a/easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb index 861f11bb8c..618bac0055 100644 --- a/easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb @@ -21,9 +21,6 @@ dependencies = [ ('SAMtools', '1.11'), ] -download_dep_fail = True -use_pip = True - # inject Bowtie2/SAMtools version in scripts that check for known version preinstallopts = """sed -i "s@,'2.2.9'@,'2.2.9', '$EBVERSIONBOWTIE2'@g" scripts/qsub_srst2.py && """ preinstallopts += """sed -i "s@,'2.2.9'@,'2.2.9', '$EBVERSIONBOWTIE2'@g" scripts/slurm_srst2.py && """ @@ -47,6 +44,4 @@ sanity_check_commands = [ "slurm_srst2.py -h", ] -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb index bcceac76a1..8875e06bdc 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb @@ -14,9 +14,6 @@ dependencies = [ ('Python', '2.7.18'), ] -use_pip = True -sanity_pip_check = True - # order is important! exts_list = [ ('numpy', '1.16.6', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb index 7266b75a30..853bb1acf3 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb @@ -16,9 +16,6 @@ dependencies = [ ('pybind11', '2.6.0'), # required by scipy ] -use_pip = True -sanity_pip_check = True - # order is important! exts_list = [ ('numpy', '1.19.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb index 4505176611..e62424957d 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb @@ -16,9 +16,6 @@ dependencies = [ ('pybind11', '2.6.0'), # required by scipy ] -use_pip = True -sanity_pip_check = True - # order is important! exts_list = [ ('numpy', '1.19.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb index d37d76cfc3..1d52db5cfc 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('pybind11', '2.6.0'), # required by scipy ] -use_pip = True - # order is important! exts_list = [ ('numpy', '1.19.4', { @@ -58,6 +56,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb index d5dd17674e..ff90550cef 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('pybind11', '2.6.0'), # required by scipy ] -use_pip = True - # order is important! exts_list = [ ('numpy', '1.19.4', { @@ -58,6 +56,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb index 0c2f044494..459c6f9824 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb @@ -21,8 +21,4 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb index 5b326ff282..67c930bb20 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb @@ -21,8 +21,4 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb index 6f3585c583..3b4ccb971c 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb @@ -21,8 +21,4 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb index cf633da88f..36cf7b4171 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb @@ -21,8 +21,4 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb index 94387013b4..5911f2c7c8 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb @@ -22,8 +22,4 @@ dependencies = [ ('matplotlib', '2.2.5', versionsuffix), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb index c578663248..e0a2925a92 100644 --- a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb @@ -38,9 +38,6 @@ components = [ 'start_dir': '%(namelower)s-%(version)s/python', 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True, }), ] diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb index cac4a8093f..43ae68f448 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb @@ -17,8 +17,4 @@ dependencies = [ ('GEOS', '3.9.1'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb index a87575e17a..e6517c9c29 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb @@ -19,8 +19,4 @@ dependencies = [ ('GEOS', '3.9.1'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb b/easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb index 88e82bb578..d85497c992 100644 --- a/easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('FMM3D', '20211018'), ] -use_pip = True - exts_list = [ (name, version, { 'source_urls': ['https://github.com/simnibs/simnibs/archive/'], @@ -26,8 +24,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/headreco', 'bin/simnibs'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb index c5815aa76a..8f6ed227e6 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -27,8 +27,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_urls': [PYPI_SOURCE], - 'download_dep_fail': True, - 'use_pip': True, } exts_list = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index e08aae3577..56919581d9 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -27,8 +27,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_urls': [PYPI_SOURCE], - 'download_dep_fail': True, - 'use_pip': True, } exts_list = [ diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb index 76924dcf22..f6273b752b 100644 --- a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -13,14 +13,10 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True - exts_list = [ ('sphinx_rtd_theme', version, { 'checksums': ['6146c845f1e1947b3c3dd4432c28998a1693ccc742b4f9ad7c63129f0757c103'], }), ] -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb index f599ebcc9b..250a1d0118 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.7.2-foss-2020b.eb @@ -27,8 +27,6 @@ dependencies = [ ('leidenalg', '0.8.3'), ] -use_pip = True - exts_list = [ ('natsort', '7.1.1', { 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], @@ -67,8 +65,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb index bc44c5abc4..9755e8b8fc 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb @@ -27,8 +27,6 @@ dependencies = [ ('leidenalg', '0.8.3'), ] -use_pip = True - exts_list = [ ('natsort', '7.1.1', { 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], @@ -54,8 +52,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb index 092fe559f0..ade17a2ca7 100644 --- a/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb @@ -23,11 +23,6 @@ dependencies = [ ('zarr', '2.8.1'), ] -download_dep_fail = True -use_pip = True - options = {'modulename': 'allel'} -sanity_pip_check = True - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb index aeec62fa9d..d4cfc0b74f 100644 --- a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb @@ -18,9 +18,6 @@ dependencies = [ ('h5py', '3.1.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('msgpack', '1.0.1', { 'checksums': ['7033215267a0e9f60f4a5e4fb2228a932c404f237817caff8dc3115d9e7cd975'], diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb index 755057a371..3b406a03e3 100644 --- a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb @@ -13,9 +13,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('distro', '1.5.0', { 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb index b3b51a2d4b..7c7bb3d6a9 100644 --- a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb @@ -13,9 +13,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('distro', '1.5.0', { 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb index be3e7b09c4..347af49b27 100644 --- a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb @@ -13,9 +13,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('distro', '1.5.0', { 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb index 6ed9c54bce..c8e047ef95 100644 --- a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb @@ -13,9 +13,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('distro', '1.5.0', { 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb index 459369823e..374a7bdf7d 100644 --- a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb @@ -17,9 +17,6 @@ dependencies = [ ('Python', '3.8.6'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('distro', '1.7.0', { 'checksums': ['151aeccf60c216402932b52e40ee477a939f8d58898927378a02abbe852c1c39'], diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb index ae0e8510b8..cf9b309d92 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb @@ -16,9 +16,6 @@ dependencies = [ ('dask', '2021.2.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('PyWavelets', '1.1.1', { 'modulename': 'pywt', diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb index bb3613e276..9e0cc9610a 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb @@ -16,9 +16,6 @@ dependencies = [ ('dask', '2021.2.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('PyWavelets', '1.1.1', { 'modulename': 'pywt', diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb index e72dbff85f..bcfbbed25d 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb @@ -16,9 +16,6 @@ dependencies = [ ('dask', '2021.2.0'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('PyWavelets', '1.1.1', { 'modulename': 'pywt', diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb index 7b0b41a3f5..506331c06b 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb @@ -17,9 +17,6 @@ dependencies = [ ('PyWavelets', '1.1.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('imageio', '2.9.0', { 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb index 77f71dfdbf..3a663de17d 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb @@ -20,10 +20,6 @@ dependencies = [ ('SciPy-bundle', '2020.11', versionsuffix) ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - options = {'modulename': 'sklearn'} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb index 5d67c894a4..2a26f91b08 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb @@ -19,10 +19,6 @@ dependencies = [ ('SciPy-bundle', '2020.11') ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - options = {'modulename': 'sklearn'} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb index 52fc2890fd..a85846ece6 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb @@ -19,10 +19,6 @@ dependencies = [ ('SciPy-bundle', '2020.11') ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - options = {'modulename': 'sklearn'} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb index b851222523..182bc21820 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb @@ -19,10 +19,6 @@ dependencies = [ ('SciPy-bundle', '2020.11') ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - options = {'modulename': 'sklearn'} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb index 5b5729dd0a..1f8fcbce02 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb @@ -19,10 +19,6 @@ dependencies = [ ('SciPy-bundle', '2020.11') ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - options = {'modulename': 'sklearn'} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb index 251b68a8ce..57260d097c 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb @@ -22,9 +22,6 @@ dependencies = [ ('PyOpenCL', '2021.1.2'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('hdf5plugin', '2.3.1', { 'checksums': ['2f6d886012c37bf7e8e002173dd6b16e6879b8e0e9f7d2f2ef9f79db97ed28d2'], diff --git a/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb index fc63b3528e..47a36d0354 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb @@ -22,9 +22,6 @@ dependencies = [ ('PyOpenCL', '2021.1.2'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('hdf5plugin', '2.3.1', { 'checksums': ['2f6d886012c37bf7e8e002173dd6b16e6879b8e0e9f7d2f2ef9f79db97ed28d2'], diff --git a/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb index 75357f2279..8d2df8c73c 100644 --- a/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb @@ -16,10 +16,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -sanity_pip_check = True -download_dep_fail = True - sanity_check_paths = { 'files': ['lib/python%(pyshortver)s/site-packages/sklearn_som/som.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn_som'], diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb index c821961ac3..89aac47183 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-6.1.0-foss-2020b.eb @@ -16,9 +16,6 @@ dependencies = [ ('IPython', '7.18.1'), ] -use_pip = True -sanity_pip_check = True - # snakemake-6.1.0_fix_jobs.patch is needed for clusters that do not support copying the full env into the batch job exts_list = [ ('wrapt', '1.12.1', { diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb index 460c5ccc1f..c3fbf16ad8 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb @@ -17,11 +17,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - options = {'modulename': 'spglib'} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb index fb660979cf..dd188b91fe 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb @@ -17,11 +17,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - options = {'modulename': 'spglib'} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb index bc1f8c26b1..93d1d182bd 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb @@ -20,11 +20,6 @@ dependencies = [ # required because we're building a Python package using Intel compilers on top of Python built with GCC check_ldshared = True -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - options = {'modulename': 'spglib'} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb index 143c22861d..c416d4588c 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb @@ -14,9 +14,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('patsy', '0.5.1', { 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb index 7a62cf629c..5d61ef7b22 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True - exts_list = [ ('patsy', '0.5.1', { 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], @@ -27,6 +25,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb index 2b3ea0cbc3..e596e62187 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb @@ -14,9 +14,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('patsy', '0.5.1', { 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], diff --git a/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb b/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb index 9ec8b94f25..8579f9457b 100644 --- a/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb +++ b/easybuild/easyconfigs/s/suave/suave-20160529-foss-2020b.eb @@ -29,10 +29,6 @@ dependencies = [ preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ -use_pip = True -sanity_pip_check = True -download_dep_fail = True - sanity_check_paths = { 'files': ['bin/suave_server', 'bin/suave_bam_to_h5'], 'dirs': ['lib/python%(pyshortver)s/site-packages/templates'], diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index a6339d51f1..05d97fb731 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -20,9 +20,6 @@ dependencies = [ ('ImageMagick', '7.0.10-35'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('reportlab', '3.6.9', { 'patches': ['reportlab-3.6.12-fontconfig.patch'], diff --git a/easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb index c379d2ef49..4ac4712853 100644 --- a/easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb +++ b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb @@ -27,7 +27,4 @@ exts_list = [ }), ] -sanity_pip_check = True -use_pip = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb index 083b6cf060..df935fe0c8 100644 --- a/easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb @@ -27,7 +27,4 @@ exts_list = [ }), ] -sanity_pip_check = True -use_pip = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb index f1c552b054..208b51d417 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-foss-2020b.eb @@ -20,13 +20,8 @@ dependencies = [ ('gmpy2', '2.1.0b5'), ] -download_dep_fail = True -use_pip = True - runtest = 'python setup.py test' -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/isympy'], 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb index 8e61d9b6f4..5267623a56 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb @@ -20,13 +20,8 @@ dependencies = [ ('gmpy2', '2.1.0b5'), ] -download_dep_fail = True -use_pip = True - runtest = 'python setup.py test' -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/isympy'], 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], diff --git a/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb index 27cae837ee..60cc0f859a 100644 --- a/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb @@ -29,10 +29,6 @@ dependencies = [ preinstallopts = "sed -i 's/pysam==/pysam>=/g' requirements.txt && " preinstallopts += "sed -i 's/pysam==/pysam>=/g' setup.py && " -download_dep_fail = True -use_pip = True - -sanity_pip_check = True sanity_check_commands = ['talon_label_reads -h'] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb index c3f0e23f2d..7341f756cd 100644 --- a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -28,9 +28,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_urls': [PYPI_SOURCE], - 'download_dep_fail': True, - 'use_pip': True, - 'sanity_pip_check': True, } exts_list = [ diff --git a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb index 37bf2e3548..62453d378d 100644 --- a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb +++ b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -7,7 +7,6 @@ version = '1.1.4' _mumergever = '1.1.0' versionsuffix = '-muMerge-%s' % _mumergever - homepage = 'https://github.com/Dowell-Lab/TFEA' description = """Transcription Factor Enrichment Analysis """ @@ -25,9 +24,6 @@ dependencies = [ ('XZ', '5.2.5'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('ujson', '5.5.0', { 'checksums': ['b25077a971c7da47bd6846a912a747f6963776d90720c88603b1b55d81790780'], diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb index 862d4fe55c..b140b09b63 100644 --- a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -24,9 +24,6 @@ dependencies = [ ('svist4get', '1.3.1'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('adjustText', '0.7.3', { 'checksums': ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index a41e687495..29bf154b7a 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -43,9 +43,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -sanity_pip_check = True -use_pip = True - exts_list = [ # TF <= 2.4 needs h5py 2.10, later versions allow 3.x ('h5py', '2.10.0', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index b37d88e8be..d10a63134e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -44,10 +44,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -sanity_pip_check = True -use_pip = True - - # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d exts_list = [ diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 110b07df5a..e804f1d30d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -46,9 +46,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -use_pip = True -sanity_pip_check = True - # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d exts_list = [ diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 503325ea6d..160fa7f0ab 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -42,9 +42,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -use_pip = True -sanity_pip_check = True - # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d exts_list = [ diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 3ca12b1e63..ba53dc20ab 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -44,9 +44,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -use_pip = True -sanity_pip_check = True - # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d exts_list = [ diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb index 840804ddc2..10b775ad9c 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb @@ -19,10 +19,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb index 7acce00ef7..ee1184a31f 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb @@ -23,10 +23,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb index 9b07b02d78..b23c422240 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb @@ -20,10 +20,6 @@ dependencies = [ ('mkl-service', '2.3.0'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb index fdcf696edd..3203335051 100644 --- a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb @@ -14,8 +14,6 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True - exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} exts_list = [ @@ -38,8 +36,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_commands = ["python -c 'import tofu.geom'"] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb index 1f32acaf35..cfcc638deb 100644 --- a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb @@ -14,8 +14,6 @@ dependencies = [ ('matplotlib', '3.3.3'), ] -use_pip = True - exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} exts_list = [ @@ -38,8 +36,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_commands = ["python -c 'import tofu.geom'"] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb index c41886f626..0ba7aedbe6 100644 --- a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb @@ -28,9 +28,6 @@ dependencies = [ options = {'modulename': '%(name)s'} -use_pip = True -download_dep_fail = True - postinstallcmds = ["cp -r %s %%(installdir)s" % d for d in ['docs', 'examples', 'tests']] sanity_check_paths = { @@ -38,6 +35,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages', 'docs', 'examples', 'tests'], } -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb index 5083f88938..7c67aace7f 100644 --- a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb @@ -28,9 +28,6 @@ dependencies = [ options = {'modulename': '%(name)s'} -use_pip = True -download_dep_fail = True - postinstallcmds = ["cp -r %s %%(installdir)s" % d for d in ['docs', 'examples', 'tests']] sanity_check_paths = { @@ -38,6 +35,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages', 'docs', 'examples', 'tests'], } -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb index e398062f1d..e54e62f630 100644 --- a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -28,9 +28,6 @@ dependencies = [ options = {'modulename': '%(name)s'} -use_pip = True -download_dep_fail = True - postinstallcmds = ["cp -r %s %%(installdir)s" % d for d in ['docs', 'examples', 'tests']] sanity_check_paths = { @@ -38,6 +35,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages', 'docs', 'examples', 'tests'], } -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb index 8996e23128..1fea1b5a53 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb @@ -24,8 +24,6 @@ dependencies = [ ('dm-tree', '0.1.5'), ] -use_pip = True - exts_list = [ ('cloudpickle', '1.6.0', { 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], @@ -41,6 +39,4 @@ exts_list = [ sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb index c31071c495..2364e43ecf 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb @@ -24,8 +24,6 @@ dependencies = [ ('dm-tree', '0.1.5'), ] -use_pip = True - exts_list = [ ('cloudpickle', '1.6.0', { 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], @@ -41,6 +39,4 @@ exts_list = [ sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb index 0ba85a72a5..aed48cf251 100644 --- a/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb @@ -25,8 +25,4 @@ dependencies = [ ('PyTorch', local_pytorch_version), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb index 1b2083358f..5c3fdce9f2 100644 --- a/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -25,8 +25,4 @@ dependencies = [ ('PyTorch', local_pytorch_version), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb index a2d3ea9fb7..afdcc67cd0 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb @@ -31,8 +31,4 @@ dependencies = [ # Disable bundled libraries to use those from EB: RE2, SentencePiece preinstallopts = "sed -i '/third_party/d;/BuildExtension/d' setup.py &&" -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb index e9c3ae26bc..98085d7ab2 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb @@ -35,8 +35,4 @@ dependencies = [ # Disable bundled libraries to use those from EB: RE2, SentencePiece preinstallopts = "sed -i '/third_party/d;/BuildExtension/d' setup.py &&" -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb index 05a3968437..417f592c53 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb @@ -39,8 +39,4 @@ dependencies = [ # Disable bundled libraries to use those from EB: RE2, SentencePiece preinstallopts = "sed -i '/third_party/d;/BuildExtension/d' setup.py &&" -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb index faa6ef0376..85258f3eb0 100644 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb @@ -15,8 +15,4 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb index ab14afd56f..574f1dde7c 100644 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb @@ -15,8 +15,4 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb index 444c6ce3c6..5e8501b1e5 100644 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb @@ -15,8 +15,4 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb index ab94cdba53..de2fa5f272 100644 --- a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb @@ -17,9 +17,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('pynvml', '11.0.0', { 'checksums': ['d5fc4a22d355b40c341d6ba0aa888a2d4d2253177d243900f8401b7e6cacb1bb'], diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb index 80d6fbc581..5249d3e47c 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb @@ -22,11 +22,6 @@ dependencies = [ ('numba', '0.52.0'), ] -download_dep_fail = True -use_pip = True - options = {'modulename': 'umap'} -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb index 5c5bc73b02..af8a0366f2 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb @@ -22,11 +22,6 @@ dependencies = [ ('numba', '0.52.0'), ] -download_dep_fail = True -use_pip = True - options = {'modulename': 'umap'} -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb index e3de10224d..de5c3745c4 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb @@ -24,8 +24,6 @@ dependencies = [ ('tqdm', '4.56.2'), ] -use_pip = True - exts_list = [ ('pynndescent', '0.5.7', { 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], @@ -36,6 +34,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb index 8bdc452acc..f2e533ad29 100644 --- a/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('PyQt5', '5.15.1'), ] -use_pip = True - exts_list = [ ('freetype_py', '2.2.0', { 'modulename': 'freetype', @@ -29,6 +27,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb index 6ae981a021..617ff51f77 100644 --- a/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb +++ b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('PyQt5', '5.15.1'), ] -use_pip = True - exts_list = [ ('freetype_py', '2.2.0', { 'modulename': 'freetype', @@ -29,6 +27,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb b/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb index 0989ba04d1..e556409d9a 100644 --- a/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb +++ b/easybuild/easyconfigs/v/voltools/voltools-0.4.2-foss-2020b.eb @@ -15,9 +15,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('GPUtil', '1.4.0', { 'modulename': 'GPUtil', diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb index 1cdcd817b6..684b63bf29 100644 --- a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb @@ -22,9 +22,6 @@ dependencies = [ ('pyfaidx', '0.5.9.5'), ] -use_pip = True -sanity_pip_check = True - exts_list = [ ('isal', '0.10.0', { 'checksums': ['3f89471065c2837d1235877dbdcdbd8b7649068723026b0582010fa106a71ff3'], @@ -38,7 +35,6 @@ exts_list = [ }), ] - sanity_check_paths = { 'files': ['bin/whatshap'], 'dirs': ['bin', 'lib'], diff --git a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb index eb57ec2b02..1d3d0f33d8 100644 --- a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb @@ -19,9 +19,6 @@ dependencies = [ ('Python', '3.8.6'), ] -download_dep_fail = True -use_pip = True - sanity_check_paths = { 'files': ['bin/vba_extract.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], @@ -29,6 +26,4 @@ sanity_check_paths = { sanity_check_commands = ['vba_extract.py --help'] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-intel-2020b.eb b/easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-intel-2020b.eb index 6777e058f4..f311ed6b71 100644 --- a/easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-intel-2020b.eb @@ -18,9 +18,4 @@ dependencies = [ ('xarray', '0.16.2'), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb index e3caa965c4..7a57ff6c68 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb @@ -18,9 +18,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # required for numpy, pandas ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb index 00d0c4eb93..0d73906af0 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-fosscuda-2020b.eb @@ -20,9 +20,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # required for numpy, pandas ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb index 805300f989..b106b0275b 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-intel-2020b.eb @@ -18,9 +18,4 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # required for numpy, pandas ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb index a98f29a352..8039b6ee3e 100644 --- a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb @@ -23,9 +23,4 @@ dependencies = [ ('PyYAML', '5.3.1'), ] -use_pip = True -download_dep_fail = True - -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb index 03214bbd47..2539d3a9c5 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -27,9 +27,6 @@ dependencies = [ ('molmod', '1.4.8'), ] -use_pip = True -sanity_pip_check = True - local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " local_runtest += "python setup.py build_ext -i; nosetests -v" @@ -51,5 +48,4 @@ exts_list = [ }), ] - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb index ab0584e8a8..3b5d31e99a 100644 --- a/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb @@ -23,8 +23,6 @@ dependencies = [ ('GMP', '6.2.0'), ] -use_pip = True - _fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py &&""" _enable_gmp = "sed -i 's/^GMP=.*/GMP=True/' core/scripts/mk_util.py &&" @@ -43,8 +41,6 @@ postinstallcmds = [ "cd %%(installdir)s/lib && ln -s ../%s/lib/libz3.so libz3.so" % _z3_site_path, ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.8.1-foss-2020b.eb b/easybuild/easyconfigs/z/zarr/zarr-2.8.1-foss-2020b.eb index 31ce9c5cb0..9776bc7590 100644 --- a/easybuild/easyconfigs/z/zarr/zarr-2.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/z/zarr/zarr-2.8.1-foss-2020b.eb @@ -14,8 +14,6 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ] -use_pip = True - exts_list = [ ('asciitree', '0.3.3', { 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], @@ -36,6 +34,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'data' From fbb58404a59c5ca08a01a48c5c22e34a513cd815 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 25 Nov 2023 11:16:27 +0100 Subject: [PATCH 2240/2365] adding easyconfigs: python-xxhash-2.0.2-GCCcore-10.2.0.eb --- .../python-xxhash-2.0.2-GCCcore-10.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e094054b20 --- /dev/null +++ b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'python-xxhash' +version = '2.0.2' + +homepage = 'https://github.com/ifduyue/python-xxhash' +description = """Python bindings for xxHash. xxHash is an extremely fast +non-cryptographic hash algorithm, working at RAM speed limit.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('xxHash', '0.8.1'), +] + +use_pip = True + +exts_list = [ + ('xxhash', version, { + 'preinstallopts': 'XXHASH_LINK_SO=1', + 'checksums': ['b7bead8cf6210eadf9cecf356e17af794f57c0939a3d420a00d87ea652f87b49'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 3a5908a932df6101dfbdff75a64bdced87a79d74 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Dec 2023 09:29:17 +0100 Subject: [PATCH 2241/2365] fix PAPI test step hanging on some systems --- easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb index f94945b421..9db23efc5a 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb @@ -34,9 +34,7 @@ builddependencies = [ start_dir = 'src' -parallel = 1 - -runtest = 'fulltest' +runtest = 'test' sanity_check_paths = { 'files': ["bin/papi_%s" % x From 9b6eda484b99dfd3eec42e7036ce5ee314798c21 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Dec 2023 10:59:12 +0100 Subject: [PATCH 2242/2365] Add comment why we run only 'test' --- easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb index 9db23efc5a..3c3d70d453 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb @@ -34,6 +34,8 @@ builddependencies = [ start_dir = 'src' +# There is also "fulltest" that is a superset of "test" but hangs on some processors +# indefinitely with a defunct `make` process. So use only "test". runtest = 'test' sanity_check_paths = { From b7fcfa044e971909fa4c78ba5f37662a1fc3c256 Mon Sep 17 00:00:00 2001 From: Mikhail Vorobyov Date: Thu, 7 Dec 2023 19:14:03 +0300 Subject: [PATCH 2243/2365] Revive iperf2 An updated copy of easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-goolf-1.4.10.eb --- .../i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..488ff44fd6 --- /dev/null +++ b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'iperf' +version = '2.1.9' + +homepage = 'http://iperf2.sourceforge.net/' +description = """Iperf-2.1.9: TCP and UDP bandwidth performance measurement tool""" + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/iperf2/files', 'download')] +checksums = ['5c0771aab00ef14520013aef01675977816e23bb8f5d9fde016f90eb2f1be788'] +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sanity_check_paths = { + 'files': ['bin/iperf'], + 'dirs': [] +} + +moduleclass = 'tools' From 2a989f1dca7866fac16c9b69daba7641089e29ba Mon Sep 17 00:00:00 2001 From: Mikhail Vorobyov Date: Thu, 7 Dec 2023 19:05:22 +0300 Subject: [PATCH 2244/2365] Easyconfig for Intel MPI Benchmarks on gompi-2020b Copy of IMB-2021.3-gompi-2021b with changed toolchain version --- .../i/IMB/IMB-2021.3-gompi-2020b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2020b.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2020b.eb b/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2020b.eb new file mode 100644 index 0000000000..9db2f7831f --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '2021.3' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +docurls = ['https://software.intel.com/en-us/imb-user-guide'] + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/intel/mpi-benchmarks/archive/'] +sources = ['IMB-v%(version)s.tar.gz'] +checksums = ['9b58a4a7eef7c0c877513152340948402fd87cb06270d2d81308dc2ef740f4c7'] + +buildopts = 'all CC="$MPICC"' + +parallel = 1 + +files_to_copy = [(['IMB-*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-MT', + 'bin/IMB-NBC', 'bin/IMB-P2P', 'bin/IMB-RMA'], + 'dirs': [], +} + +moduleclass = 'perf' From f9a4868cf734658ebafc1bda3c9e978c4f1f6347 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Sat, 9 Dec 2023 22:29:35 +0100 Subject: [PATCH 2245/2365] fix for sanity check when rpath linking is enabled --- easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb index 6e3105ea15..916636547c 100644 --- a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -22,12 +22,16 @@ builddependencies = [ ] postinstallcmds = [ + # copy the LercTest source file to a LercTest subdir in the installation directory and compile it + # (needs to be done here instead of in the sanity check, else it won't work when RPATH linking is enabled) "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", - "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/test.c", + "mkdir %(installdir)s/LercTest", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/LercTest/main.cpp", + "cd %(installdir)s/LercTest && g++ main.cpp -o LercTest -I../include -L../lib -lLerc", ] sanity_check_commands = [ - "mkdir -p %(builddir)s && cd %(builddir)s && g++ %(installdir)s/test.c -o lerctest -lLerc && ./lerctest", + "%(installdir)s/LercTest/LercTest", ] sanity_check_paths = { From 7193bf6f3b6ee5c948e3141fe623799de2179f3b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Sun, 10 Dec 2023 10:32:25 +0100 Subject: [PATCH 2246/2365] always install libraries to 'lib/' --- easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb index 916636547c..d97e184c8e 100644 --- a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -21,6 +21,8 @@ builddependencies = [ ('CMake', '3.18.4'), ] +configopts = '-DCMAKE_INSTALL_LIBDIR=lib' + postinstallcmds = [ # copy the LercTest source file to a LercTest subdir in the installation directory and compile it # (needs to be done here instead of in the sanity check, else it won't work when RPATH linking is enabled) From b4a892b9987b65be67f090801bf4310f30616028 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Sun, 10 Dec 2023 10:33:09 +0100 Subject: [PATCH 2247/2365] use CXX and CXXFLAGS instead of hardcoded values --- easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb index d97e184c8e..a75e046b3d 100644 --- a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -29,7 +29,7 @@ postinstallcmds = [ "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", "mkdir %(installdir)s/LercTest", "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/LercTest/main.cpp", - "cd %(installdir)s/LercTest && g++ main.cpp -o LercTest -I../include -L../lib -lLerc", + "cd %(installdir)s/LercTest && ${CXX} ${CXXFLAGS} main.cpp -o LercTest -I../include -L../lib -lLerc", ] sanity_check_commands = [ From 71acac9b5989e28eb6afff90a2a6f61642e87f8a Mon Sep 17 00:00:00 2001 From: "U-ADF\\BranfoSJ" Date: Tue, 12 Dec 2023 13:50:29 +0000 Subject: [PATCH 2248/2365] move kim-api/2.2.1-GCCcore-10.2.0 to GCC --- .../k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..a3d76ec464 --- /dev/null +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'kim-api' +version = '2.2.1' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +KIM is an API and OpenKIM is a collection of interatomic models (potentials) for +atomistic simulations. This is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild only installs the API, the models can be installed with the +package openkim-models, or the user can install them manually by running + kim-api-collections-management install user MODELNAME +or + kim-api-collections-management install user OpenKIM +to install them all. + """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://s3.openkim.org/kim-api/'] +sources = ['%(name)s-%(version)s.txz'] +checksums = ['1d5a12928f7e885ebe74759222091e48a7e46f77e98d9147e26638c955efbc8e'] + +dependencies = [ + ('CMake', '3.18.4'), # Also needed to install models, thus not just a builddependency. +] + +parallel = 1 + +modextravars = { + 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' +} + +sanity_check_paths = { + 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'chem' From be76e5f05acc0515122f6c1ec5c101b43d80dc53 Mon Sep 17 00:00:00 2001 From: "U-ADF\\BranfoSJ" Date: Tue, 12 Dec 2023 13:52:15 +0000 Subject: [PATCH 2249/2365] and move deps --- .../openkim-models-20190725-GCC-10.2.0.eb | 50 +++++++++++++++++++ .../openkim-models-20210128-GCC-10.2.0.eb | 50 +++++++++++++++++++ 2 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/o/openkim-models/openkim-models-20190725-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/openkim-models/openkim-models-20210128-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/o/openkim-models/openkim-models-20190725-GCC-10.2.0.eb b/easybuild/easyconfigs/o/openkim-models/openkim-models-20190725-GCC-10.2.0.eb new file mode 100644 index 0000000000..90c5ae682e --- /dev/null +++ b/easybuild/easyconfigs/o/openkim-models/openkim-models-20190725-GCC-10.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'openkim-models' +version = '20190725' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +OpenKIM is an API and a collection of interatomic models (potentials) for +atomistic simulations. It is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild installs the models. The API itself is in the kim-api +package. + """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('kim-api', '2.2.1'), +] + +source_urls = ['https://s3.openkim.org/archives/collection/'] +sources = ['openkim-models-2019-07-25.txz'] +checksums = ['50338084ece92ec0fb13b0bbdf357b5d7450e26068ba501f23c315f814befc26'] + +separate_build_dir = True +abs_path_compilers = True # Otherwise some KIM-API magic breaks cmake. +configopts = '-DKIM_API_INSTALL_COLLECTION=SYSTEM ' +configopts += '-DKIM_API_PORTABLE_MODEL_INSTALL_PREFIX=%(installdir)s/lib/kim-api/portable-models ' +configopts += '-DKIM_API_SIMULATOR_MODEL_INSTALL_PREFIX=%(installdir)s/lib/kim-api/simulator-models ' +configopts += '-DKIM_API_MODEL_DRIVER_INSTALL_PREFIX=%(installdir)s/lib/kim-api/model-drivers ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/kim-api/model-drivers', 'lib/kim-api/portable-models', 'lib/kim-api/simulator-models'] +} + +modextravars = { + 'KIM_API_MODEL_DRIVERS_DIR': '%(installdir)s/lib/kim-api/model-drivers', + 'KIM_API_PORTABLE_MODELS_DIR': '%(installdir)s/lib/kim-api/portable-models', + 'KIM_API_SIMULATOR_MODELS_DIR': '%(installdir)s/lib/kim-api/simulator-models', +} + + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/openkim-models/openkim-models-20210128-GCC-10.2.0.eb b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210128-GCC-10.2.0.eb new file mode 100644 index 0000000000..2e2b058ef6 --- /dev/null +++ b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210128-GCC-10.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'openkim-models' +version = '20210128' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +OpenKIM is an API and a collection of interatomic models (potentials) for +atomistic simulations. It is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild installs the models. The API itself is in the kim-api +package. + """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('kim-api', '2.2.1'), +] + +source_urls = ['https://s3.openkim.org/archives/collection/'] +sources = ['openkim-models-2021-01-28.txz'] +checksums = ['8824adee02ae4583bd378cc81140fbb49515c5965708ee98d856d122d48dd95f'] + +separate_build_dir = True +abs_path_compilers = True # Otherwise some KIM-API magic breaks cmake. +configopts = '-DKIM_API_INSTALL_COLLECTION=SYSTEM ' +configopts += '-DKIM_API_PORTABLE_MODEL_INSTALL_PREFIX=%(installdir)s/lib/kim-api/portable-models ' +configopts += '-DKIM_API_SIMULATOR_MODEL_INSTALL_PREFIX=%(installdir)s/lib/kim-api/simulator-models ' +configopts += '-DKIM_API_MODEL_DRIVER_INSTALL_PREFIX=%(installdir)s/lib/kim-api/model-drivers ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/kim-api/model-drivers', 'lib/kim-api/portable-models', 'lib/kim-api/simulator-models'] +} + +modextravars = { + 'KIM_API_MODEL_DRIVERS_DIR': '%(installdir)s/lib/kim-api/model-drivers', + 'KIM_API_PORTABLE_MODELS_DIR': '%(installdir)s/lib/kim-api/portable-models', + 'KIM_API_SIMULATOR_MODELS_DIR': '%(installdir)s/lib/kim-api/simulator-models', +} + + +moduleclass = 'chem' From 20448b7482ea95c4e696e3fb842badebe5adc331 Mon Sep 17 00:00:00 2001 From: "U-ADF\\BranfoSJ" Date: Tue, 12 Dec 2023 14:33:08 +0000 Subject: [PATCH 2250/2365] need an iccifort/2020.4.304 kim-api --- .../kim-api-2.2.1-iccifort-2020.4.304.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..825a324d75 --- /dev/null +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'kim-api' +version = '2.2.1' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +KIM is an API and OpenKIM is a collection of interatomic models (potentials) for +atomistic simulations. This is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild only installs the API, the models can be installed with the +package openkim-models, or the user can install them manually by running + kim-api-collections-management install user MODELNAME +or + kim-api-collections-management install user OpenKIM +to install them all. + """ + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://s3.openkim.org/kim-api/'] +sources = ['%(name)s-%(version)s.txz'] +checksums = ['1d5a12928f7e885ebe74759222091e48a7e46f77e98d9147e26638c955efbc8e'] + +dependencies = [ + ('CMake', '3.18.4'), # Also needed to install models, thus not just a builddependency. +] + +parallel = 1 + +modextravars = { + 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' +} + +sanity_check_paths = { + 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'chem' From c8a67daba8e141288d7ed1e7d5ff7fd0d80df789 Mon Sep 17 00:00:00 2001 From: Mikhail Vorobyov Date: Wed, 27 Dec 2023 19:43:12 +0300 Subject: [PATCH 2251/2365] Update easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb Accepting build dependencies and code style fixes. Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb index 488ff44fd6..6a3bf59792 100644 --- a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb @@ -18,10 +18,13 @@ version = '2.1.9' homepage = 'http://iperf2.sourceforge.net/' description = """Iperf-2.1.9: TCP and UDP bandwidth performance measurement tool""" +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/iperf2/files', 'download')] checksums = ['5c0771aab00ef14520013aef01675977816e23bb8f5d9fde016f90eb2f1be788'] -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] sanity_check_paths = { 'files': ['bin/iperf'], From fc2499b183f3d0975451d987dd2581975de7e7f0 Mon Sep 17 00:00:00 2001 From: Mikhail Vorobyov Date: Wed, 27 Dec 2023 19:43:12 +0300 Subject: [PATCH 2252/2365] Update easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb index 6a3bf59792..3c1a46a9ec 100644 --- a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'iperf' version = '2.1.9' -homepage = 'http://iperf2.sourceforge.net/' +homepage = 'https://sourceforge.net/projects/iperf2/' description = """Iperf-2.1.9: TCP and UDP bandwidth performance measurement tool""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From c271b12c71b07cc23b1f83a7e835ba7ae7de1ca8 Mon Sep 17 00:00:00 2001 From: Mikhail Vorobyov Date: Wed, 27 Dec 2023 19:43:12 +0300 Subject: [PATCH 2253/2365] Update easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb Substitute a variable with more general one. Co-authored-by: Sam Moors --- easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb index 3c1a46a9ec..857c5c3a6d 100644 --- a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ description = """Iperf-2.1.9: TCP and UDP bandwidth performance measurement tool toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] source_urls = [('http://sourceforge.net/projects/iperf2/files', 'download')] checksums = ['5c0771aab00ef14520013aef01675977816e23bb8f5d9fde016f90eb2f1be788'] From a4088d81c4e1bf447d5765edeb66c7c45f21b357 Mon Sep 17 00:00:00 2001 From: Mikhail Vorobyov Date: Wed, 27 Dec 2023 19:43:12 +0300 Subject: [PATCH 2254/2365] Update easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb Use HTTPS. Co-authored-by: Sam Moors --- easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb index 857c5c3a6d..60578ae9ea 100644 --- a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb @@ -21,7 +21,7 @@ description = """Iperf-2.1.9: TCP and UDP bandwidth performance measurement tool toolchain = {'name': 'GCCcore', 'version': '10.2.0'} sources = [SOURCE_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/iperf2/files', 'download')] +source_urls = [('https://sourceforge.net/projects/iperf2/files', 'download')] checksums = ['5c0771aab00ef14520013aef01675977816e23bb8f5d9fde016f90eb2f1be788'] builddependencies = [('binutils', '2.35')] From 51e01ece3c0ab9912a9a0e0fedd9cb37248ff40c Mon Sep 17 00:00:00 2001 From: Mikhail Vorobyov Date: Wed, 27 Dec 2023 19:43:12 +0300 Subject: [PATCH 2255/2365] Update iperf-2.1.9-GCCcore-10.2.0.eb Remove exact version from description. --- easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb index 60578ae9ea..2a76957904 100644 --- a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ name = 'iperf' version = '2.1.9' homepage = 'https://sourceforge.net/projects/iperf2/' -description = """Iperf-2.1.9: TCP and UDP bandwidth performance measurement tool""" +description = """Iperf 2: TCP and UDP bandwidth performance measurement tool""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From e6e9eed5ff81a2dc64c37037ea7ddc004b8b2b2b Mon Sep 17 00:00:00 2001 From: Mikhail Vorobyov Date: Thu, 28 Dec 2023 02:38:29 +0300 Subject: [PATCH 2256/2365] Update iperf-2.1.9-GCCcore-10.2.0.eb Add sanity check calling "--help". --- easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb index 2a76957904..baf0cfe8d0 100644 --- a/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = ["iperf --help"] + moduleclass = 'tools' From 6936e1a8f7d1b4da843300a2d89fb9a2e02047ee Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 9 Jan 2024 08:41:21 +0000 Subject: [PATCH 2257/2365] bypass .mod file in GeneMark-ET (#19500) --- .../g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb index f6cc1e0092..110477c056 100644 --- a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb @@ -22,6 +22,8 @@ sanity_check_paths = { 'dirs': ['lib'], } +skip_mod_files_sanity_check = True + modextrapaths = {'PATH': ''} moduleclass = 'bio' From 3b7ed7e94b63fdc1708179fb1ede6458fb2706fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 11 Jan 2024 20:14:13 +0100 Subject: [PATCH 2258/2365] change homepage for argtable (#19551) * change homepage * add missing checksum --- .../easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb index 896c622188..bf680a03bd 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'argtable' version = '2.13' -homepage = 'http://argtable.sourceforge.net/' +homepage = 'https://argtable.sourceforge.io/' description = """ Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. """ From d894efdbfd7a5cec6da9fa655fb52e521084a888 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 20:22:26 +0100 Subject: [PATCH 2259/2365] remove Python versionsuffix for PCMSolver with iimpi/2020b --- .../PCMSolver/PCMSolver-1.2.3-iimpi-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b.eb new file mode 100644 index 0000000000..2ee4d8e8eb --- /dev/null +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'PCMSolver' +version = '1.2.3' + +homepage = 'https://pcmsolver.readthedocs.org' +description = """An API for the Polarizable Continuum Model.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +# we have to disable use of -march=native to ensure a correct build on recent Intel systems +# see also https://github.com/PCMSolver/pcmsolver/issues/159 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d1ef6bdc268a2e719b36c85125c3543df7a26e1a738daf4483f4ded0c76f5b60'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Eigen', '3.3.8'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('zlib', '1.2.11'), + ('Boost', '1.74.0'), +] + +configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN ' + +# The spherical test fails regardless of how it is compiled. +# Instead of patching the tests to skip it just don't run the tests for now. +# runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/run_pcm', 'lib/libpcm.a', 'lib/libpcm.%s' % SHLIB_EXT], + 'dirs': ['include/PCMSolver'] +} + +moduleclass = 'chem' From 6e1e42100ff8c60bc53d22a33012b1ee734830e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jan 2024 12:16:15 +0100 Subject: [PATCH 2260/2365] use https source URL for alsa-lib --- .../easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb index a96a6a054d..e679e46298 100644 --- a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb @@ -9,7 +9,7 @@ description = """The Advanced Linux Sound Architecture (ALSA) provides audio and toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] sources = [SOURCE_TAR_BZ2] checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347'] From f2e25251b58e25b69b35bf936909d3fe3f1b9842 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jan 2024 21:05:05 +0100 Subject: [PATCH 2261/2365] don't enable download_dep_fail, use_pip, sanity_pip_check in recent easyconfigs --- .../easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb | 4 ---- easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb | 4 ---- .../p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb | 4 ---- easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb | 4 ---- 4 files changed, 16 deletions(-) diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb index 3a7d86ba8d..cfce3200f6 100644 --- a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -22,8 +22,4 @@ dependencies = [ ('Z3', '4.8.10', '-Python-%(pyver)s'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb index ce60ce71e3..d9654ab450 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb @@ -16,8 +16,6 @@ dependencies = [ ('NiBabel', '3.2.1'), ] -use_pip = True - exts_list = [ ('traits', '6.2.0', { 'checksums': ['16fa1518b0778fd53bf0547e6a562b1787bf68c8f6b7995a13bd1902529fdb0c'], @@ -80,6 +78,4 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import nipype.interfaces'"] -sanity_pip_check = True - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb index e094054b20..3f7b7fc300 100644 --- a/easybuild/easyconfigs/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb @@ -18,8 +18,6 @@ dependencies = [ ('xxHash', '0.8.1'), ] -use_pip = True - exts_list = [ ('xxhash', version, { 'preinstallopts': 'XXHASH_LINK_SO=1', @@ -27,6 +25,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb index d6014a40f3..1bfd6bcd46 100644 --- a/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb @@ -17,8 +17,4 @@ builddependencies = [ dependencies = [('Python', '3.8.6')] -use_pip = True -download_dep_fail = True -sanity_pip_check = True - moduleclass = 'tools' From 3bb736e9feea5824f4f2ec0dc733552fec917dd4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Jan 2024 16:52:44 +0100 Subject: [PATCH 2262/2365] add missing dm-tree dependency for dm-reverb 0.2.0 --- easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb index aa3a70ea80..39199d15af 100644 --- a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb @@ -27,6 +27,7 @@ dependencies = [ ('Python', '3.8.6'), ('TensorFlow', '2.4.1'), ('protobuf', '3.14.0'), + ('dm-tree', '0.1.5'), ('snappy', '1.1.8'), ('zlib', '1.2.11'), ] From 8fb1184a2fe151048fc563c7de13adc12a1a0fd8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 25 Jan 2024 13:21:46 +0100 Subject: [PATCH 2263/2365] adding easyconfigs: TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb, TAMkin-1.2.6-foss-2020b.eb, TAMkin-1.2.6-foss-2021a.eb, TAMkin-1.2.6-foss-2021b.eb --- .../t/TAMkin/TAMkin-1.2.6-foss-2020b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb new file mode 100644 index 0000000000..1287bce559 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['TAMkin-1.2.6_fix-python38.patch'] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, +] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.5.1'), + ('molmod', '1.4.8'), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' From b2d14f302603e7fd8428cb2d7eedbccb5fd7660f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 25 Jan 2024 13:54:19 +0100 Subject: [PATCH 2264/2365] Use matplotlib 3.3.3 for 2020b --- easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb index 1287bce559..022abda9c0 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb @@ -20,7 +20,7 @@ checksums = [ dependencies = [ ('Python', '3.8.6'), - ('matplotlib', '3.5.1'), + ('matplotlib', '3.3.3'), ('molmod', '1.4.8'), ] From 71293cf31d7a305d78d4efdd4bd1618fa475f777 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 27 Jan 2024 20:11:06 +0000 Subject: [PATCH 2265/2365] remove `easybuild_version = '3.5.0'` from R easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 4 ---- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 4 ---- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 4 ---- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 4 ---- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 4 ---- easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 4 ---- 6 files changed, 24 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 782f039b49..463201babd 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -58,10 +58,6 @@ configopts = "--with-pic --enable-threads --enable-R-shlib" # we're installing them anyway below configopts += " --with-recommended-packages=no" -# specify that at least EasyBuild v3.5.0 is required, -# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK -easybuild_version = '3.5.0' - exts_default_options = { 'source_urls': [ 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index db5d9c9e47..0d911cfe91 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -67,10 +67,6 @@ configopts = "--with-pic --enable-threads --enable-R-shlib" # we're installing them anyway below configopts += " --with-recommended-packages=no" -# specify that at least EasyBuild v3.5.0 is required, -# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK -easybuild_version = '3.5.0' - exts_default_options = { 'source_urls': [ 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index c7d07e5f2a..ccd7f677ec 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -65,10 +65,6 @@ configopts = "--with-pic --enable-threads --enable-R-shlib" # we're installing them anyway below configopts += " --with-recommended-packages=no" -# specify that at least EasyBuild v3.5.0 is required, -# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK -easybuild_version = '3.5.0' - exts_default_options = { 'source_urls': [ 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index afc6216b0b..fbc7276de1 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -69,10 +69,6 @@ configopts = "--with-pic --enable-threads --enable-R-shlib" # we're installing them anyway below configopts += " --with-recommended-packages=no" -# specify that at least EasyBuild v3.5.0 is required, -# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK -easybuild_version = '3.5.0' - exts_default_options = { 'source_urls': [ 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index bf2b31d78e..e084c7875e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -62,10 +62,6 @@ configopts = "--with-pic --enable-threads --enable-R-shlib" # we're installing them anyway below configopts += " --with-recommended-packages=no" -# specify that at least EasyBuild v3.5.0 is required, -# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK -easybuild_version = '3.5.0' - exts_default_options = { 'source_urls': [ 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index be10c211dc..dd1c62b806 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -72,10 +72,6 @@ configopts = "--with-pic --enable-threads --enable-R-shlib" # we're installing them anyway below configopts += " --with-recommended-packages=no" -# specify that at least EasyBuild v3.5.0 is required, -# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK -easybuild_version = '3.5.0' - exts_default_options = { 'source_urls': [ 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive From 0f26e37864120036481151ddff2bd4b6d9c2ad6e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 29 Jan 2024 20:44:38 +0000 Subject: [PATCH 2266/2365] stop using custom easyblock for Doxygen --- .../d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb index f972f6c1aa..245da26746 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'CMakeMake' + name = 'Doxygen' version = '1.8.20' @@ -25,4 +27,11 @@ dependencies = [('libiconv', '1.16')] configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + moduleclass = 'devel' From f8fd66d5059db8a716b2143d5abaf7c74c585fc4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 17:22:51 +0100 Subject: [PATCH 2267/2365] don't enable download_dep_fail, use_pip, sanity_pip_check in recent easyconfigs --- .../c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 3 --- .../g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb | 3 --- .../i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 3 +-- .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb | 3 +-- .../o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb | 2 -- .../easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb | 3 --- 6 files changed, 2 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 5150980005..2e6d9914d6 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -43,9 +43,6 @@ dependencies = [ preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " -exts_default_options = { -} - exts_list = [ ('opt-einsum', '3.3.0', { 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 9d5d923af6..8455c32dfa 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -53,9 +53,6 @@ skipsteps = ['test'] exts_defaultclass = 'PythonPackage' -exts_default_options = { -} - local_genomeworks_preinstallopts = "sed -i 's/[=~]=/>=/g' requirements.txt && " local_genomeworks_preinstallopts += "export GW_INSTALL_DIR=%(installdir)s && " local_genomeworks_preinstallopts += "export GW_VERSION=%(version)s && " diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index aab9ec0426..d35d5a3e44 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -38,8 +38,7 @@ dependencies = [ ('tqdm', '4.56.2'), ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] -exts_default_options = { -} + exts_defaultclass = 'PythonPackage' exts_list = [ ('fire', '0.4.0', { diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index 542cfc7bf1..c533dcb1b5 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -24,8 +24,7 @@ dependencies = [ ] exts_defaultclass = 'PythonPackage' -exts_default_options = { -} + exts_list = [ (name, version, { 'modulename': 'pygpu', diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb index 2b699a6f1b..c14c203d7e 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -16,8 +16,6 @@ dependencies = [ ] builddependencies = [('binutils', '2.35')] -exts_default_options = { -} exts_list = [ ('pbr', '5.6.0', { 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index d4e87b9a1c..df5b2f160e 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -21,9 +21,6 @@ dependencies = [ ('Python', '3.8.6'), ] -exts_default_options = { -} - exts_list = [ ('Logbook', '1.5.3', { 'checksums': ['66f454ada0f56eae43066f604a222b09893f98c1adc18df169710761b8f32fe8'], From ac3ef9d5156ccd8a2f8a55554a6b8660eb34507d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 18:49:57 +0100 Subject: [PATCH 2268/2365] make sure that Brunsli libraries are installed into /lib (#19805) --- .../easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index f90442fc54..22f38cbf5f 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -27,7 +27,10 @@ dependencies = [ # skip use of third_party directory, since we provide Brotli via a proper dependency preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " -configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" @@ -35,8 +38,8 @@ buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" postinstallcmds = [ "mkdir %(installdir)s/bin", "cp dbrunsli %(installdir)s/bin/", - "cp libbrunsli*.a %(installdir)s/lib*/", - "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, ] sanity_check_paths = { From 603a70dfff76c3042a79dd12838d06f85e426639 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 14:09:56 +0100 Subject: [PATCH 2269/2365] remove numa configure option from hwloc 2.2+ --- easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb index ddabd3a738..f3d9db107b 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb @@ -35,8 +35,7 @@ dependencies = [ ('libpciaccess', '0.16'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', From d892dbcb771827e0485dba7217008bb36869d45b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 16:46:36 +0100 Subject: [PATCH 2270/2365] fix MS_RDONLY error in OpenMPI 4.0.5 --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 2 ++ .../o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 2 ++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb | 2 ++ .../easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb | 2 ++ 4 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb index 1536146190..184de98e33 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz @@ -20,6 +21,7 @@ checksums = [ '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb index 383370dd6f..bb1fb2730a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -14,6 +14,7 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz @@ -22,6 +23,7 @@ checksums = [ '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb index 3746daadf8..838b2563b3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz @@ -20,6 +21,7 @@ checksums = [ '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb index de0f5b3d2e..08a4dbccb2 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz @@ -20,6 +21,7 @@ checksums = [ '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] builddependencies = [ From 8a9b0833de9f8ae95fb0866625e54c3c3d8541fd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 12 Feb 2024 18:44:51 +0000 Subject: [PATCH 2271/2365] all but the latest Perls --- .../easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb | 2 +- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb index 882c2de902..bd93ea380e 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 34e3a3e297..f24535bf5c 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -9,7 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.35'), From 45971321b0c7c16171512c69b174c663381eed51 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 12 Feb 2024 18:49:46 +0000 Subject: [PATCH 2272/2365] checksums --- .../easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb index bd93ea380e..d3674a9d64 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb @@ -14,6 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.32.0.tar.gz': 'efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index f24535bf5c..7340496b8a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -10,6 +10,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.32.0.tar.gz': 'efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.35'), From ffcea8187c96a63817096e4d9e74a5112c45b35a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 18 Feb 2024 09:22:22 +0000 Subject: [PATCH 2273/2365] add `download_instructions` to WIEN2k easyconfigs --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb index 5e5f66e861..161a212ba3 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb @@ -19,6 +19,10 @@ dependencies = [ ('libxc', '4.3.4'), ] +download_instructions = """ +WIEN2k can be ordered at http://susi.theochem.tuwien.ac.at/index.html. +""" + osdependencies = [('glibc-static', 'libc6-dev')] # required for libpthread.a remote = 'pbsssh' From 350bf2f6889c384f3407a74907e175613d758db6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 18 Feb 2024 09:35:41 +0000 Subject: [PATCH 2274/2365] add `download_instructions` to TetGen easyconfig --- .../easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb index 08661910bc..8880b56b40 100644 --- a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb @@ -3,14 +3,16 @@ easyblock = 'CMakeMake' name = 'TetGen' version = '1.6.0' -homepage = 'http://wias-berlin.de/software/index.jsp?id=TetGen' +homepage = 'https://wias-berlin.de/software/index.jsp?id=TetGen' description = """ A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -# Fill in a form and download from above URL sources = ['tetgen1.6.0.tar.gz'] checksums = ['87b5e61ebd3a471fc4f2cdd7124c2b11dd6639f4feb1f941a5d2f5110d05ce39'] +download_instructions = f"""{name} requires manual download from {homepage} +Required download: {' '.join(sources)}""" + builddependencies = [ ('CMake', '3.18.4'), From 2533d723a66e6dd9fa44255cbdf0a175459221f2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 18 Feb 2024 15:52:16 +0000 Subject: [PATCH 2275/2365] add `download_instructions` to AMS easyconfigs --- .../easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb index 0d9ba4e2d4..76091ce5f2 100644 --- a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb +++ b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'iimpi', 'version': '2020b'} sources = ['ams%(version)s.pc64_linux.intelmpi.bin.tgz'] checksums = ['8a68eef268d7eb53ea1e10f66a48a8280f4dadae585999096ba1c246e88989db'] +download_instructions = f"""{name} requires manual download from {homepage} +Required download: {' '.join(sources)}""" dependencies = [('libGLU', '9.0.1')] From 83492c238c4267f57892befbfee5c1435ca83659 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 18 Feb 2024 20:11:30 +0000 Subject: [PATCH 2276/2365] add `download_instructions` to GeneMark-ET easyconfigs --- .../g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb index 110477c056..7ff097babf 100644 --- a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb @@ -8,11 +8,14 @@ description = "Eukaryotic gene prediction suite with automatic training" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -# download via http://exon.gatech.edu/GeneMark/license_download.cgi -# rename gmes_linux_64.tar.gz to gmes_linux_64-4.65.tar.gz sources = ['gmes_linux_64-%(version)s.tar.gz'] checksums = ['62ea2dfa1954ab25edcc118dbeaeacf15924274fb9ed47bc54716cfd15ad04fe'] +download_instructions = """ +1. complete the license form: http://exon.gatech.edu/GeneMark/license_download.cgi +2. rename the tarball: `mv gmes_linux_64.tar.gz gmes_linux_64-%(version)s.tar.gz` +""" + dependencies = [('Perl', '5.32.0')] fix_perl_shebang_for = ['*.pl'] From 739a2e3ff43a2deb555f54bc6de6bacd1316b5b3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 19 Feb 2024 15:55:04 +0000 Subject: [PATCH 2277/2365] add `download_instructions` to IMOD easyconfigs --- .../easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb | 14 +++++++------- .../i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 14 +++++++------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index d3a1580f52..dc4310036d 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -16,13 +16,6 @@ Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'openmp': True} -# download manually from mercurial repository and create source tarball: -# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD -# get lunch -# cd IMOD -# hg update -r IMOD_4-11-5 -# cd .. -# tar czf IMOD-4.11.5.tar.gz IMOD sources = [SOURCE_TAR_GZ] patches = ['IMOD-%(version)s_fix-csvtohtml-py3.patch'] checksums = [ @@ -30,6 +23,13 @@ checksums = [ None, # IMOD-4.11.5.tar.gz '8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971', # IMOD-4.11.5_fix-csvtohtml-py3.patch ] +download_instructions = f"""{name} requires manual download from mercurial repository and creating source tarball: +1. hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD +2. get lunch +3. cd IMOD +4. hg update -r IMOD_{version.replace('.', '-')} +5. cd .. +6. tar czf {name}-{version}.tar.gz IMOD""" dependencies = [ ('LibTIFF', '4.1.0'), diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index 1f1c6e82c8..4180e68700 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -18,13 +18,6 @@ toolchainopts = {'pic': True, 'openmp': True} # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] -# download manually from mercurial repository and create source tarball: -# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD -# get lunch -# cd IMOD -# hg update -r IMOD_4-11-5 -# cd .. -# tar czf IMOD-4.11.5.tar.gz IMOD sources = [SOURCE_TAR_GZ] # can't include a valid checksum, since tarball has to be created manually patches = ['IMOD-%(version)s_fix-csvtohtml-py3.patch'] @@ -33,6 +26,13 @@ checksums = [ None, # IMOD-4.11.5.tar.gz '8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971', # IMOD-4.11.5_fix-csvtohtml-py3.patch ] +download_instructions = f"""{name} requires manual download from mercurial repository and creating source tarball: +1. hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD +2. get lunch +3. cd IMOD +4. hg update -r IMOD_{version.replace('.', '-')} +5. cd .. +6. tar czf {name}-{version}.tar.gz IMOD""" dependencies = [ ('LibTIFF', '4.1.0'), From 847967b5684e6377484b83f17f5045f0ff5dce8b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 19 Feb 2024 16:43:00 +0000 Subject: [PATCH 2278/2365] add `download_instructions` to MotionCor2 easyconfigs --- .../easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb index 0bbb8322a6..280bf3a6dd 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb @@ -21,11 +21,11 @@ BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -# No longer directly downloadable, available from https://msg.ucsf.edu/software sources = [ '%(name)s_%(version)s.zip', ] checksums = ['5a1b952f46816e396b918b92fcb118376c02be3636371bd6fcef00f315685b8d'] +download_instructions = """Visit https://msg.ucsf.edu/software and fill in the form to download %s""" % sources[0] # CUDA is a build dependency to make sure it gets installed. # It's actually a runtime dependency, but that's handled in the wrapper to diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb index 836b2d4668..c4d1ce0d0d 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb @@ -23,8 +23,8 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} sources = ['%(name)s_%(version)s.zip'] checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] +download_instructions = """Visit https://msg.ucsf.edu/software and fill in the form to download %s""" % sources[0] -# No longer directly downloadable, available from https://msg.ucsf.edu/software # CUDA is a build dependency to make sure it gets installed. # It's actually a runtime dependency, but that's handled in the wrapper to # make sure it doesn't conflict with whatever toolchain happens to be loaded. From 12c0cb14336cd294ad5240db55af7e4b0246cc04 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 19 Feb 2024 19:52:45 +0000 Subject: [PATCH 2279/2365] add `download_instructions` to Amber easyconfigs --- .../a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb | 4 +++- .../a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb index 1f0d542911..a752ce9cab 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb @@ -6,7 +6,7 @@ patchlevels = (3, 11) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) -homepage = 'http://ambermd.org/amber.html' +homepage = 'http://ambermd.org/' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.""" @@ -59,6 +59,8 @@ checksums = [ # AmberTools-21_dont_include_config.h_in_top_Makefile.patch 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', ] +download_instructions = f"""{name} requires manual download from https://ambermd.org/GetAmber.php +Required downloads: {sources[0]} {sources[1]['filename']}""" builddependencies = [ ('Bison', '3.7.1'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb index 638decc861..522bcf6e78 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb @@ -6,7 +6,7 @@ patchlevels = (3, 11) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) -homepage = 'http://ambermd.org/amber.html' +homepage = 'http://ambermd.org/' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.""" @@ -31,6 +31,8 @@ checksums = [ # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', ] +download_instructions = f"""{name} requires manual download from https://ambermd.org/GetAmber.php +Required downloads: {' '.join(sources)}""" builddependencies = [ ('Bison', '3.7.1'), From 1223a01ae6b21b7c1758322cf0e6961080723629 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 20 Feb 2024 08:54:12 +0000 Subject: [PATCH 2280/2365] https --- .../a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb | 4 ++-- .../a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb index a752ce9cab..3e43c7245a 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb @@ -1,12 +1,12 @@ name = 'Amber' local_amber_ver = 20 local_ambertools_ver = 21 -# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php patchlevels = (3, 11) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) -homepage = 'http://ambermd.org/' +homepage = 'https://ambermd.org/' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.""" diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb index 522bcf6e78..a3ba577980 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb @@ -1,12 +1,12 @@ name = 'Amber' local_amber_ver = 20 local_ambertools_ver = 21 -# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php patchlevels = (3, 11) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) -homepage = 'http://ambermd.org/' +homepage = 'https://ambermd.org/' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.""" From 4d5f6ff8e1cb23d31f9d9724508bbd0d61c438d8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 20 Feb 2024 11:49:36 +0100 Subject: [PATCH 2281/2365] add OpenMPI-4.1.x_add_atomic_wmb.patch and update checksums accordingly --- .../o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 18 ++++++++++-------- .../o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb | 6 +++++- 2 files changed, 15 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index b82c542c42..ec897b5c4c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -13,16 +13,18 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ - '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a', # openmpi-4.1.0.tar.gz - # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch - 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', - # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch - 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch - # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch - 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', + {'openmpi-4.1.0.tar.gz': '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a'}, + {'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch': + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e'}, + {'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch': + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb'}, + {'OpenMPI-4.x_fix_pmix_discovery.patch': '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b'}, + {'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch': + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb index 5148de10aa..d0d18bc3a0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb @@ -8,7 +8,11 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['9b78c7cf7fc32131c5cf43dd2ab9740149d9d87cadb2e2189f02685749a6b527'] +patches = ['OpenMPI-4.1.x_add_atomic_wmb.patch'] +checksums = [ + {'openmpi-4.1.2.tar.bz2': '9b78c7cf7fc32131c5cf43dd2ab9740149d9d87cadb2e2189f02685749a6b527'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, +] builddependencies = [ ('pkg-config', '0.29.2'), From 08149efd812c147e27fc6932b0f439d6722ea2a9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 21 Feb 2024 15:48:13 +0100 Subject: [PATCH 2282/2365] Remove --disable-libdeflate option from LibTIFF 4.1.0 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb index f5661b0938..9e430cbd05 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -37,7 +37,7 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += "--disable-webp --disable-libdeflate " +configopts += "--disable-webp " sanity_check_paths = { 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, From aeac4ab4b67ce6ee9c4a12a04b57ce4aa0be4b45 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 21 Feb 2024 16:55:15 +0100 Subject: [PATCH 2283/2365] Remove git version check and fix test command for molmod 1.4.8 --- easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb index 1aa8772b2a..c8bfec5a59 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -10,8 +10,10 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.8_fix-git-version-check.patch'] checksums = [ - '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8', # molmod-1.4.8.tar.gz + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'}, ] dependencies = [ @@ -24,6 +26,6 @@ download_dep_fail = True sanity_pip_check = True runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" -runtest += "python setup.py build_ext -i; pytest -ra" +runtest += "python setup.py build_ext -i && pytest -ra" moduleclass = 'math' From e27adf5a6a5da9ac666613a87a01077833ddbbb6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 28 Feb 2024 12:16:54 +0100 Subject: [PATCH 2284/2365] Fix test_vsa_no_mass --- easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb index 022abda9c0..385046a56c 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb @@ -12,10 +12,14 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -patches = ['TAMkin-1.2.6_fix-python38.patch'] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] checksums = [ {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, ] dependencies = [ From 1573e11092233b69b7d92405c4a4442257126e59 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Feb 2024 09:45:13 +0100 Subject: [PATCH 2285/2365] Remove --disable-docs configure option from FriBidi 1.0.5+ --- .../easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb index 40e6ff9157..c0dd7325a8 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb @@ -23,8 +23,6 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], From a4c5fe4d2888a5e09e42c65585305f4da20fde3b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 1 Mar 2024 21:28:33 +0100 Subject: [PATCH 2286/2365] use system architecture template in DB_File --- easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb index 0b79bde69a..3c7b085c1a 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ dependencies = [ preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { - 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], 'dirs': [], } From e2e4a996f474c10cc032aa8fea850095b2b976ea Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 3 Mar 2024 08:58:19 +0000 Subject: [PATCH 2287/2365] update homepage and source_urls for SPAdes --- .../s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb | 4 ++-- easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb index 54ab5e1ceb..a2f6af4df2 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb @@ -13,12 +13,12 @@ name = 'SPAdes' version = '3.15.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['e93b43951a814dc7bd6a246e1e863bbad6aac4bfe1928569402c131b2af99d0d'] diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb index d1300d60a1..4a3432922a 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb @@ -12,12 +12,12 @@ easyblock = 'CMakeMake' name = 'SPAdes' version = '3.15.2' -homepage = 'https://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['e93b43951a814dc7bd6a246e1e863bbad6aac4bfe1928569402c131b2af99d0d'] From 8b609387c5d64d5dd9334a66c73a77898e5ebcfc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 4 Mar 2024 15:30:06 +0100 Subject: [PATCH 2288/2365] Remove disable-visibility configure flag from GTK3 --- easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb index 9eaad73eab..627eb4f9fe 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb @@ -44,7 +44,7 @@ components = [ (name, version, { 'source_urls': [FTPGNOME_SOURCE], 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes", }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], From 36676239f4b40d166823d6ab765d4f4af3a38825 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 5 Mar 2024 09:18:36 +0100 Subject: [PATCH 2289/2365] Remove mpi configure option from libfdf 0.2.2 --- .../easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb | 2 -- .../l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb index 71cbe3216a..4f17eb894d 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb @@ -13,8 +13,6 @@ source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed9 sources = ['libfdf-%(version)s.tar.gz'] checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] -configopts = ' --without-mpi ' - sanity_check_paths = { 'files': ['include/fdf.mod', 'lib/libfdf.a'], 'dirs': [''], diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb index bb206d03e6..12c8f37583 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb @@ -13,8 +13,6 @@ source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed9 sources = ['libfdf-%(version)s.tar.gz'] checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] -configopts = ' --without-mpi ' - sanity_check_paths = { 'files': ['include/fdf.mod', 'lib/libfdf.a'], 'dirs': [''], From 6e69d8270104c996e48a7afd7aeb60ebbada026e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Mar 2024 09:05:44 +0100 Subject: [PATCH 2290/2365] Fix configure option and gpertools dependency of MIRA 5.0 --- easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb index 69c6533045..062d990ae9 100644 --- a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb @@ -13,11 +13,9 @@ sources = ['mira-V5rc2.tar.bz2'] source_urls = ['https://github.com/bachev/mira/releases/download/V5rc2/'] checksums = ['4255aa9c4f09ec686b1c717bffe2dd124d3ef9b87f00e74d1bcd51b8599b8e44'] -preconfigopts = 'export CFLAGS="$CFLAGS -fpermissive" && ' -preconfigopts += 'export CXXFLAGS="$CXXFLAGS -fpermissive" && ' +preconfigopts = 'export CXXFLAGS="$CXXFLAGS -fpermissive" && ' configopts = '--with-boost=$EBROOTBOOST --with-expat=$EBROOTEXPAT --with-zlib=$EBROOTZLIB ' -configopts += '--with-tcmalloc-dir=$EBROOTGPERFTOOLS/lib ' builddependencies = [ ('flex', '2.6.4'), @@ -26,7 +24,6 @@ dependencies = [ ('Boost', '1.74.0'), ('zlib', '1.2.11'), ('expat', '2.2.9'), - ('gperftools', '2.9.1'), ] sanity_check_paths = { From eed8b46e718b4d263bbd363a66279dd1b2052dbc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 20 Mar 2024 13:44:26 +0000 Subject: [PATCH 2291/2365] Switch libxc sources to gitlab --- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb | 5 +++-- .../easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb | 5 +++-- 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb index 2d16f4413b..7932a1b81b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_lm-fix.patch', @@ -17,7 +17,8 @@ patches = [ 'libxc-%(version)s_fix-timeout.patch', ] checksums = [ - 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', + '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb index 81cacc26ca..a3d4087938 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_rename-F03.patch', @@ -18,7 +18,8 @@ patches = [ 'libxc-%(version)s_fix-timeout.patch', ] checksums = [ - 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', + '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz 'e494be3ca2026998f2dd7c6b03a4e662f204fd3d963271e588f9f0d5739e76b5', # libxc-4.3.4_rename-F03.patch 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb index e62a0ad0fa..3e72f2dcfb 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['180d52b5552921d1fac8a10869dd30708c0fb41dc202a3bbee0e36f43872718a'] +checksums = [('180d52b5552921d1fac8a10869dd30708c0fb41dc202a3bbee0e36f43872718a', + '3fe05ccf7033622112f7d6ab28ac82301f5840b8d1bbe8b6df1022dbc732883f')] builddependencies = [ ('CMake', '3.18.4'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb index 8aa007ac6f..820cf82860 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] +checksums = [('0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd', + '53cbccae4227794c4f4e042d0c20c3171894d8eacd13fd78aab376d5971a966c')] builddependencies = [ ('CMake', '3.18.4'), From 0cbd15a86d74e4bee6ae52c81da37f37b74ed561 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 20 Mar 2024 13:51:58 +0000 Subject: [PATCH 2292/2365] New homepage --- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb index 7932a1b81b..46b4a89581 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb index a3d4087938..bd9018d08a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb index 3e72f2dcfb..02f66c082a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '5.1.2' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb index 820cf82860..311998a80a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '5.1.3' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" From c220f3a56f5694c54642061d35f5d81600bc5203 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Mar 2024 09:08:00 +0100 Subject: [PATCH 2293/2365] clean up easyconfigs that explicitly set `use_pip`, `sanity_pip_check` and `download_dep_fail` --- easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb index 385046a56c..508b9103e1 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb @@ -28,9 +28,6 @@ dependencies = [ ('molmod', '1.4.8'), ] -download_dep_fail = True -use_pip = True - # disable tests that require X11 by specifying "backend: agg" in matplotlibrc runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' @@ -40,6 +37,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_pip_check = True - moduleclass = 'chem' From f3e51c0ea801643564200fc5e870449f5d9e7c69 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Sun, 14 Apr 2024 12:50:21 +0200 Subject: [PATCH 2294/2365] Move all legacy QuantumESPRESSO easyconfigs to the legacy easyblock --- .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb | 2 ++ .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb index 02147ccb84..c954f1ce9a 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb @@ -1,3 +1,5 @@ +easyblock = "EB_QuantumESPRESSO_autotools" + name = 'QuantumESPRESSO' version = '6.6' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb index 43a880080a..f34b824285 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb @@ -1,6 +1,8 @@ ## # Author: Robert Mijakovic ## +easyblock = "EB_QuantumESPRESSO_autotools" + name = 'QuantumESPRESSO' version = '6.7' From 2abd0977369291e57f229f8b2ed380d2d382c32e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Apr 2024 18:07:28 +0200 Subject: [PATCH 2295/2365] make sure that libjpeg-turbo libraries are installed in 'lib' subdirectory --- .../l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb index 1214eaa1d2..49f121b7a6 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb @@ -27,7 +27,11 @@ dependencies = [ ('NASM', '2.15.05'), ] -configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' +# make sure that libraries are installed to /lib (instead of /lib64), +# which helps with avoiding problems when libjpeg-turbo is a dependency that +# gets linked via RPATH and Meson/Ninja are involved, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16256 +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1 -DCMAKE_INSTALL_LIBDIR:PATH=lib' runtest = "test" From ce78dff81c5c78901cddd30952108f41ccd1156a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2024 22:08:10 +0200 Subject: [PATCH 2296/2365] add patch to fix CVE in R v4.0.x --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 6 +++++- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 6 +++++- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 6 +++++- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 6 +++++- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 6 +++++- easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 6 +++++- 6 files changed, 30 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 782f039b49..d8b9d1c97f 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -9,7 +9,11 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d'] +patches = ['R-4.x_fix-CVE-2024-27322.patch'] +checksums = [ + {'R-4.0.3.tar.gz': '09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d'}, + {'R-4.x_fix-CVE-2024-27322.patch': 'd8560e15c3c5716f99e852541901014d406f2a73136b0b74f11ba529f7a7b00d'}, +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index db5d9c9e47..3437fa7f9d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -9,7 +9,11 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d'] +patches = ['R-4.x_fix-CVE-2024-27322.patch'] +checksums = [ + {'R-4.0.3.tar.gz': '09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d'}, + {'R-4.x_fix-CVE-2024-27322.patch': 'd8560e15c3c5716f99e852541901014d406f2a73136b0b74f11ba529f7a7b00d'}, +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index c7d07e5f2a..c5a5374239 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -15,7 +15,11 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e'] +patches = ['R-4.x_fix-CVE-2024-27322.patch'] +checksums = [ + {'R-4.0.4.tar.gz': '523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e'}, + {'R-4.x_fix-CVE-2024-27322.patch': 'd8560e15c3c5716f99e852541901014d406f2a73136b0b74f11ba529f7a7b00d'}, +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index afc6216b0b..5930c93042 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -9,7 +9,11 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e'] +patches = ['R-4.x_fix-CVE-2024-27322.patch'] +checksums = [ + {'R-4.0.4.tar.gz': '523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e'}, + {'R-4.x_fix-CVE-2024-27322.patch': 'd8560e15c3c5716f99e852541901014d406f2a73136b0b74f11ba529f7a7b00d'}, +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index bf2b31d78e..a3d990d65b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef'] +patches = ['R-4.x_fix-CVE-2024-27322.patch'] +checksums = [ + {'R-4.0.5.tar.gz': '0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef'}, + {'R-4.x_fix-CVE-2024-27322.patch': 'd8560e15c3c5716f99e852541901014d406f2a73136b0b74f11ba529f7a7b00d'}, +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index be10c211dc..9fbcf1785f 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef'] +patches = ['R-4.x_fix-CVE-2024-27322.patch'] +checksums = [ + {'R-4.0.5.tar.gz': '0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef'}, + {'R-4.x_fix-CVE-2024-27322.patch': 'd8560e15c3c5716f99e852541901014d406f2a73136b0b74f11ba529f7a7b00d'}, +] builddependencies = [ ('pkg-config', '0.29.2'), From ccea7caecf7932c29ddb81eb90f1452e6949acea Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 6 May 2024 11:19:41 +0200 Subject: [PATCH 2297/2365] remove CMAKE_INSTALL_LIBDIR settings from configopts as those are now set by the CMakeMake easyblock --- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb | 2 +- .../easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 2 +- .../easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 3 --- easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb | 2 -- .../l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb | 6 +----- easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 1 - easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb | 1 - 8 files changed, 4 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb index e4a039c796..62f9440cbe 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -36,7 +36,7 @@ start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 941c31686a..1d338c2f60 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -40,7 +40,7 @@ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index 0551ea8b33..bd481cac4d 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -36,7 +36,7 @@ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index 22f38cbf5f..35ff65577e 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -29,9 +29,6 @@ preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(versio configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' -# make sure that libraries end up in /lib (not lib64) -configopts += "-DCMAKE_INSTALL_LIBDIR=lib " - buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" # also install dbrunsli binary and missing libraries diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb index a75e046b3d..a731819812 100644 --- a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -21,8 +21,6 @@ builddependencies = [ ('CMake', '3.18.4'), ] -configopts = '-DCMAKE_INSTALL_LIBDIR=lib' - postinstallcmds = [ # copy the LercTest source file to a LercTest subdir in the installation directory and compile it # (needs to be done here instead of in the sanity check, else it won't work when RPATH linking is enabled) diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb index 49f121b7a6..1214eaa1d2 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb @@ -27,11 +27,7 @@ dependencies = [ ('NASM', '2.15.05'), ] -# make sure that libraries are installed to /lib (instead of /lib64), -# which helps with avoiding problems when libjpeg-turbo is a dependency that -# gets linked via RPATH and Meson/Ninja are involved, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16256 -configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1 -DCMAKE_INSTALL_LIBDIR:PATH=lib' +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' runtest = "test" diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb index c92d21af64..bb470835e7 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -57,7 +57,6 @@ configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb index 3d7c9e1937..56d278e80e 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb @@ -56,7 +56,6 @@ configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " From 446b715dfa1bef6164c8b7204188a4a5e74b36ec Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 25 May 2024 09:49:22 +0100 Subject: [PATCH 2298/2365] add `build_info_msg` abour kernel modules to GDRCopy --- .../GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb | 30 +++++++++---------- .../GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb | 30 +++++++++---------- .../g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb | 30 +++++++++---------- 3 files changed, 45 insertions(+), 45 deletions(-) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb index c99c15a13e..915d01b254 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -27,21 +27,21 @@ dependencies = [ ('Check', '0.15.2'), ] -# This easyconfig only installs the library and binaries of GDRCopy. Please -# keep in mind that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library and binaries of GDRCopy. Please +keep in mind that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb index accc04a5bd..443bbdd4af 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -27,21 +27,21 @@ dependencies = [ ('Check', '0.15.2'), ] -# This easyconfig only installs the library and binaries of GDRCopy. Please -# keep in mind that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library and binaries of GDRCopy. Please +keep in mind that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb index 85810e2394..f6498b61ef 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb @@ -20,21 +20,21 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library of GDRCopy. Please keep in mind +that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] From 24fb66a349659dd8c5977eb4c91b77022ed043c1 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 13 Jun 2024 16:14:27 +0200 Subject: [PATCH 2299/2365] Easyblock update means most changes are no longer required --- .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb | 2 -- .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb index c954f1ce9a..02147ccb84 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb @@ -1,5 +1,3 @@ -easyblock = "EB_QuantumESPRESSO_autotools" - name = 'QuantumESPRESSO' version = '6.6' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb index f34b824285..43a880080a 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb @@ -1,8 +1,6 @@ ## # Author: Robert Mijakovic ## -easyblock = "EB_QuantumESPRESSO_autotools" - name = 'QuantumESPRESSO' version = '6.7' From f67cb7d71e95800a617a5282d643ed9591e20aea Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 17 Jul 2024 11:29:41 +0200 Subject: [PATCH 2300/2365] phonopy changed their homepage from version 2.5 --- easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb index 3a1f3d0bc3..2aa223e2c8 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'phonopy' version = '2.12.0' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'foss', 'version': '2020b'} From bee857e42f47911ea3309f00b12ff14278242612 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 1 Aug 2024 21:36:15 +0000 Subject: [PATCH 2301/2365] Fix download URLs for old Intel software (2018-23) Intel changed "irc_nas" to "IRC_NAS". Newer packages (2023.1+) already use that, but older ones need changing. Mirrors https://github.com/spack/spack/pull/43286 Fixes #21104 --- easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb | 2 +- .../i/impi/impi-2019.12.320-iccifort-2020.4.304.eb | 2 +- .../easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb | 2 +- .../easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb | 2 +- .../i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb | 2 +- .../easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb | 4 ++-- 13 files changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb index fbd8bc1719..056539c7f7 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17117/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17117/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb index 75ac380269..71a9f0f37b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'NVHPC', 'version': '21.2'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb index 541c3c12ae..1526523c78 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb index e07323d8ee..570499af77 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompic', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb index e1f7dd0c3f..15ccb6b8c7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb index a350ab4a6e..73aac3a85e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb index 89d0c991d8..68e2a157d3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb index 737f7462d7..363e95f7dc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2020.12'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17402/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17402/'] sources = ['l_onemkl_p_%(version)s.52_offline.sh'] checksums = ['818b6bd9a6c116f4578cda3151da0612ec9c3ce8b2c8a64730d625ce5b13cc0c'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb index a5ba5409ff..2bf8b19fb2 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17836/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17836/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['8108fbf2353a9f1926036bb67647b65c0e4933a3eb66e1dc933960e5b055f320'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb index d4a9ef76ae..d723d12dc1 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb index 3305cf60a8..7082d103ec 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb index 1a0fbe3b03..d8a92d6db7 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.1.2'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17397/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17397/'] sources = ['l_mpi_oneapi_p_%(version)s.76_offline.sh'] checksums = ['8b7693a156c6fc6269637bef586a8fd3ea6610cac2aae4e7f48c1fbb601625fe'] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb index 820a237e44..67a5c1f570 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17513/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17513/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.63_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17508/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17508/'], 'filename': 'l_fortran-compiler_p_%(version)s.62_offline.sh', }, ] From b5d89bd6bcfe2d7a0a3fd0a84bdd0fa4be942b28 Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Mon, 5 Aug 2024 13:42:42 +0200 Subject: [PATCH 2302/2365] Szip: Update source and homepage URLs --- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb index 88e067c36e..576e48c80b 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] From 73a2b3fbe7049a72d78dcf13f01d98148e1216c0 Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Tue, 6 Aug 2024 13:54:52 +0200 Subject: [PATCH 2303/2365] HDF URLs (Issue #21131) Squash of: * Change URLs * revert archive changes * Adding missing checksums * h4toh5/2.2.2: Revert changes (no longer available upstream) --- easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb | 4 ++-- easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb index bdb2cb878e..91e084fc23 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb index 8e8e8c7f70..50fe19e455 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] From 31858becebef863fe3a4d183b28667341fcc0719 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Aug 2024 17:41:07 +0200 Subject: [PATCH 2304/2365] adding easyconfigs: VSEARCH-2.28.1-GCC-10.2.0.eb --- .../v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..14ed6e6d97 --- /dev/null +++ b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'VSEARCH' +version = '2.28.1' + +homepage = 'https://github.com/torognes/vsearch' +description = """VSEARCH supports de novo and reference based chimera detection, + clustering, full-length and prefix dereplication, rereplication, + reverse complementation, masking, all-vs-all pairwise global alignment, + exact and global alignment searching, shuffling, subsampling and sorting. + It also supports FASTQ file analysis, filtering, + conversion and merging of paired-end reads.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/torognes/vsearch/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-pdfman ' + +sanity_check_paths = { + 'files': ['bin/vsearch'], + 'dirs': [], +} + +sanity_check_commands = ['vsearch --help'] + +moduleclass = 'bio' From a2f8b3196b7d7a93c1acdd826b72f911de2feb1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Aug 2024 14:59:47 +0200 Subject: [PATCH 2305/2365] add versionsuffix for spektral 1.2.0 since it depends on TensorFlow 2.5.0 --- ...l-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..75446a8cbf --- /dev/null +++ b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'spektral' +version = '1.2.0' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-%s' % local_tf_version + +homepage = 'https://graphneural.network' +description = "Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('lxml', '4.6.2'), + ('networkx', '2.5'), + ('scikit-learn', '0.23.2'), + ('tqdm', '4.56.2'), + ('TensorFlow', local_tf_version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['215f148e5d5067081bc28abe282bfd0942ed8be6d68f128fd7786006a884abf7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 9223503cab9aa015df42d7b2c6cccc4dc35a6cb5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 26 Aug 2024 13:11:09 +0100 Subject: [PATCH 2306/2365] remove unnecessary use of an easyblock for BamTools --- .../b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb | 7 +++++++ .../b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb | 10 +++++++++- 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb index df8599b794..db3318f6ff 100644 --- a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb @@ -1,4 +1,6 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'CMakeMake' + name = 'BamTools' version = '2.5.1' @@ -16,4 +18,9 @@ checksums = ['4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc'] builddependencies = [('CMake', '3.18.4')] +sanity_check_paths = { + 'files': ['bin/bamtools', 'include/bamtools/shared/bamtools_global.h', 'lib/libbamtools.a'], + 'dirs': ['include/bamtools/api', 'lib/pkgconfig'], +} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb index ad901666a4..4122753e13 100644 --- a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb @@ -1,4 +1,5 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'CMakeMake' name = 'BamTools' version = '2.5.1' @@ -9,7 +10,9 @@ description = "BamTools provides both a programmer's API and an end-user's toolk toolchain = {'name': 'iccifort', 'version': '2020.4.304'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/pezmaster31/bamtools/archive'] +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' +source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc'] @@ -18,4 +21,9 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] +sanity_check_paths = { + 'files': ['bin/bamtools', 'include/bamtools/shared/bamtools_global.h', 'lib/libbamtools.a'], + 'dirs': ['include/bamtools/api', 'lib/pkgconfig'], +} + moduleclass = 'bio' From a78b7b18f4347a3ff7c6437572209b70d44a539d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 28 Aug 2024 16:36:58 +0100 Subject: [PATCH 2307/2365] add 'bamtools --help' sanity check --- easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb | 2 ++ .../b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb index db3318f6ff..832de6cddb 100644 --- a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': ['include/bamtools/api', 'lib/pkgconfig'], } +sanity_check_commands = ["bamtools --help"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb index 4122753e13..7e8593030c 100644 --- a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['include/bamtools/api', 'lib/pkgconfig'], } +sanity_check_commands = ["bamtools --help"] + moduleclass = 'bio' From 16a6be0d26c94ae14d751e6e2c5a1a2f08f24d20 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 30 Aug 2024 16:51:12 +0200 Subject: [PATCH 2308/2365] Move exts_default_options to top-level parameters forPythonBundle ECs It is easier in the top-level and might cause confusion with https://github.com/easybuilders/easybuild-easyblocks/pull/3428 --- .../cell2location-0.05-alpha-fosscuda-2020b.eb | 6 ------ .../OpenStackClient-5.5.0-GCCcore-10.2.0.eb | 7 +++---- .../p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb | 7 ++----- 3 files changed, 5 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 9a0eeba162..1556b0f9da 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -45,12 +45,6 @@ preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " use_pip = True -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} - exts_list = [ ('opt-einsum', '3.3.0', { 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb index b013362d2e..50dab938d4 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -16,9 +16,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.35')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pbr', '5.6.0', { 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], @@ -121,7 +121,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index ee4425b49c..96d813edcc 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -21,9 +21,8 @@ dependencies = [ ('Python', '3.8.6'), ] -exts_default_options = { - 'use_pip': True -} +sanity_pip_check = True +use_pip = True exts_list = [ ('Logbook', '1.5.3', { @@ -37,6 +36,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' From 824e65b61fe9ffe10b3cdfb1b977bba999dd5cc8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Sep 2024 19:56:19 +0200 Subject: [PATCH 2309/2365] remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all --- easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index 22f38cbf5f..9e505b4df5 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -21,7 +21,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency From 59bb89a3b8206c8abd7a4fd9d3f2cfa900d9f9e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Sep 2024 15:53:02 +0200 Subject: [PATCH 2310/2365] clean up easyconfigs that explicitly set `use_pip`, `sanity_pip_check`, and `download_dep_fail` --- .../spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb index 75446a8cbf..91006d1a37 100644 --- a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -20,14 +20,10 @@ dependencies = [ ('TensorFlow', local_tf_version), ] -use_pip = True - exts_list = [ (name, version, { 'checksums': ['215f148e5d5067081bc28abe282bfd0942ed8be6d68f128fd7786006a884abf7'], }), ] -sanity_pip_check = True - moduleclass = 'ai' From 58d676267ce49f0dd241995ef4a60ef2486baa2d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Sep 2024 10:03:19 +0200 Subject: [PATCH 2311/2365] avoid missing symbol in mclust extension of R-4.0.3-foss-2020b --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index d8b9d1c97f..9d09c81951 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -57,6 +57,10 @@ dependencies = [ osdependencies = [OS_PKG_OPENSSL_DEV] +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + configopts = "--with-pic --enable-threads --enable-R-shlib" # some recommended packages may fail in a parallel build (e.g. Matrix), and # we're installing them anyway below From ce96758bed92efb3c6a2b2610b5069aaa0128449 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Sep 2024 12:56:22 +0200 Subject: [PATCH 2312/2365] Fix repeated sanity check runs in manta --- .../m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb index 4587e8e91d..ff224b45ba 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb @@ -62,9 +62,7 @@ sanity_check_paths = { 'dirs': ['libexec'], } -sanity_check_commands = [ - 'python %(installdir)s/bin/runMantaWorkflowDemo.py' -] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', From 5523e5ddcf15340a12f49f429be6d9527917fca3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 3 Jul 2024 19:41:15 +0200 Subject: [PATCH 2313/2365] Drop manually specified PYTHONPATH from ParaView --- .../easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb index 4d1f402364..bed1948538 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb @@ -52,6 +52,4 @@ sanity_check_paths = { sanity_check_commands = ['python -c "import paraview"'] -modextrapaths = {'PYTHONPATH': ['lib64/python%(pyshortver)s/site-packages', 'lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' From 6588b959525978bda3bcabfea05132365f75bf0f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 4 Jul 2024 00:11:17 +0200 Subject: [PATCH 2314/2365] Drop manual default PYTHONPATH's from modextrapaths --- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb | 2 -- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 2 -- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 -- easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb | 2 -- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb | 2 -- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb | 2 -- easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb | 4 ---- .../easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb | 4 ---- .../easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb | 4 ---- .../g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb | 2 -- .../easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb | 2 -- .../i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 1 - .../j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb | 2 -- .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb | 2 -- .../l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 4 ---- easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb | 2 -- easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb | 1 - easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb | 1 - easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb | 1 - easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb | 1 - easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb | 1 - easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb | 1 - .../easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb | 4 ---- .../s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb | 4 ---- .../easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb | 2 -- .../easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 2 -- easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 2 -- easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb | 2 -- 33 files changed, 70 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb index 62f9440cbe..c5b59f6ec8 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -48,8 +48,6 @@ local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 1d338c2f60..03b39ad84d 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -51,8 +51,6 @@ local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index bd481cac4d..381b36a6c1 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -48,8 +48,6 @@ local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index d4ce0c41bf..c4dc7d4789 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -42,8 +42,6 @@ configopts = " ".join([ ]) prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['bin/ecflow_client', 'bin/ecflow_server'], 'dirs': ['lib/python%(pyshortver)s/site-packages/ecflow', 'share/ecflow/etc'], diff --git a/easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb b/easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb index 32ce0d7089..6b34a42a98 100644 --- a/easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb +++ b/easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb @@ -40,6 +40,4 @@ sanity_check_commands = [ "cd %(builddir)s/FMM3D-* && python python/test/test_lfmm.py", ] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb index 2484b33b3c..8453e7a125 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -53,8 +53,6 @@ configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jas configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb index a2b483559e..183a5e05d0 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb @@ -53,8 +53,6 @@ configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jas configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb index 1168e3faf6..b03dcaa460 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb @@ -59,8 +59,6 @@ configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' prebuildopts = "env LDSHARED='icc -shared' " -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb index 9bdccacd92..491b8b4a24 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-foss-2020b.eb @@ -78,8 +78,4 @@ exts_list = [ }), ] -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb index b4dd34b1bf..86fb64c1c5 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb @@ -79,8 +79,4 @@ exts_list = [ }), ] -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb index 03155a5055..b194b5deb3 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb @@ -79,8 +79,4 @@ exts_list = [ }), ] -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 8455c32dfa..c33ec23288 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -86,6 +86,4 @@ sanity_check_commands = [ "python -c 'import genomeworks'", ] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb index 1f8bfba881..923a257f23 100644 --- a/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HAL/HAL-2.1-foss-2020b.eb @@ -106,6 +106,4 @@ sanity_check_commands = [ "python -c 'from hal.stats.halStats import getHalGenomes'" ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb index b96581acb3..cff2e2a3ab 100644 --- a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb @@ -35,8 +35,6 @@ files_to_copy = [ 'include', 'LICENSE.txt', ] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['bin/hpdbscan', 'lib/libhpdbscan.%s' % SHLIB_EXT, 'include/hpdbscan.h'], 'dirs': [], diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index d35d5a3e44..57d730009e 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -50,7 +50,6 @@ exts_list = [ modextrapaths = { 'PATH': 'lib/python%(pyshortver)s/site-packages/IsoNet/bin', - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/' } sanity_check_commands = [ 'isonet.py check', diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb index fbd9f14c94..9879509ec7 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -101,8 +101,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/jupyterhub'], 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index c533dcb1b5..f1ee0b724d 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -33,8 +33,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['lib/libgpuarray.%s' % SHLIB_EXT, 'lib/libgpuarray-static.a'], 'dirs': ['include/gpuarray', 'lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index cca7752cf8..b6bbb0b3fd 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -72,8 +72,4 @@ sanity_check_commands = [ 'source %(installdir)s/scripts/dependencies.sh && longread_umi_version_dump', ] -modextrapaths = { - 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb index 0b54a76009..28f24d9a3b 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb @@ -47,6 +47,4 @@ sanity_check_commands = [ "python -c 'import meep'", ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb index fb7a82f563..8a8eafaed2 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb @@ -48,7 +48,6 @@ sanity_check_paths = { sanity_check_commands = ["python -m simtk.testInstallation"] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', } diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb index a7be917c4f..b9e09be200 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb @@ -56,7 +56,6 @@ sanity_check_paths = { sanity_check_commands = ["python -m simtk.testInstallation"] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', } diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb index 0620868684..c771c0aa1d 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb @@ -52,7 +52,6 @@ sanity_check_paths = { sanity_check_commands = ["python -m simtk.testInstallation"] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', } diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb index 15672d7342..177ce80391 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb @@ -50,7 +50,6 @@ sanity_check_paths = { sanity_check_commands = ["python -m simtk.testInstallation"] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', } diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb index 439ac03341..a0469cd4a4 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb @@ -58,7 +58,6 @@ sanity_check_paths = { sanity_check_commands = ["python -m simtk.testInstallation"] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', } diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index b2fab8f4e4..fd2d0b018d 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -82,7 +82,6 @@ sanity_check_commands = [ ] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'QT_INSTALL_DATA': 'qsci', } diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb index 307a924374..5f11b9d4cf 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb @@ -102,7 +102,6 @@ sanity_check_commands = [ ] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'QT_INSTALL_DATA': 'qsci', } diff --git a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb index 560b073c28..b482c0cbb4 100644 --- a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb @@ -48,10 +48,6 @@ components = [ }), ] -modextrapaths = { - 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] -} - postinstallcmds = ["chmod a+x %(installdir)s/bin/rmats.py"] sanity_check_commands = [ diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb index e0a2925a92..7b54e4be6f 100644 --- a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb @@ -55,8 +55,4 @@ sanity_check_commands = [ "python -c 'import sentencepiece'", ] -modextrapaths = { - 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb index 0ad9b52ffd..0f3d1bad69 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb @@ -37,8 +37,6 @@ postinstallcmds = [ "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb index f51b83860c..6fcd01d902 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb @@ -37,8 +37,6 @@ postinstallcmds = [ "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb index 7341f756cd..3d91b35cbf 100644 --- a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -46,8 +46,6 @@ postinstallcmds = [ "mv %(installdir)s/default_motifs %(installdir)s/share ", ] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['bin/train_model_default.sh', 'bin/train_classifier.py', 'bin/create_features.py', 'bin/idr'], diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb index bb470835e7..d317dccff8 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -67,8 +67,6 @@ postinstallcmds = [ 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] local_vtk_exec += ['vtkpython'] diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb index 56d278e80e..6098da53a7 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb @@ -66,8 +66,6 @@ postinstallcmds = [ 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] local_vtk_exec += ['vtkpython'] From 39f318105b1b06b15f563f6af835b339ae0447e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 6 Jul 2024 21:23:50 +0200 Subject: [PATCH 2315/2365] Remove additional manually specified PYTHONPATH's --- ...SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb | 2 -- easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 2 +- 3 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb index 410cd5034d..d865aa10a2 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb @@ -38,8 +38,6 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import snappy'"] -modextrapaths = {'PYTHONPATH': [local_pysite]} - local_javaopts = " -Dsnap.pythonExecutable=python" local_javaopts += " -Dsnap.pythonModuleDir=%s" % local_pyinstalldir diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb index 8f6ed227e6..5ef5383cb5 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -45,7 +45,7 @@ sanity_check_commands = [ "python -c 'import pyspark'", ] -modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} +modextrapaths = {'PYTHONPATH': 'python'} modextravars = {'SPARK_HOME': '%(installdir)s'} diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index 56919581d9..5c43460341 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -45,7 +45,7 @@ sanity_check_commands = [ "python -c 'import pyspark'", ] -modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} +modextrapaths = {'PYTHONPATH': 'python'} modextravars = {'SPARK_HOME': '%(installdir)s'} From d5488293640646b5dc2b6297371801653106aa1f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 23 Sep 2024 09:16:35 +0200 Subject: [PATCH 2316/2365] Fix compilation of HPDBSCAN --- .../easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb index b96581acb3..5a0f068b7d 100644 --- a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb @@ -12,7 +12,11 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/Markus-Goetz/hpdbscan/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}] -checksums = ['52ff343f77aeea5a425a911d88a57314c6bc877c18209eb53819d114421a868d'] +patches = ['HPDBSCAN-20210826_fix-numpy-headers.patch'] +checksums = [ + {'HPDBSCAN-20210826.tar.gz': '52ff343f77aeea5a425a911d88a57314c6bc877c18209eb53819d114421a868d'}, + {'HPDBSCAN-20210826_fix-numpy-headers.patch': 'cceb6a8cc15cb9bfbf92e5944f0398c1ac9db85a04fea3f7b1e0a0595fb530b1'}, +] builddependencies = [ ('CMake', '3.18.4'), From eb416cd0bb25da42e8d04bb8b6efd0a258ae3736 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Sep 2024 14:48:44 +0200 Subject: [PATCH 2317/2365] use x instead of l in list comprehensions, since l is an ambiguous variable name reported by pycodestyle --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb | 2 +- easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb | 2 +- easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb | 2 +- .../easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb | 4 ++-- .../easyconfigs/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb | 4 ++-- .../easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb | 4 ++-- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb | 2 +- .../o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb | 2 +- .../s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb | 4 ++-- easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb | 2 +- 15 files changed, 19 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb index 427e25ee82..3ed520be5c 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb @@ -53,7 +53,7 @@ configopts += '--with-cgl-lib="-lCgl" ' configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' sanity_check_paths = { - 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Cbc', 'CbcSolver', 'OsiCbc']], 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb index 4a649579d2..b3d64ec60c 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb @@ -45,7 +45,7 @@ configopts += '--with-osi-lib="-lOsi" ' configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' sanity_check_paths = { - 'files': ['bin/clp'] + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['Clp', 'ClpSolver', 'OsiClp']], + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Clp', 'ClpSolver', 'OsiClp']], 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb index b1f3baccd6..2e5b24b063 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ testopts = " && rm -r %(installdir)s/lib" runtest = 'check' sanity_check_paths = { - 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + 'files': ['lib/lib%s.%s' % (x, e) for x in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + ['include/gmp.h', 'include/gmpxx.h'], 'dirs': ['share'], } diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb index df76b6b84f..22b310f46f 100644 --- a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb @@ -31,7 +31,7 @@ _bins = ['bin/igzip'] _includes = ['include/%(namelower)s.h'] _includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', 'mem_routines', 'raid', 'test', 'types']] -_libs = ['lib/libisal.%s' % l for l in ['a', 'la', SHLIB_EXT]] +_libs = ['lib/libisal.%s' % x for x in ['a', 'la', SHLIB_EXT]] sanity_check_paths = { 'files': _bins + _includes + _libs, diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb index 4ad17d850e..b689599457 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb @@ -53,7 +53,7 @@ local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF sanity_check_paths = { 'files': ['bin/itkTestDriver'] + - ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (x, SHLIB_EXT) for x in local_lib_names], 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], } diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb index 0d9fe14e51..a72a767497 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb @@ -53,7 +53,7 @@ local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF sanity_check_paths = { 'files': ['bin/itkTestDriver'] + - ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (x, SHLIB_EXT) for x in local_lib_names], 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], } diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb index 1be5c814b9..9392190354 100644 --- a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb @@ -29,10 +29,10 @@ _solinks = [ "libaio.%s.1" % SHLIB_EXT, ] -postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, x) for x in _solinks] sanity_check_paths = { - 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], + 'files': ['lib/%s' % x for x in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb index 06e2a0c516..1e22cfc835 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb @@ -28,8 +28,8 @@ configopts = "--enable-libwebpmux" sanity_check_paths = { 'files': ['include/webp/%s' % f for f in ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h']] + - ['lib/lib%s.a' % l for l in ['webp', 'webpdemux', 'webpmux']] + - ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['webp', 'webpdemux', 'webpmux']], + ['lib/lib%s.a' % x for x in ['webp', 'webpdemux', 'webpmux']] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['webp', 'webpdemux', 'webpmux']], 'dirs': ['lib/'] } diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb index f46954badf..2c3c97317d 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb @@ -41,8 +41,8 @@ preinstallopts = 'EBFLAGS="$CFLAGS" ' sanity_check_paths = { 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + - [('lib/libncbi-%s.%s' % (l, e), 'lib64/libncbi-%s.%s' % (l, e)) - for l in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + [('lib/libncbi-%s.%s' % (x, e), 'lib64/libncbi-%s.%s' % (x, e)) + for x in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb index 2ef2ac3431..3e4cbc865c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ configopts = [ # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for x in libncurses{.,_,w}*; do ln -s "${x}" "${x/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb index f866015943..526c20bde1 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb @@ -77,7 +77,7 @@ local_contrib_libs = [ ] sanity_check_paths = { - 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], 'dirs': [], } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb index 6bd1dad125..45c90226c4 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb @@ -77,7 +77,7 @@ local_contrib_libs = [ ] sanity_check_paths = { - 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb index ba95e2ddc3..4c6e55fba4 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb @@ -90,8 +90,8 @@ local_bin = ['abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg- sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bin] + ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + - [('lib/libncbi-%s.%s' % (l, e), 'lib64/libncbi-%s.%s' % (l, e)) - for l in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + [('lib/libncbi-%s.%s' % (x, e), 'lib64/libncbi-%s.%s' % (x, e)) + for x in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], 'dirs': [] } diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb index bb470835e7..8d0089e3af 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -76,7 +76,7 @@ local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] sanity_check_paths = { 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + - ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in local_vtk_libs], 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], } diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb index 56d278e80e..74baca5cff 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb @@ -75,7 +75,7 @@ local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] sanity_check_paths = { 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + - ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in local_vtk_libs], 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], } From 6847e77213cd1803397fc8a515e51830b7447aa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Sep 2024 15:45:06 +0200 Subject: [PATCH 2318/2365] fix long lines --- easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb | 4 ++-- .../q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb index 08a161c2dc..ebc1a1481a 100644 --- a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb @@ -4,8 +4,8 @@ name = 'QtPy' version = '1.9.0' homepage = "https://github.com/spyder-ide/qtpy" -description = """QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. -It provides support for PyQt5, PyQt4, PySide2 and PySide.""" +description = """QtPy is a small abstraction layer that lets you write applications using a single API call + to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb index 005a376969..c9cbce1585 100644 --- a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb @@ -4,10 +4,10 @@ name = 'Qtconsole' version = '5.0.2' homepage = 'https://jupyter.org/' -description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. -The Qtconsole is a very lightweight application that largely feels like a terminal, -but provides a number of enhancements only possible in a GUI, -such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more.""" +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media output, + session export, and more. The Qtconsole is a very lightweight application that largely feels like a terminal, + but provides a number of enhancements only possible in a GUI, such as inline figures, proper multiline editing + with syntax highlighting, graphical calltips, and more.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From d4e39a0f515ef705a513c343528124a305538dff Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Dec 2023 14:31:30 +0100 Subject: [PATCH 2319/2365] Replace `parallel` by `maxparallel` The latter is the new, better option which makes it clear how it works with `--parallel` passed in the config or commandline. --- easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb | 2 +- .../easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb | 2 +- .../easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb | 2 +- .../easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb | 2 +- easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb | 2 +- easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb | 2 +- easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb | 2 +- easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb | 2 +- .../easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb | 2 +- easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb | 2 +- .../h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb | 2 +- .../h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb | 2 +- .../h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb | 2 +- .../h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb | 2 +- .../h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb | 2 +- .../h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb | 2 +- easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2020b.eb | 2 +- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb | 2 +- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb | 2 +- easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb | 2 +- easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb | 2 +- .../easyconfigs/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb | 2 +- easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb | 2 +- .../l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb | 2 +- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb | 2 +- .../l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb | 2 +- easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 2 +- .../n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb | 2 +- .../n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb | 2 +- .../n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb | 2 +- easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb | 2 +- easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb | 2 +- .../easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb | 2 +- .../t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb | 2 +- .../easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb | 2 +- .../w/WannierTools/WannierTools-2.5.1-intel-2020b.eb | 2 +- easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb | 2 +- 64 files changed, 64 insertions(+), 64 deletions(-) diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb index b06c4f9ab4..0c83158cf8 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('BWA', '0.7.17'), ] -parallel = 1 +maxparallel = 1 buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' buildopts += '&& make standalone CXX="$CXX" CXXFLAGS="$CXXFLAGS"' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb index 4934bcbe29..418c3a32ed 100644 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb @@ -27,6 +27,6 @@ sanity_check_paths = { 'dirs': ["include/apr-1"], } -parallel = 1 +maxparallel = 1 moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb index ef4cb6bb24..51520b0c75 100644 --- a/easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb @@ -13,7 +13,7 @@ sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] checksums = ['f20a0a021157d911bea06666911763b737c4ff38b39e793b8560f940fe391b8e'] buildopts = '-f makefile.lnx_ifort FFLAGS="$FFLAGS" LINK="-static-intel"' -parallel = 1 +maxparallel = 1 files_to_copy = [(['bader'], 'bin')] diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb index 978e186cf1..9f5fe72dfb 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb @@ -38,7 +38,7 @@ dependencies = [ configopts = '--enable-openmp ' -parallel = 1 +maxparallel = 1 sanity_check_paths = { 'files': ['bin/ctffind'], diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb index e32b7fad6c..bc7a3b0e4f 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb @@ -48,7 +48,7 @@ dependencies = [ configopts = " --with-hpdf=$EBROOTLIBHARU " # jemboss.jar does not build in a parallel build -parallel = 1 +maxparallel = 1 sanity_check_paths = { 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + diff --git a/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb b/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb index c9a3c391ab..510d8d37be 100644 --- a/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb +++ b/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb @@ -19,7 +19,7 @@ builddependencies = [ preconfigopts = './cleanup && ./bootstrap && ' -parallel = 1 +maxparallel = 1 sanity_check_paths = { 'files': ['lib/libEigenExa.%s' % x for x in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb b/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb index c1b6581087..551f52c847 100644 --- a/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb +++ b/easybuild/easyconfigs/e/Elk/Elk-7.0.12-foss-2020b.eb @@ -42,7 +42,7 @@ buildopts = 'all' runtest = 'test' -parallel = 1 +maxparallel = 1 files_to_copy = [( [ diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb index 39bd452716..e0ca399fda 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb @@ -27,7 +27,7 @@ builddependencies = [('pkg-config', '0.29.2')] dependencies = [('GLib', '2.66.1')] # parallel build fails -parallel = 1 +maxparallel = 1 sanity_check_paths = { 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb index d03c231209..c1affd1cd7 100644 --- a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb @@ -21,7 +21,7 @@ checksums = ['a4afb925d7ced8d083be12ca58911bb16d5348754e7c2f6431127138338ee02a'] unpack_options = '--strip-components=1' -parallel = 1 +maxparallel = 1 dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb b/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb index 2a62a4bc71..8e08523b89 100644 --- a/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb +++ b/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2020b.eb @@ -28,7 +28,7 @@ local_options = "-DFFTLIB_THREADSAFE " # use this when multiple threads access start_dir = 'src' -parallel = False +maxparallel = 1 build_cmd = "$CXX $CXXFLAGS -I../include -I$EBROOTFFTW/include %s -c fftlib.cpp -o fftlib.o" % local_options diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb index fc27032402..6e3b75a3c9 100644 --- a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb @@ -18,7 +18,7 @@ checksums = [ dependencies = [('Lua', '5.4.2')] -parallel = 1 +maxparallel = 1 local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' buildopts = 'liball %s' % local_comp_flags diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb index ffd6dc3cff..7ef6dccb66 100644 --- a/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb @@ -18,7 +18,7 @@ checksums = [ dependencies = [('Lua', '5.4.2')] -parallel = 1 +maxparallel = 1 local_comp_flags = 'VENDOR="intel" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' buildopts = 'liball %s' % local_comp_flags diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb index ca2a334a1a..197298d43e 100644 --- a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb @@ -33,7 +33,7 @@ prebuildopts = 'cd src &&' preinstallopts = 'cd src &&' -parallel = 1 +maxparallel = 1 modextravars = { "GLI_WSTYPE": "217", diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb index 1ccb3cd073..e549e59d5b 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb @@ -19,6 +19,6 @@ dependencies = [ ] # parallel build tends to fail -parallel = 1 +maxparallel = 1 moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb index 9f965a3a42..d1f966b463 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb @@ -27,6 +27,6 @@ buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FC=$FC CC=$CC ' buildopts += 'FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -fallow-argument-mismatch -I."' # parallel build tends to fail -parallel = 1 +maxparallel = 1 moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb index 795f421b23..25dd11aae6 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb @@ -50,6 +50,6 @@ extra_native_libs = [ ('zlib', 'lib*/libz.%s*' % SHLIB_EXT), ] -parallel = 1 +maxparallel = 1 moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb index 609faa926b..cf272d473d 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb @@ -23,7 +23,7 @@ dependencies = [ preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend +maxparallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend exts_list = [ ('cloudpickle', '1.5.0', { diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb index 32757cca2c..c318277eb4 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb @@ -23,7 +23,7 @@ dependencies = [ preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend +maxparallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend exts_list = [ ('cloudpickle', '1.6.0', { diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb index b4c2e230ac..fc64a6544d 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -23,7 +23,7 @@ dependencies = [ preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend +maxparallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend exts_list = [ ('cloudpickle', '1.6.0', { diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb index 5f3f66b801..475597d798 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -24,7 +24,7 @@ dependencies = [ preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend +maxparallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend exts_list = [ ('cloudpickle', '1.6.0', { diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb index 08775cbcd4..8d34023ef1 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -24,7 +24,7 @@ dependencies = [ preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend +maxparallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend exts_list = [ ('cloudpickle', '1.6.0', { diff --git a/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2020b.eb b/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2020b.eb index 9db2f7831f..9b368a912c 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2020b.eb @@ -18,7 +18,7 @@ checksums = ['9b58a4a7eef7c0c877513152340948402fd87cb06270d2d81308dc2ef740f4c7'] buildopts = 'all CC="$MPICC"' -parallel = 1 +maxparallel = 1 files_to_copy = [(['IMB-*'], 'bin')] diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index dc4310036d..30ad59c9e1 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -40,7 +40,7 @@ dependencies = [ ] # parallel build sometimes fails -parallel = 1 +maxparallel = 1 # modify all qmake pro files in order to pass CFLAGS local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&" diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index 4180e68700..61718b6104 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -43,7 +43,7 @@ dependencies = [ ] # parallel build sometimes fails -parallel = 1 +maxparallel = 1 # replace hardcoded CUDA compute capabilitites in machines/rhlinux. local_cuda_replace = 'echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb index 116f07001d..6f6d3ac31d 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb @@ -22,7 +22,7 @@ source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(versi sources = [SOURCELOWER_TAR_GZ] checksums = ['e195b7cf7ba42a90e5e112c0ed27894cd7ac864476dc5fb45ab169f5b930ea5a'] -parallel = 1 +maxparallel = 1 # The tests for the Bloom filter are statistical tests and can randomly fail, # they actually don't make a lot of sense diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb index 491b5541b7..fafcee6308 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb @@ -26,7 +26,7 @@ dependencies = [('HDF5', '1.10.7')] preconfigopts = "cd ../%(name)s-%(version)s/ext/htslib/ && autoreconf && cd - &&" -parallel = 1 +maxparallel = 1 separate_build_dir = True diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb index d57bbc1de7..b8b39f95ff 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb @@ -27,7 +27,7 @@ dependencies = [('HDF5', '1.10.7')] preconfigopts = "cd ../%(name)s-%(version)s/ext/htslib/ && autoreconf && cd - &&" configopts = '-DUSE_HDF5=ON' -parallel = 1 +maxparallel = 1 separate_build_dir = True diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb index a3d76ec464..12adff577b 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb @@ -28,7 +28,7 @@ dependencies = [ ('CMake', '3.18.4'), # Also needed to install models, thus not just a builddependency. ] -parallel = 1 +maxparallel = 1 modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb index 825a324d75..e2f93a06fe 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb @@ -28,7 +28,7 @@ dependencies = [ ('CMake', '3.18.4'), # Also needed to install models, thus not just a builddependency. ] -parallel = 1 +maxparallel = 1 modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' diff --git a/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb index 40c4ad0139..6128a9ac49 100644 --- a/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ checksums = ['c32bed5807000c0b7161c276e50d9ca0af0cb248df2c1affb2f6fc02471b51d0'] dependencies = [('binutils', '2.35')] # parallel build fails -parallel = 1 +maxparallel = 1 buildopts = "all" diff --git a/easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb index 1f09fb058e..991bb64101 100644 --- a/easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ dependencies = [ ('PCRE2', '10.35'), ] -parallel = 1 +maxparallel = 1 start_dir = 'src/nmath/standalone' diff --git a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb index 2823fc5897..ea4e98a511 100644 --- a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ('binutils', '2.35'), ] -parallel = 1 +maxparallel = 1 separate_build_dir = True diff --git a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb index c2da1b819d..4e37d805f1 100644 --- a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb @@ -27,7 +27,7 @@ dependencies = [ ('libbaseencode', '1.0.11'), ] -parallel = 1 +maxparallel = 1 separate_build_dir = True diff --git a/easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb index 60a3b0255b..49b562a9cb 100644 --- a/easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb @@ -28,6 +28,6 @@ sanity_check_paths = { 'dirs': [], } -parallel = 1 +maxparallel = 1 moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb index 507b4b404b..02a5143fe7 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb @@ -40,7 +40,7 @@ builddependencies = [ dependencies = [('libpng', '1.6.37')] -parallel = 1 +maxparallel = 1 sanity_check_paths = { 'files': ['lib/libhpdf.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb index f9a79031af..eb26611a6f 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -33,7 +33,7 @@ separate_build_dir = True local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" -parallel = 1 +maxparallel = 1 # make sure that built libraries (libmbd.so) in build directory are picked when running tests # this is required when RPATH linking is used diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb index f33ad17bec..b215da5eb6 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -33,7 +33,7 @@ separate_build_dir = True local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" -parallel = 1 +maxparallel = 1 # make sure that built libraries (libmbd.so) in build directory are picked when running tests # this is required when RPATH linking is used diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb index f93fd92279..d783490e21 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ('binutils', '2.35'), ] -parallel = 1 +maxparallel = 1 sanity_check_paths = { 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb index e9d1b83c72..414380e8b4 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb @@ -28,6 +28,6 @@ sanity_check_paths = { 'dirs': ['include'], } -parallel = 1 +maxparallel = 1 moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb index 46b4a89581..0df5335e2e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb @@ -31,7 +31,7 @@ builddependencies = [ separate_build_dir = True -parallel = 1 +maxparallel = 1 local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb index bd9018d08a..6253121a11 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb @@ -45,7 +45,7 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] -parallel = 1 +maxparallel = 1 # make sure that built libraries (libxc*.so*) in build directory are picked when running tests # this is required when RPATH linking is used diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb index 02f66c082a..70940c1854 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb @@ -29,7 +29,7 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] -parallel = 1 +maxparallel = 1 # make sure that built libraries (libxc*.so*) in build directory are picked when running tests # this is required when RPATH linking is used diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb index 311998a80a..5b2dc43c0a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb @@ -29,7 +29,7 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] -parallel = 1 +maxparallel = 1 # make sure that built libraries (libxc*.so*) in build directory are picked when running tests # this is required when RPATH linking is used diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb index 788e37ba40..771db93b9f 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb @@ -25,7 +25,7 @@ dependencies = [ ('METIS', '5.1.0'), ] -parallel = 1 +maxparallel = 1 # fix 'Type mismatch between actual argument' errors with GCC 10.x prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb index 2ccfcf5826..aa6dcc6644 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -25,7 +25,7 @@ dependencies = [ ('METIS', '5.1.0'), ] -parallel = 1 +maxparallel = 1 # fix 'Type mismatch between actual argument' errors with GCC 10.x prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb index 29f68f317f..a1e88b5290 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb @@ -31,7 +31,7 @@ dependencies = [ ] # makefile is not parallel safe -parallel = 1 +maxparallel = 1 sanity_check_paths = { 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb index 2ae4e5ed5c..e642d4a9c2 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb @@ -34,7 +34,7 @@ local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit inte buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' buildopts += 'INT=%s ' % local_intlength -parallel = 1 +maxparallel = 1 files_to_copy = ['bin', 'dox', 'man', 'tests'] diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 8e2acaccc7..110f64221c 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -28,7 +28,7 @@ dependencies = [ ] # building in parallel fails -parallel = 1 +maxparallel = 1 # fix for not being able to find header files buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" NSS_ENABLE_WERROR=0 ' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb index a4fe7306cb..423dff0c34 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb @@ -20,6 +20,6 @@ builddependencies = [ dependencies = [('netCDF', '4.7.4')] # (too) parallel build fails, but single-core build is fairly quick anyway (~1min) -parallel = 1 +maxparallel = 1 moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb index ca40c6a2e2..c9ca60d0c3 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb @@ -20,6 +20,6 @@ builddependencies = [ dependencies = [('netCDF', '4.7.4')] # (too) parallel build fails, but single-core build is fairly quick anyway (~1min) -parallel = 1 +maxparallel = 1 moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb index 47dc0efa8e..542fca7fe9 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb @@ -20,6 +20,6 @@ builddependencies = [ dependencies = [('netCDF', '4.7.4')] # (too) parallel build fails, but single-core build is fairly quick anyway (~1min) -parallel = 1 +maxparallel = 1 moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb index 02ccca5454..9583a55268 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb @@ -28,7 +28,7 @@ preconfigopts = 'sh autogen.sh && ' configopts = ['--enable-phyml', '--enable-phytime', '--enable-phyrex', '--enable-mpi '] -parallel = 1 +maxparallel = 1 sanity_check_paths = { 'files': ['bin/phyml', 'bin/phyml-mpi', 'bin/phyrex', 'bin/phytime'], diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb index f55d1c11a2..aa41fa1532 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb @@ -35,6 +35,6 @@ modextrapaths = { 'CPATH': ['qhull/include'], } -parallel = 1 +maxparallel = 1 moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb index 02147ccb84..77c0d57fbf 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb @@ -38,6 +38,6 @@ dependencies = [ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail -parallel = 1 +maxparallel = 1 moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb index 43a880080a..6679d48bea 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb @@ -41,6 +41,6 @@ dependencies = [ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail -parallel = 1 +maxparallel = 1 moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb index 81525546aa..3a7251eef1 100644 --- a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb @@ -30,6 +30,6 @@ sanity_check_paths = { 'dirs': [], } -parallel = 1 +maxparallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb index b1ec0ee6ab..3309a308a4 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb @@ -27,7 +27,7 @@ start_dir = 'source' buildopts = ' STAR && make STARlong' -parallel = 1 +maxparallel = 1 files_to_copy = [ (['source/STAR', 'source/STARlong'], 'bin'), diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb index 0b9214740f..6d5dc00b29 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb @@ -27,7 +27,7 @@ start_dir = 'source' buildopts = ' STAR && make STARlong' -parallel = 1 +maxparallel = 1 files_to_copy = [ (['source/STAR', 'source/STARlong'], 'bin'), diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb index 987c24ea99..318b4f0281 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb @@ -26,7 +26,7 @@ start_dir = 'source' buildopts = ' STAR && make STARlong' -parallel = 1 +maxparallel = 1 files_to_copy = [ (['source/STAR', 'source/STARlong'], 'bin'), diff --git a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb index fd54246780..c754973398 100644 --- a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb @@ -23,7 +23,7 @@ checksums = [ 'dd8f861d0b6307d1f020f57a080fcefb683ac79916cad484c429df950c223524', # TagDust-2.33_extern.patch ] -parallel = 1 +maxparallel = 1 builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb index 5e3929fa84..8b97539cf5 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb @@ -37,7 +37,7 @@ dependencies = [ preconfigopts = './autogen.sh && ' configopts = '--with-boost=$EBROOTBOOST' -parallel = 1 +maxparallel = 1 sanity_check_paths = { 'files': ['bin/%(namelower)s'], diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb index 1ee9adeaf3..765c13e793 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb @@ -39,6 +39,6 @@ sanity_check_paths = { 'dirs': ['share'], } -parallel = 1 +maxparallel = 1 moduleclass = 'phys' diff --git a/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb b/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb index 64d7016da8..52ef2ed493 100644 --- a/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb @@ -30,7 +30,7 @@ buildopts = '-f Makefile.intel-mpi F90FLAGS="$F90FLAGS -fpp -DMPI" ' installopts = '-f Makefile.intel-mpi PREFIX=%(installdir)s ' # No dependecies in the Makefile -parallel = 1 +maxparallel = 1 sanity_check_paths = { 'files': ['bin/wt.x'], diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb index 207a525546..e0adab5b26 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb @@ -27,7 +27,7 @@ dependencies = [ ('bwidget', '1.9.14'), ] -parallel = 1 +maxparallel = 1 prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" From 6a289e18339bc5f5fb7e24b9d9ce06c41df9459f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 10 Oct 2024 18:10:55 +0200 Subject: [PATCH 2320/2365] Fix flags for updated mesonninja easyblock --- easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb | 2 -- easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb | 2 +- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb | 2 +- 5 files changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb index 91ba9a2e47..eb70f8215e 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb @@ -28,7 +28,7 @@ dependencies = [ ('GLib', '2.66.1'), ] -configopts = "--buildtype=release --default-library=both " +configopts = "--default-library=both " configopts += "-Dintrospection=true " sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb index f57fb4074b..6cdb2634cf 100644 --- a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb @@ -45,8 +45,6 @@ preconfigopts += 'CPPFLAGS="-I${EBROOTMULTICHOOSE}/include/multichoose ${CPPFLAG # add missing linker flags for fastahack and smithwaterman preconfigopts += 'LDFLAGS="-lsw -lfastahack ${LDFLAGS}"' -configopts = "--buildtype release" - postinstallcmds = [ # add extra scripts "cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s/", diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb index f45c527ed4..70f37bb9e8 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb @@ -40,7 +40,7 @@ dependencies = [ # avoid using hardcoded path to Python binary in build step preconfigopts = "export PYTHON=python && " -configopts = "--buildtype=release --default-library=both " +configopts = "--default-library=both " fix_python_shebang_for = ['bin/*'] diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb index 84d0566473..a931bf0671 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('X11', '20201008'), ] -configopts = "--buildtype=release --default-library=both " +configopts = "--default-library=both " configopts += "-Dgio_sniffing=false -Dgir=true -Dman=false " sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb index 815a744fab..41c1257895 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('FriBidi', '1.0.10'), ] -configopts = "--buildtype=release --default-library=both " +configopts = "--default-library=both " sanity_check_paths = { 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, From 666ebaa0c1dc8d1cf76ff85cda82093a8cbc3097 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Sep 2024 12:36:11 +0200 Subject: [PATCH 2321/2365] Remove whitespace at EOL from ECs Run the following command: `autopep8 -i -a --select W291 --max-line-length 120 $(flake8 --filename '*.eb' --select W291 -j5 --format='%(path)s' | sort -u)` --- .../almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb | 4 ++-- .../artic-ncov2019-2021.06.24-foss-2020b.eb | 2 +- .../a/astropy/astropy-4.2.1-foss-2020b.eb | 4 ++-- .../a/astropy/astropy-4.2.1-intel-2020b.eb | 4 ++-- .../a/astropy/astropy-4.2.1-intelcuda-2020b.eb | 4 ++-- .../b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb | 2 +- .../b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb | 2 +- .../easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb | 10 +++++----- .../c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb | 2 +- .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb | 14 +++++++------- .../Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb | 2 +- .../cell2location-0.05-alpha-fosscuda-2020b.eb | 2 +- .../DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb | 4 ++-- .../d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb | 4 ++-- .../dune-core/dune-core-2.8.0.post1-foss-2020b.eb | 4 ++-- .../e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb | 2 +- .../easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb | 6 +++--- .../f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb | 6 +++--- .../f/futile/futile-1.8.3-foss-2020b.eb | 2 +- .../f/futile/futile-1.8.3-intel-2020b.eb | 2 +- .../g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb | 2 +- .../g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb | 2 +- .../g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb | 4 ++-- .../g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb | 6 +++--- .../g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb | 2 +- .../g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb | 2 +- .../g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb | 2 +- .../h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 4 ++-- .../h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb | 4 ++-- .../easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb | 4 ++-- .../i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 6 +++--- ...soNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 6 +++--- .../easyconfigs/i/iVar/iVar-1.3.1-GCC-10.2.0.eb | 2 +- .../i/igraph/igraph-0.8.5-foss-2020b.eb | 4 ++-- .../i/igraph/igraph-0.9.1-fosscuda-2020b.eb | 4 ++-- .../j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb | 6 +++--- .../easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 2 +- .../k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb | 4 ++-- .../libbaseencode-1.0.11-GCCcore-10.2.0.eb | 2 +- .../l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb | 2 +- .../l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb | 2 +- .../l/libmbd/libmbd-0.10.4-foss-2020b.eb | 10 +++++----- .../l/libmbd/libmbd-0.10.4-intel-2020b.eb | 10 +++++----- .../easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb | 2 +- .../m/MITObim/MITObim-1.9.1-foss-2020b.eb | 2 +- .../easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb | 2 +- .../m/MultiQC/MultiQC-1.10.1-foss-2020b.eb | 4 ++-- .../m/medaka/medaka-1.4.3-foss-2020b.eb | 2 +- .../m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb | 4 ++-- .../m/mrcfile/mrcfile-1.3.0-foss-2020b.eb | 10 +++++----- .../m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb | 10 +++++----- .../m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb | 4 ++-- .../easyconfigs/n/NFFT/NFFT-3.1.3-foss-2020b.eb | 6 +++--- .../n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb | 6 +++--- .../n/NTPoly/NTPoly-2.5.1-foss-2020b.eb | 4 ++-- .../n/NTPoly/NTPoly-2.5.1-intel-2020b.eb | 4 ++-- .../n/NTPoly/NTPoly-2.7.1-intel-2020b.eb | 4 ++-- .../o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb | 2 +- .../o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb | 2 +- .../OpenStackClient-5.5.0-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb | 4 ++-- .../p/PhyML/PhyML-3.3.20200621-foss-2020b.eb | 2 +- .../p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb | 2 +- .../p/PyMC3/PyMC3-3.11.1-intel-2020b.eb | 2 +- .../easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 4 ++-- .../Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb | 4 ++-- .../p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb | 4 ++-- .../plotly-orca-1.3.1-GCCcore-10.2.0.eb | 2 +- .../p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb | 2 +- .../p/pygraphviz/pygraphviz-1.7-foss-2020b.eb | 4 ++-- .../q/QTLtools/QTLtools-1.3.1-foss-2020b.eb | 2 +- .../r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb | 2 +- ...request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb | 2 +- .../s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb | 2 +- .../SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb | 2 +- .../s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb | 2 +- .../s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb | 4 ++-- .../s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb | 2 +- .../easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb | 2 +- .../easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb | 2 +- .../easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb | 2 +- .../s/Sibelia/Sibelia-3.0.7-foss-2020b.eb | 6 +++--- .../s/SuperLU/SuperLU-5.3.0-foss-2020b.eb | 2 +- .../s/SuperLU/SuperLU-5.3.0-intel-2020b.eb | 2 +- .../s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb | 2 +- .../s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb | 12 ++++++------ .../segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb | 12 ++++++------ .../easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb | 2 +- .../s/silx/silx-0.14.0-fosscuda-2020b.eb | 2 +- .../s/svist4get/svist4get-1.3.1-foss-2020b.eb | 4 ++-- easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 2 +- .../t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb | 2 +- .../easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb | 2 +- .../u/umap-learn/umap-learn-0.4.6-foss-2020b.eb | 4 ++-- .../umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb | 4 ++-- .../u/umap-learn/umap-learn-0.5.3-foss-2020b.eb | 4 ++-- .../u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb | 2 +- .../v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb | 4 ++-- .../vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb | 2 +- .../w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb | 4 ++-- .../w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb | 2 +- .../x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb | 12 ++++++------ .../z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb | 2 +- 105 files changed, 196 insertions(+), 196 deletions(-) diff --git a/easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb index 70063cf416..ea9607c100 100644 --- a/easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb @@ -5,8 +5,8 @@ version = '2.0.2' homepage = 'https://github.com/horta/almosthere' description = """Progress indicator C library. -ATHR is a simple yet powerful progress indicator library that works on Windows, -Linux, and macOS. It is non-blocking as the progress update is done via a +ATHR is a simple yet powerful progress indicator library that works on Windows, +Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index f473322e5c..ac69d69016 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -11,7 +11,7 @@ local_commit = 'b3f2dda5e6d95bc1c5d95a04d4ef37d304479477' version = '2021.06.24' homepage = "https://github.com/artic-network/artic-ncov2019" -description = """Initial implementation of an ARTIC bioinformatics platform +description = """Initial implementation of an ARTIC bioinformatics platform for nanopore sequencing of nCoV2019 novel coronavirus.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb index ab2fbb4268..05cea4d686 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb @@ -4,8 +4,8 @@ name = 'astropy' version = '4.2.1' homepage = 'https://www.astropy.org/' -description = """The Astropy Project is a community effort to develop -a single core package for Astronomy in Python and foster interoperability +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb index 08411ca88a..3f8dd88d7d 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb @@ -4,8 +4,8 @@ name = 'astropy' version = '4.2.1' homepage = 'https://www.astropy.org/' -description = """The Astropy Project is a community effort to develop -a single core package for Astronomy in Python and foster interoperability +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.""" toolchain = {'name': 'intel', 'version': '2020b'} diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb index 903e0674b3..296cbb27dc 100644 --- a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intelcuda-2020b.eb @@ -4,8 +4,8 @@ name = 'astropy' version = '4.2.1' homepage = 'https://www.astropy.org/' -description = """The Astropy Project is a community effort to develop -a single core package for Astronomy in Python and foster interoperability +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.""" toolchain = {'name': 'intelcuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb index 17f091c140..c0e967c4db 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb @@ -1,5 +1,5 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# +# # Author: Jonas Demeulemeester # The Francis Crick Insitute, London, UK diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb index d04a72ec26..087e109afd 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb @@ -1,5 +1,5 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# +# # Author: Jonas Demeulemeester # The Francis Crick Insitute, London, UK diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb index 6a056e1d19..9c383f87b5 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.6.4-GCC-10.2.0.eb @@ -4,11 +4,11 @@ name = 'Beast' version = '2.6.4' homepage = 'http://beast2.org' -description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular - sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using - strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies - but is also a framework for testing evolutionary hypotheses without conditioning on a single - tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. """ toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb index 4783f6bad6..0277630cc1 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb @@ -6,7 +6,7 @@ name = 'CD-HIT' version = '4.8.1' homepage = 'http://weizhongli-lab.org/cd-hit/' -description = """ CD-HIT is a very widely used program for clustering and +description = """ CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb index e49ddd7b1d..508660721a 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ dependencies = [('cURL', '7.72.0')] builddependencies = [('binutils', '2.35')] -# make would create just static libcfitsio.a. +# make would create just static libcfitsio.a. # Let's create dynamic lib and testprog too. buildopts = '&& make shared && make testprog' diff --git a/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb index 6aa0a88629..452e52e64c 100644 --- a/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CSB/CSB-1.2.5-foss-2020b.eb @@ -6,15 +6,15 @@ version = '1.2.5' homepage = 'https://github.com/csb-toolbox' description = """Computational Structural Biology Toolbox -CSB is a python library and application framework, which can be used to solve -problems in the field of structural bioinformatics. If you are a -bioinformatician, software engineer or a researcher working in this field, -chances are you may find something useful here. Our package consists of a few +CSB is a python library and application framework, which can be used to solve +problems in the field of structural bioinformatics. If you are a +bioinformatician, software engineer or a researcher working in this field, +chances are you may find something useful here. Our package consists of a few major components: -1. Core class library - object-oriented, granular, with an emphasis on design +1. Core class library - object-oriented, granular, with an emphasis on design and clean interfaces. -2. Application framework - console applications ("protocols"), which consume -objects from the core library in order to build something executable (and +2. Application framework - console applications ("protocols"), which consume +objects from the core library in order to build something executable (and hopefully useful). 3. Test framework - ensures that the library actually works. """ diff --git a/easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb b/easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb index f705159c83..7f05717089 100644 --- a/easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb @@ -7,7 +7,7 @@ name = 'Control-FREEC' version = '11.6' homepage = 'https://github.com/BoevaLab/FREEC' -description = """Copy number and genotype annotation from whole +description = """Copy number and genotype annotation from whole genome and whole exome sequencing data.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 2e6d9914d6..0d601f949a 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -7,7 +7,7 @@ version = '0.05-alpha' local_nodejsver = '-nodejs-12.19.0' homepage = 'https://github.com/BayraktarLab/cell2location/' -description = """Comprehensive mapping of tissue cell architecture via integrated +description = """Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)""" toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb index 96dff919eb..5187e2bd4d 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb @@ -14,8 +14,8 @@ version = '4.5.2' versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/DendroPy/' -description = """A Python library for phylogenetics and phylogenetic computing: -reading, writing, simulation, processing and manipulation of phylogenetic trees +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb index fee0868898..e26ef6250b 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb @@ -13,8 +13,8 @@ name = 'DendroPy' version = '4.5.2' homepage = 'https://pypi.python.org/pypi/DendroPy/' -description = """A Python library for phylogenetics and phylogenetic computing: -reading, writing, simulation, processing and manipulation of phylogenetic trees +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb index 46586020a2..c7a15bbfaf 100644 --- a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -4,8 +4,8 @@ name = 'dune-core' version = '2.8.0.post1' homepage = "https://www.dune-project.org/groups/core/" -description = """The Dune core modules build the stable basis of Dune. -They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. +description = """The Dune core modules build the stable basis of Dune. +They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. These modules build the foundation for higher-level components. """ diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb index 39bd452716..5ab021eb86 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb @@ -13,7 +13,7 @@ version = '2.4.0' homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' description = """ Exonerate is a generic tool for pairwise sequence comparison. - It allows you to align sequences using a many alignment models, using either + It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. """ toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb index 37d3a4ba76..adfae3f450 100644 --- a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-foss-2020b.eb @@ -4,9 +4,9 @@ name = 'FabIO' version = '0.11.0' homepage = 'http://www.silx.org' -description = """FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. -FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), -for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers +description = """FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. +FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), +for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats).""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb index 12a34b0c60..72f3553560 100644 --- a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb @@ -4,9 +4,9 @@ name = 'FabIO' version = '0.11.0' homepage = 'http://www.silx.org' -description = """FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. -FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), -for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers +description = """FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. +FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), +for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats).""" toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb index 3b00140697..36a7a5ac4e 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb @@ -5,7 +5,7 @@ version = '1.8.3' homepage = 'https://launchpad.net/futile' description = """ - The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules and wrapper that encapsulate the most common low-level operations of a Fortran code. """ diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb index a06c36e332..2a39fe6802 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb @@ -5,7 +5,7 @@ version = '1.8.3' homepage = 'https://launchpad.net/futile' description = """ - The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules and wrapper that encapsulate the most common low-level operations of a Fortran code. """ diff --git a/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb index 1031e4d395..1249ce4888 100644 --- a/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb @@ -5,7 +5,7 @@ version = '0.9.9.8' homepage = 'https://github.com/g-truc/glm' description = """ -OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb index 9a861968d8..1c4af51730 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb @@ -7,7 +7,7 @@ homepage = 'https://www.gnu.org/software/glpk/' description = """The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. - It is a set of routines written in ANSI C + It is a set of routines written in ANSI C and organized in the form of a callable library.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb index b8b3910444..ac7d832cd0 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb @@ -3,7 +3,7 @@ version = '10.7.1' homepage = 'https://geant4.cern.ch/' description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. - Its areas of application include high energy, nuclear and accelerator physics, + Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb index 890b1c101c..a7024a6c42 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb @@ -3,8 +3,8 @@ version = '9.1.1' homepage = 'https://www.gurobi.com' description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. -The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern -architectures and multi-core processors, using the most advanced implementations of the +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the latest algorithms.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb index c45a19e3d0..de4750866d 100644 --- a/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb @@ -6,14 +6,14 @@ version = '0.4.5' homepage = 'https://gemmi.readthedocs.io/' description = """ -Gemmi is a library, accompanied by a set of programs, developed primarily for +Gemmi is a library, accompanied by a set of programs, developed primarily for use in macromolecular crystallography (MX). For working with: macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files), refinement -restraints (CIF files), reflection data (MTZ and mmCIF formats), data on a 3D +restraints (CIF files), reflection data (MTZ and mmCIF formats), data on a 3D grid (electron density maps, masks, MRC/CCP4 format) crystallographic symmetry. Parts of this library can be useful in structural bioinformatics (for symmetry- -aware analysis of protein models), and in other molecular-structure sciences +aware analysis of protein models), and in other molecular-structure sciences that use CIF files (we have the fastest open-source CIF parser). """ diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb index 32893834e0..e6424a8a5c 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb @@ -4,7 +4,7 @@ easyblock = 'ConfigureMake' versionsuffix = '-egl' # available: -glx, -osmesa, -egl acc. to @Micket's suggestion: -# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and # offscreen), and OSMESA (offscreen software only). name = 'glew' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb index 083e28d457..2d7aeeae60 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb @@ -4,7 +4,7 @@ easyblock = 'ConfigureMake' versionsuffix = '-glx' # available: -glx, -osmesa, -egl acc. to @Micket's suggestion: -# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and # offscreen), and OSMESA (offscreen software only). name = 'glew' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb index cb58df1067..89901c2114 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb @@ -4,7 +4,7 @@ easyblock = 'ConfigureMake' versionsuffix = '-osmesa' # available: -glx, -osmesa, -egl acc. to @Micket's suggestion: -# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and # offscreen), and OSMESA (offscreen software only). name = 'glew' diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index 3eae6fe8e4..cf409c8474 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -20,8 +20,8 @@ name = 'HH-suite' version = '3.3.0' homepage = 'https://github.com/soedinglab/hh-suite' -description = """The HH-suite is an open-source software package -for sensitive protein sequence searching based on the pairwise +description = """The HH-suite is an open-source software package +for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).""" toolchain = {'name': 'gompi', 'version': '2020b'} diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb index 5e469b0e3d..76feb218e0 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb @@ -20,8 +20,8 @@ name = 'HH-suite' version = '3.3.0' homepage = 'https://github.com/soedinglab/hh-suite' -description = """The HH-suite is an open-source software package -for sensitive protein sequence searching based on the pairwise +description = """The HH-suite is an open-source software package +for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).""" toolchain = {'name': 'gompic', 'version': '2020b'} diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index dc4310036d..8e541dfffc 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -49,7 +49,7 @@ local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += local_exports = 'export QTDIR=$EBROOTQT5 &&' local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&' local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&' -# readw_or_imod.f and others with gfortran10: +# readw_or_imod.f and others with gfortran10: # Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2)) # => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0. local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&' # required for gfortran10 @@ -57,7 +57,7 @@ local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&' # requi preconfigopts = local_exports preconfigopts += local_qmake_pass_cflags -# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. +# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. # CFLAGs are passed with -flags. configure_cmd = './setup ' configure_cmd += '-flags "$CFLAGS" ' # inject CFLAGS diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index 4180e68700..e78dafd95f 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -45,7 +45,7 @@ dependencies = [ # parallel build sometimes fails parallel = 1 -# replace hardcoded CUDA compute capabilitites in machines/rhlinux. +# replace hardcoded CUDA compute capabilitites in machines/rhlinux. local_cuda_replace = 'echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|' local_cuda_replace += ' awk \'{' local_cuda_replace += ' printf "-arch sm_"$1; ' @@ -61,7 +61,7 @@ local_exports = 'export QTDIR=$EBROOTQT5 &&' local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&' local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&' local_exports += 'export CUDA_DIR=$CUDA_HOME &&' -# readw_or_imod.f and others with gfortran10: +# readw_or_imod.f and others with gfortran10: # Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2)) # => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0. local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&' # required for gfortran10 @@ -70,7 +70,7 @@ preconfigopts = local_exports preconfigopts += local_cudaarch_sed preconfigopts += local_qmake_pass_cflags -# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. +# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. # CFLAGs are passed with -flags. configure_cmd = './setup ' configure_cmd += '-flags "$CFLAGS" ' # inject CFLAGS diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 57d730009e..52512fdf4b 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -12,9 +12,9 @@ version = '%s_%s_%s_%s' % (local_version, local_commit_date, local_commit_count, homepage = 'https://github.com/Heng-Z/IsoNet' description = """IsoNet stands for for ISOtropic reconstructioN of Electron Tomography. It trains deep convolutional neural networks to reconstruct meaningful contents in the mis -sing wedge for electron tomography, and to increase signal-to-noise ratio, -using the information learned from the original tomogram. The software requires -tomograms as input. Observing at about 30A resolution, the IsoNet generated +sing wedge for electron tomography, and to increase signal-to-noise ratio, +using the information learned from the original tomogram. The software requires +tomograms as input. Observing at about 30A resolution, the IsoNet generated tomograms are largely isotropic.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/i/iVar/iVar-1.3.1-GCC-10.2.0.eb b/easybuild/easyconfigs/i/iVar/iVar-1.3.1-GCC-10.2.0.eb index 9ff54171ea..c254db7175 100644 --- a/easybuild/easyconfigs/i/iVar/iVar-1.3.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/i/iVar/iVar-1.3.1-GCC-10.2.0.eb @@ -15,7 +15,7 @@ version = '1.3.1' homepage = 'https://github.com/andersen-lab/ivar' description = """ iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. -""" +""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb index 098e05b12a..0177350f16 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.8.5-foss-2020b.eb @@ -4,8 +4,8 @@ name = 'igraph' version = '0.8.5' homepage = 'https://igraph.org' -description = """igraph is a collection of network analysis tools with the emphasis on -efficiency, portability and ease of use. igraph is open source and free. igraph can be +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.9.1-fosscuda-2020b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.9.1-fosscuda-2020b.eb index 28cd22238a..8a232120a0 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.9.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.9.1-fosscuda-2020b.eb @@ -6,8 +6,8 @@ name = 'igraph' version = '0.9.1' homepage = 'https://igraph.org' -description = """igraph is a collection of network analysis tools with the emphasis on -efficiency, portability and ease of use. igraph is open source and free. igraph can be +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb index 116f07001d..77b868b048 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb @@ -1,8 +1,8 @@ ## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia # Homepage: https://staff.flinders.edu.au/research/deep-thought # -# Authors:: Robert Qiao +# Authors:: Robert Qiao # License:: GPLv3.0 # # Notes:: @@ -24,7 +24,7 @@ checksums = ['e195b7cf7ba42a90e5e112c0ed27894cd7ac864476dc5fb45ab169f5b930ea5a'] parallel = 1 -# The tests for the Bloom filter are statistical tests and can randomly fail, +# The tests for the Bloom filter are statistical tests and can randomly fail, # they actually don't make a lot of sense runtest = "check GTEST_FILTER=-'*Bloom*'" diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index bc3e0480ec..f99474f1c5 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -5,7 +5,7 @@ easyblock = 'PythonBundle' name = 'jax' version = '0.2.19' homepage = 'https://pypi.python.org/pypi/jax' -description = """Composable transformations of Python+NumPy programs: +description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb index 4838f91cda..9bd5a84885 100644 --- a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb @@ -1,6 +1,6 @@ # Contribution from the Crick HPC team # uploaded by J. Sassmannshausen -# this is a bug fix to make sure the symlinks in bin are not getting destroyed +# this is a bug fix to make sure the symlinks in bin are not getting destroyed # by Easybuild when it is tidying up # This build also links updateTaxonomy.sh and updateAccessions.sh in the bin folder # so users can install their own Taxonomy database @@ -11,7 +11,7 @@ name = 'KronaTools' version = '2.8' homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' -description = """Krona Tools is a set of scripts to create Krona charts from +description = """Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb index 2823fc5897..d8dfa0a2c7 100644 --- a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb @@ -8,7 +8,7 @@ name = 'libbaseencode' version = '1.0.11' homepage = 'https://github.com/paolostivanin/libbaseencode' -description = """Library written in C for encoding and decoding +description = """Library written in C for encoding and decoding data using base32 or base64 according to RFC-4648""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb index d7da6e3a9e..5deaf391f9 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb @@ -29,7 +29,7 @@ osdependencies = [OS_PKG_IBVERBS_DEV] # Disable deprecated "sockets" provider configopts = "--disable-sockets " -# Disable usNIC provider by default as this requires specific osdependencies +# Disable usNIC provider by default as this requires specific osdependencies # If you want to enable this provider you need to uncomment the following line: # osdependencies.append(('libnl3-devel', 'libnl3-dev')) configopts += "--disable-usnic " diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb index bee537ec24..53c4550ea8 100644 --- a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb @@ -1,6 +1,6 @@ # Contribution from the NIHR Biomedical Research Centre # Guy's and St Thomas' NHS Foundation Trust and King's College London -# based on libgcrypt-1.8.5-GCCcore-8.3.0.eb +# based on libgcrypt-1.8.5-GCCcore-8.3.0.eb # uploaded by J. Sassmannshausen diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb index f9a79031af..54e3b5af45 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -7,15 +7,15 @@ homepage = 'https://libmbd.github.io/index.html' description = """ Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - - The Fortran implementation is the reference, most advanced implementation, with support for analytical - gradients and distributed parallelism, and additional functionality beyond the MBD method itself. - It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. -The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. """ diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb index f33ad17bec..c687ad0f0e 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -7,15 +7,15 @@ homepage = 'https://libmbd.github.io/index.html' description = """ Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - - The Fortran implementation is the reference, most advanced implementation, with support for analytical - gradients and distributed parallelism, and additional functionality beyond the MBD method itself. - It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. -The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. """ diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb index b30c960112..e192b5b004 100644 --- a/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb @@ -4,7 +4,7 @@ name = 'lz4' version = '1.9.2' homepage = 'https://lz4.github.io/lz4/' -description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb b/easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb index 6711cda43d..283dde5a2d 100644 --- a/easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb @@ -5,7 +5,7 @@ version = '1.9.1' homepage = "https://github.com/chrishah/MITObim" description = """The MITObim procedure (mitochondrial baiting and iterative mapping) represents - a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms + a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb index ba802ba558..9c3d7a9f59 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb @@ -2,7 +2,7 @@ name = 'MPICH' version = '3.3.2' homepage = 'https://www.mpich.org/' -description = """MPICH is a high-performance and widely portable implementation +description = """MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb index 1f38d2c832..9dee95e4e4 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb @@ -3,7 +3,7 @@ # The Francis Crick Institute # Elements derived from work by Pablo Escobar # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics # Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. # See: https://click.palletsprojects.com/en/7.x/python3/ @@ -14,7 +14,7 @@ name = 'MultiQC' version = '1.10.1' homepage = 'https://multiqc.info' -description = """Aggregate results from bioinformatics analyses across many samples into a single +description = """Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 5fe1f8f7b4..5859e4cb68 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -20,7 +20,7 @@ builddependencies = [('Autotools', '20200321')] dependencies = [ ('Python', '3.8.6'), # includes cffi # TensorFlow 2.2.3 required by medaka 1.4.3, see requirements.txt - # We need to patch medaka to use that version, see below. + # We need to patch medaka to use that version, see below. ('TensorFlow', '2.2.3'), ('Biopython', '1.78'), # Pysam 0.16.0.1 is strictly required, see requirements.txt diff --git a/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb index d692be29e5..06408c9c90 100644 --- a/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb @@ -6,8 +6,8 @@ version = '1.0.0' homepage = 'https://mmtf.rcsb.org/' description = """ -The Macromolecular Transmission Format (MMTF) is a new compact binary format to -transmit and store biomolecular structures for fast 3D visualization and +The Macromolecular Transmission Format (MMTF) is a new compact binary format to +transmit and store biomolecular structures for fast 3D visualization and analysis. """ diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb index 0cbc428952..c60ba7e918 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb @@ -3,15 +3,15 @@ easyblock = 'PythonPackage' name = 'mrcfile' version = '1.3.0' homepage = 'https://github.com/ccpem/mrcfile' -description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in +description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. -It allows MRC files to be created and opened easily using a very simple API, -which exposes the file’s header and data as numpy arrays. The code runs in +It allows MRC files to be created and opened easily using a very simple API, +which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard- compliant MRC files in Python as easily as possible, and with no dependencies on -any compiled libraries except numpy. You can use it interactively to inspect -files, correct headers and so on, or in scripts and larger software packages to +any compiled libraries except numpy. You can use it interactively to inspect +files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions. """ toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb index 679837b053..ede48f5e30 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb @@ -3,15 +3,15 @@ easyblock = 'PythonPackage' name = 'mrcfile' version = '1.3.0' homepage = 'https://github.com/ccpem/mrcfile' -description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in +description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. -It allows MRC files to be created and opened easily using a very simple API, -which exposes the file’s header and data as numpy arrays. The code runs in +It allows MRC files to be created and opened easily using a very simple API, +which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard- compliant MRC files in Python as easily as possible, and with no dependencies on -any compiled libraries except numpy. You can use it interactively to inspect -files, correct headers and so on, or in scripts and larger software packages to +any compiled libraries except numpy. You can use it interactively to inspect +files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions. """ toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb index 73c851471f..c85cf60f99 100644 --- a/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb @@ -6,8 +6,8 @@ version = '3.3.0' homepage = 'http://msgpack.org/' description = """MessagePack is an efficient binary serialization format, which lets you exchange -data among multiple languages like JSON, except that it's faster and smaller. -Small integers are encoded into a single byte while typical short strings +data among multiple languages like JSON, except that it's faster and smaller. +Small integers are encoded into a single byte while typical short strings require only one extra byte in addition to the strings themselves.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-foss-2020b.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-foss-2020b.eb index 600e4ec0ab..011d4f4624 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-foss-2020b.eb @@ -3,9 +3,9 @@ name = 'NFFT' version = '3.1.3' homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' -description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier -transform) is a C subroutine library for computing the nonequispaced -discrete Fourier transform (NDFT) and its generalisations in one or more +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier +transform) is a C subroutine library for computing the nonequispaced +discrete Fourier transform (NDFT) and its generalisations in one or more dimensions, of arbitrary input size, and of complex data.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb index 2d7c67fc27..4550457df6 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb @@ -3,9 +3,9 @@ name = 'NFFT' version = '3.1.3' homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' -description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier -transform) is a C subroutine library for computing the nonequispaced -discrete Fourier transform (NDFT) and its generalisations in one or more +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier +transform) is a C subroutine library for computing the nonequispaced +discrete Fourier transform (NDFT) and its generalisations in one or more dimensions, of arbitrary input size, and of complex data.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb index 40c8715239..f2706a745d 100644 --- a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb @@ -4,8 +4,8 @@ name = 'NTPoly' version = '2.5.1' homepage = 'https://github.com/william-dawson/NTPoly' -description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on -polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions in NTPoly can be computed in linear time.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb index b7e6e5f85e..e6a73c74e3 100644 --- a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb @@ -4,8 +4,8 @@ name = 'NTPoly' version = '2.5.1' homepage = 'https://github.com/william-dawson/NTPoly' -description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on -polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions in NTPoly can be computed in linear time.""" toolchain = {'name': 'intel', 'version': '2020b'} diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb index 09ce90d741..1aca5fd3cf 100644 --- a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb @@ -4,8 +4,8 @@ name = 'NTPoly' version = '2.7.1' homepage = 'https://github.com/william-dawson/NTPoly' -description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on -polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions in NTPoly can be computed in linear time.""" toolchain = {'name': 'intel', 'version': '2020b'} diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb index d0d18bc3a0..153e0299b7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb @@ -31,7 +31,7 @@ dependencies = [ # disable MPI1 compatibility for now, see what breaks... # configopts = '--enable-mpi1-compatibility ' -# to enable SLURM integration use e.g. --try-amend="configopts=--with-slurm" +# to enable SLURM integration use e.g. --try-amend="configopts=--with-slurm" # configopts = '--with-slurm --with-pmi=/usr --with-pmi-libdir=/usr/lib64' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb index b233ee7281..ea54770e27 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ version = '1.1.1h' homepage = 'https://www.openssl.org/' description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, - and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb index c14c203d7e..5927a9835b 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -6,7 +6,7 @@ version = '5.5.0' homepage = 'https://docs.openstack.org/python-openstackclient/latest/' description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the -command set for Compute, Identity, Image, Network, Object Store and Block +command set for Compute, Identity, Image, Network, Object Store and Block Storage APIs together in a single shell with a uniform command structure.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb index ee59ac1eae..87a94a348d 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb @@ -9,8 +9,8 @@ name = 'PRANK' version = '170427' homepage = 'http://wasabiapp.org/software/prank/' -description = """ PRANK is a probabilistic multiple alignment program for DNA, - codon and amino-acid sequences. PRANK is based on a novel algorithm that treats +description = """ PRANK is a probabilistic multiple alignment program for DNA, + codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb index 02ccca5454..79852e030e 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics # Updated to version 3.3.20200621 # J. Sassmannshausen (GSTT/NHS) diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb index 21449c04d5..a62733510b 100644 --- a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb @@ -6,7 +6,7 @@ name = 'PyMC3' version = '3.11.1' homepage = 'https://docs.pymc.io/' -description = """Probabilistic Programming in Python: +description = """Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano""" toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb index 890f1ea942..9da8425123 100644 --- a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb @@ -7,7 +7,7 @@ name = 'PyMC3' version = '3.11.1' homepage = 'https://docs.pymc.io/' -description = """Probabilistic Programming in Python: +description = """Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano""" toolchain = {'name': 'intel', 'version': '2020b'} diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb index 017acd4449..da23337767 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -5,9 +5,9 @@ version = '2.5.0' homepage = 'https://github.com/schrodinger/pymol-open-source' description = """ -PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D +PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. -It also includes molecular editing, ray tracing, and movies. Open Source PyMOL +It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone! """ diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb index 9877aa9b6f..7a71f6aeeb 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics # 0.9.1.4: # Modified by: Adam Huffman # The Francis Crick Institute @@ -15,7 +15,7 @@ version = '0.16.0.1' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/pysam-developers/pysam' -description = """Pysam is a python module for reading and manipulating Samfiles. +description = """Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb index f3859c5755..3729fe4b2d 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics # 0.9.1.4: # Modified by: Adam Huffman # The Francis Crick Institute @@ -14,7 +14,7 @@ name = 'Pysam' version = '0.16.0.1' homepage = 'https://github.com/pysam-developers/pysam' -description = """Pysam is a python module for reading and manipulating Samfiles. +description = """Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-10.2.0.eb index 6815d1259d..5131a11ee7 100644 --- a/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-10.2.0.eb @@ -7,7 +7,7 @@ name = 'plotly-orca' version = '1.3.1' homepage = 'https://github.com/plotly/orca' -description = """Orca is an Electron app that generates images and reports of Plotly things like +description = """Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb index 9eddf8c8ef..c3601acf52 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -1,6 +1,6 @@ # include patch to fix failing test jobs due to additional white space # see https://github.com/pybind/pybind11/issues/3680 -# Authors: J. Sassmannshausen / Alexander Grund +# Authors: J. Sassmannshausen / Alexander Grund name = 'pybind11' version = '2.6.0' diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb index a2dfa4a36a..1be2410d55 100644 --- a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb @@ -4,8 +4,8 @@ name = 'pygraphviz' version = '1.7' homepage = 'https://pygraphviz.github.io/' -description = """PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. -With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz +description = """PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. +With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb index e71d826080..58dc2a8e8b 100644 --- a/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb @@ -9,7 +9,7 @@ version = '1.3.1' homepage = "https://qtltools.github.io/qtltools/" description = """QTLtools is a tool set for molecular QTL discovery and analysis. -It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) +It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb index a29ce5a975..2f0f3a144e 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb @@ -1,6 +1,6 @@ # EasyBuild easyconfig # -# Contributed from Fred Hutchinson Cancer Research Center, Seattle WA, US +# Contributed from Fred Hutchinson Cancer Research Center, Seattle WA, US # John Dey jfdey@fredhutch.org # easyblock = 'CMakeMake' diff --git a/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb b/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb index a7e257c4ff..a19833b9b3 100644 --- a/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb +++ b/easybuild/easyconfigs/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb @@ -8,7 +8,7 @@ local_nodejsver = '12.19.0' versionsuffix = '-nodejs-%s' % local_nodejsver homepage = 'https://github.com/request/request/' -description = """Request is designed to be the simplest way possible to make http calls. +description = """Request is designed to be the simplest way possible to make http calls. It supports HTTPS and follows redirects by default.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb index 9fd7bf2d7a..735d3fa7c1 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb @@ -12,7 +12,7 @@ name = 'SAMtools' version = '1.11' homepage = 'https://www.htslib.org/' -description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb index 1c73a42bfa..39a2d0ca01 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb @@ -12,7 +12,7 @@ name = 'SAMtools' version = '1.11' homepage = 'https://www.htslib.org/' -description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.""" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb index 4501b991b2..5d5ff21de9 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb @@ -12,7 +12,7 @@ name = 'SAMtools' version = '1.12' homepage = 'https://www.htslib.org/' -description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb index 020040b808..e1bb43fce3 100644 --- a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb @@ -6,7 +6,7 @@ version = '3.0.0' homepage = 'https://simplecryoem.com/' description = """Single-particle IMage Processing Linux Engine SIMPLE is an open-source software -package for analysis of cryogenic transmission electron microscopy (cryo-EM) +package for analysis of cryogenic transmission electron microscopy (cryo-EM) movies of single-particles (Single-Particle Analysis, SPA).""" toolchain = {'name': 'foss', 'version': '2020b'} @@ -23,7 +23,7 @@ dependencies = [ ('LibTIFF', '4.1.0'), ('jbigkit', '2.1'), ] -# Avoid using problematic FindOpenMP_Fortran.cmake; +# Avoid using problematic FindOpenMP_Fortran.cmake; # Instead OpenMP_Fortran_FLAGS will be set in configopts. preconfigopts = 'sed -i "s/unset (OpenMP_Fortran_FLAGS CACHE)/#&/g" ../*/cmake/Modules/ZSetParallelLibrary.cmake &&' diff --git a/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb index 6767efd60c..09eb61a850 100644 --- a/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb @@ -5,7 +5,7 @@ version = '20190603' _commit = 'daf76ba' homepage = 'https://korflab.github.io/' -description = """SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. +description = """SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb index b1ec0ee6ab..2adade16b5 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb @@ -1,6 +1,6 @@ # Contribution from the NIHR Biomedical Research Centre # Guy's and St Thomas' NHS Foundation Trust and King's College London -# Based on STAR-2.7.3a-GCC-8.3.0.eb +# Based on STAR-2.7.3a-GCC-8.3.0.eb # uploaded by J. Sassmannshausen diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb index 0b9214740f..610184133c 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb @@ -1,6 +1,6 @@ # Contribution from the NIHR Biomedical Research Centre # Guy's and St Thomas' NHS Foundation Trust and King's College London -# Based on STAR-2.7.3a-GCC-8.3.0.eb +# Based on STAR-2.7.3a-GCC-8.3.0.eb # uploaded by J. Sassmannshausen diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb index 987c24ea99..842eda34ac 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb @@ -1,6 +1,6 @@ # Contribution from the NIHR Biomedical Research Centre # Guy's and St Thomas' NHS Foundation Trust and King's College London -# Based on STAR-2.7.7a-GCC-10.2.0.eb +# Based on STAR-2.7.7a-GCC-10.2.0.eb # uploaded by J. Sassmannshausen easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb b/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb index 4ee05dcdc0..fbc2e24bc0 100644 --- a/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb @@ -4,9 +4,9 @@ name = 'Sibelia' version = '3.0.7' homepage = 'http://bioinf.spbau.ru/en/%(namelower)s' -description = """Sibelia: A comparative genomics tool: It assists biologists in analysing - the genomic variations that correlate with pathogens, or the genomic changes that help - microorganisms adapt in different environments. Sibelia will also be helpful for the +description = """Sibelia: A comparative genomics tool: It assists biologists in analysing + the genomic variations that correlate with pathogens, or the genomic changes that help + microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb index 41d145da7e..cc945eb512 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb @@ -2,7 +2,7 @@ name = 'SuperLU' version = '5.3.0' homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb index 2328a04942..8504a4cba5 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb @@ -2,7 +2,7 @@ name = 'SuperLU' version = '5.3.0' homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb index cc04b3f897..d70754c056 100644 --- a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb @@ -1,6 +1,6 @@ # easybuild easyconfig # -# John Dey jfdey@fredhutch.org fizwit@github.com +# John Dey jfdey@fredhutch.org fizwit@github.com easyblock = 'MakeCp' name = 'samblaster' diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb index 80454f74e0..4cbca7d3c1 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb @@ -4,12 +4,12 @@ name = 'segemehl' version = '0.3.4' homepage = 'https://www.bioinf.uni-leipzig.de/Software/segemehl/' -description = """segemehl is a software to map short sequencer reads to reference genomes. - Unlike other methods, segemehl is able to detect not only mismatches but also insertions - and deletions. Furthermore, segemehl is not limited to a specific read length and is able - to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching - strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads - gziped queries to save both disk and memory space and allows bisulfite sequencing mapping +description = """segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb index e9ae1cd887..8e58b77ae0 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb @@ -4,12 +4,12 @@ name = "segemehl" version = "0.3.4" homepage = 'https://www.bioinf.uni-leipzig.de/Software/segemehl/' -description = """segemehl is a software to map short sequencer reads to reference genomes. - Unlike other methods, segemehl is able to detect not only mismatches but also insertions - and deletions. Furthermore, segemehl is not limited to a specific read length and is able - to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching - strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads - gziped queries to save both disk and memory space and allows bisulfite sequencing mapping +description = """segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.""" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} diff --git a/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb index 57260d097c..b7fdd41233 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.14.0-foss-2020b.eb @@ -4,7 +4,7 @@ name = 'silx' version = '0.14.0' homepage = "http://www.silx.org/" -description = """The silx project provides a collection of Python packages to support the +description = """The silx project provides a collection of Python packages to support the development of data assessment, reduction and analysis applications at synchrotron radiation facilities.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb index 47a36d0354..9dc87add1b 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb @@ -4,7 +4,7 @@ name = 'silx' version = '0.14.0' homepage = "http://www.silx.org/" -description = """The silx project provides a collection of Python packages to support the +description = """The silx project provides a collection of Python packages to support the development of data assessment, reduction and analysis applications at synchrotron radiation facilities.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index 05d97fb731..3656ed6804 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -6,8 +6,8 @@ name = 'svist4get' version = '1.3.1' homepage = 'https://github.com/art-egorov/svist4get' -description = """Svist4get is a simple bioinformatics tool for visualization of -genomic signal tracks in user-defined genomic windows, either arbitrary selected +description = """Svist4get is a simple bioinformatics tool for visualization of +genomic signal tracks in user-defined genomic windows, either arbitrary selected by genomic coordinates or anchored to particular transcripts or genes.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb index 3d91b35cbf..1fa2407bbb 100644 --- a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -7,7 +7,7 @@ version = '1.0' homepage = 'https://github.com/jenhantao/tba' description = """TBA (a Transcription factor Binding Analysis): -TBA is a multi-functional machine learning tool for identifying +TBA is a multi-functional machine learning tool for identifying transcription factors associated with genomic features""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb index b140b09b63..08129698d7 100644 --- a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -6,7 +6,7 @@ name = 'TOBIAS' version = '0.14.0' homepage = 'https://github.com/loosolab/TOBIAS' -description = """TOBIAS is a collection of command-line bioinformatics tools +description = """TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb b/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb index 3c336471f3..13dbafb70c 100644 --- a/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb +++ b/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb @@ -4,7 +4,7 @@ name = 'UShER' version = '0.4.1' homepage = 'https://github.com/yatisht/usher' -description = """UShER is now a package consisting of a family of programs for +description = """UShER is now a package consisting of a family of programs for rapid phylogenetic analyses, particularly suitable for the SARS-CoV-2 genomes.""" toolchain = {'name': 'gompi', 'version': '2020b'} diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb index 5249d3e47c..42b0ba96af 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb @@ -6,8 +6,8 @@ name = 'umap-learn' version = '0.4.6' homepage = 'https://pypi.org/project/umap-learn/' -description = """Uniform Manifold Approximation and Projection (UMAP) is a -dimension reduction technique that can be used for visualisation similarly to t-SNE, +description = """Uniform Manifold Approximation and Projection (UMAP) is a +dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb index af8a0366f2..292ef5cd39 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb @@ -6,8 +6,8 @@ name = 'umap-learn' version = '0.4.6' homepage = 'https://pypi.org/project/umap-learn/' -description = """Uniform Manifold Approximation and Projection (UMAP) is a -dimension reduction technique that can be used for visualisation similarly to t-SNE, +description = """Uniform Manifold Approximation and Projection (UMAP) is a +dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb index de5c3745c4..be1b827f91 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb @@ -9,8 +9,8 @@ version = '0.5.3' homepage = 'https://umap-learn.readthedocs.io/en/latest/' description = """ -Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique -that can be used for visualisation similarly to t-SNE, but also for general non-linear +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique +that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction. """ diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb index 7b350bf610..280230633a 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb @@ -4,7 +4,7 @@ name = 'utf8proc' version = '2.5.0' homepage = 'https://github.com/JuliaStrings/utf8proc' -description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb index faf8ac8607..4f24e03b47 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb @@ -4,8 +4,8 @@ name = 'VCFtools' version = '0.1.16' homepage = "https://vcftools.github.io" -description = """The aim of VCFtools is to provide - easily accessible methods for working with complex +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex genetic variation data in the form of VCF files.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb index aef3494ecb..04e98360f2 100644 --- a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb @@ -6,7 +6,7 @@ version = '0.0.1' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/cc2qe/vawk' -description = """An awk-like VCF parser +description = """An awk-like VCF parser """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb index e0b1909d58..55747ac92b 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb @@ -4,8 +4,8 @@ buildtype = 'dmpar' versionsuffix = '-%s' % buildtype homepage = 'http://www.wrf-model.org' -description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is - a next-generation mesoscale numerical weather prediction system designed to serve both operational +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb index 90a7f361f2..6e3ea0c67a 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb @@ -49,7 +49,7 @@ preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext configopts = '--enable-intl --enable-ipv6 ' # Options required by wxPython configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' -# Note: the configure step might claim to find OpenGL headers in +# Note: the configure step might claim to find OpenGL headers in # /usr/include, but it will still use the ones from the Mesa dependency above configopts += '--with-opengl ' configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb index efe8235a51..b74cb1a349 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -8,17 +8,17 @@ version = '1-1-b59' homepage = 'https://www.census.gov/data/software/x13as.About_X-13.html' description = """ -X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, +X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, and maintained by the Census Bureau. Features of X-13ARIMA-SEATS include: - - Extensive time series modeling and model selection capabilities for + - Extensive time series modeling and model selection capabilities for linear regression models with ARIMA errors (regARIMA models); - - The capability to generate ARIMA model-based seasonal adjustment - using a version of the SEATS software originally developed by Victor - Gómez and Agustín Maravall at the Bank of Spain, as well as nonparametric + - The capability to generate ARIMA model-based seasonal adjustment + using a version of the SEATS software originally developed by Victor + Gómez and Agustín Maravall at the Bank of Spain, as well as nonparametric adjustments from the X-11 procedure; - - Diagnostics of the quality and stability of the adjustments + - Diagnostics of the quality and stability of the adjustments achieved under the options selected; - The ability to efficiently process many series at once. """ diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb index af251418ce..ad7e1f5e18 100644 --- a/easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb @@ -4,7 +4,7 @@ name = 'zstd' version = '1.4.5' homepage = 'https://facebook.github.io/zstd' -description = """Zstandard is a real-time compression algorithm, providing high compression ratios. +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.""" From 8076eed00be0b58aa7083ef94b5bbcff0d024953 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 6 Nov 2024 18:25:25 +0100 Subject: [PATCH 2322/2365] Update libvdwxc webpage as old URL has been taken over by evildoers. --- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb index 9dee6b6ef2..0e414c5d72 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb index 751488a072..a610d3ec77 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" From 8069089c02f2cb4e9e71e648b9f84a20cf45838d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 19 Dec 2024 19:08:15 +0100 Subject: [PATCH 2323/2365] Fix TCLLIBPATH delimiter to use spaces instead of : --- .../easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb | 2 +- .../g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb index 14d2aeee87..da0ad0bb0a 100644 --- a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Tk', '8.6.10')] -modextrapaths = {'TCLLIBPATH': '.'} +modextrapaths = {'TCLLIBPATH': {'path': '', 'delimiter': ' '} sanity_check_paths = { 'files': ['button.tcl'], diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb index 740e71bf49..b5f2ab9ada 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb @@ -85,7 +85,7 @@ modextrapaths = { 'CLASSPATH': 'lib/graphviz/java', 'LD_LIBRARY_PATH': 'lib/graphviz/java', 'PYTHONPATH': 'lib/graphviz/python%s' % local_pyver_major, - 'TCLLIBPATH': 'lib/graphviz/tcl', + 'TCLLIBPATH': {'path': 'lib/graphviz/tcl', 'delimiter': ' '}, } moduleclass = 'vis' From d670781ba4f34315d036b4bf3bd5ad572ca378b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 19 Dec 2024 19:09:14 +0100 Subject: [PATCH 2324/2365] Add missing TCLLIBPATH to Tk, fix missing brace --- .../easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb index da0ad0bb0a..9353b81cc5 100644 --- a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Tk', '8.6.10')] -modextrapaths = {'TCLLIBPATH': {'path': '', 'delimiter': ' '} +modextrapaths = {'TCLLIBPATH': {'path': '', 'delimiter': ' '}} sanity_check_paths = { 'files': ['button.tcl'], diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb index c72c3a8465..759668c39f 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb @@ -35,6 +35,8 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = {'TCLLIBPATH': {'path': 'lib', 'delimiter': ' '}} + start_dir = 'unix' moduleclass = 'vis' From 2c9108a174d27f1066e2d73e715da8af1543b1ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 19 Dec 2024 19:09:30 +0100 Subject: [PATCH 2325/2365] Fix path -> paths typo --- .../easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb | 2 +- .../g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb index 9353b81cc5..91da342e8f 100644 --- a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Tk', '8.6.10')] -modextrapaths = {'TCLLIBPATH': {'path': '', 'delimiter': ' '}} +modextrapaths = {'TCLLIBPATH': {'paths': '', 'delimiter': ' '}} sanity_check_paths = { 'files': ['button.tcl'], diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb index b5f2ab9ada..8fd6567150 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb @@ -85,7 +85,7 @@ modextrapaths = { 'CLASSPATH': 'lib/graphviz/java', 'LD_LIBRARY_PATH': 'lib/graphviz/java', 'PYTHONPATH': 'lib/graphviz/python%s' % local_pyver_major, - 'TCLLIBPATH': {'path': 'lib/graphviz/tcl', 'delimiter': ' '}, + 'TCLLIBPATH': {'paths': 'lib/graphviz/tcl', 'delimiter': ' '}, } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb index 759668c39f..3c3f3db77b 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb @@ -35,7 +35,7 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = {'TCLLIBPATH': {'path': 'lib', 'delimiter': ' '}} +modextrapaths = {'TCLLIBPATH': {'paths': 'lib', 'delimiter': ' '}} start_dir = 'unix' From d21f15668f966f38e7a31dace23a313032fd91d4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 2 Jan 2025 11:41:02 +0000 Subject: [PATCH 2326/2365] remove `install_pip=True` from Python easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 2 -- easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index 05777350e9..41a5b4d0ad 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -28,8 +28,6 @@ dependencies = [ osdependencies = [OS_PKG_OPENSSL_DEV] -install_pip = True - exts_default_options = { 'source_urls': [PYPI_SOURCE], } diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index bf47608722..9540cbf9f3 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -35,8 +35,6 @@ dependencies = [ osdependencies = [OS_PKG_OPENSSL_DEV] -install_pip = True - exts_default_options = { 'source_urls': [PYPI_SOURCE], } From 20e7fb120f3c3d0204c4bbea7742715e65ff9967 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 16 Jan 2025 14:48:11 +0000 Subject: [PATCH 2327/2365] update homepage and source_urls for libxsmm --- easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb | 4 ++-- .../l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb index cc99b62c39..0d233d0fee 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxsmm' version = '1.16.1' -homepage = 'https://github.com/hfp/libxsmm' +homepage = 'https://github.com/libxsmm/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://github.com/hfp/libxsmm/archive/'] +source_urls = ['https://github.com/libxsmm/libxsmm/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['93dc7a3ec40401988729ddb2c6ea2294911261f7e6cd979cf061b5c3691d729d'] diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb index fba1cdf479..4d9093e4d2 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxsmm' version = '1.16.1' -homepage = 'https://github.com/hfp/libxsmm' +homepage = 'https://github.com/libxsmm/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).""" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://github.com/hfp/libxsmm/archive/'] +source_urls = ['https://github.com/libxsmm/libxsmm/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['93dc7a3ec40401988729ddb2c6ea2294911261f7e6cd979cf061b5c3691d729d'] From 142a9d9c466bed81bfcc1df02fac86e7ae3d85c3 Mon Sep 17 00:00:00 2001 From: Pierre Beaujean Date: Thu, 30 Jan 2025 10:42:01 +0100 Subject: [PATCH 2328/2365] Change source_urls for Boost from boostorg.jfrog.io to archives.boost.io (fix #22152) --- .../b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 2 +- .../easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb index ca9a6e5edc..9ca9d5f851 100644 --- a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb @@ -10,7 +10,7 @@ description = """Boost.Python is a C++ library which enables seamless interopera toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +source_urls = ['https://archives.boost.io/release/%(version)s/source/'] sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] patches = ['Boost-1.71.0_fix-Python3.patch'] checksums = [ diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index 963017ac24..164df10bb3 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +source_urls = ['https://archives.boost.io/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] patches = ['Boost-%(version)s-library_version_type_serialization.patch'] checksums = [ diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb index 8a46e2591d..088daf7c7f 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'iccifort', 'version': '2020.4.304'} # add C++ compiler option as workaround for "error: no instance of constructor .* matches the argument list" errors toolchainopts = {'pic': True, 'extra_cxxflags': '-DBOOST_ASIO_USE_TS_EXECUTOR_AS_DEFAULT=1'} -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +source_urls = ['https://archives.boost.io/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] patches = ['Boost-%(version)s-library_version_type_serialization.patch'] checksums = [ From 3f69ee07425a713254514c9eb02cfddf3e33ce1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Feb 2025 09:20:13 +0100 Subject: [PATCH 2329/2365] avoid using `buildcmd` in PySide2 easyconfig --- .../easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb index 956583ecc4..1505bcb68e 100644 --- a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -29,7 +29,7 @@ use_pip = False preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' -buildcmd = 'build --parallel=%(parallel)s' +buildopts = '--parallel=%(parallel)s' preinstallopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' install_target = 'install --parallel=%(parallel)s' From aa2a9bb26cf1fcd01e3a68545810bd423c437e85 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 27 Feb 2025 19:44:51 +0100 Subject: [PATCH 2330/2365] remove deprecated allow_prepend_abs_path from libglvnd easyconfigs --- .../easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb index d0f0184cab..7495fa8b56 100644 --- a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb @@ -22,8 +22,9 @@ builddependencies = [ dependencies = [('X11', '20201008')] # Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. -allow_prepend_abs_path = True -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} +modextrapaths = { + "__EGL_VENDOR_LIBRARY_DIRS": ['/etc/glvnd/egl_vendor.d', '/usr/share/glvnd/egl_vendor.d'], +} sanity_check_paths = { 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], From 773a2ce9b15951582b20a55a3444ea59e0345c80 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 27 Feb 2025 21:57:05 +0100 Subject: [PATCH 2331/2365] replace hardcoded CPATH in modextravars with global MODULE_LOAD_ENV_HEADERS --- easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb | 2 +- easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb | 2 +- easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb | 2 +- easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb | 2 +- .../easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb | 2 +- .../c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb | 2 +- .../g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb | 2 +- .../MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb | 2 +- easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb | 2 +- 20 files changed, 20 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb index 89ab6d27b0..a82ddd0362 100644 --- a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb @@ -33,6 +33,6 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = {'CPATH': 'include/ac'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/ac'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb index 92ff63b1db..9917d88d4a 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb @@ -29,6 +29,6 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = {'CPATH': 'include/blis'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/blis'} moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb index 4e65c62993..767f214dca 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb @@ -46,6 +46,6 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = {'CPATH': 'include/blis'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/blis'} moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb index 3ed520be5c..26a9185dc8 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb @@ -58,6 +58,6 @@ sanity_check_paths = { } # other coin-or projects expect instead of -modextrapaths = {'CPATH': 'include/coin'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/coin'} moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb index e9e8533a7c..3a65e5ac28 100644 --- a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb @@ -45,6 +45,6 @@ sanity_check_paths = { } # other coin-or projects expect instead of -modextrapaths = {'CPATH': 'include/coin'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/coin'} moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb index b3d64ec60c..ff0a3292b0 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb @@ -50,6 +50,6 @@ sanity_check_paths = { } # other coin-or projects expect instead of -modextrapaths = {'CPATH': 'include/coin'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/coin'} moduleclass = "math" diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb index ebc08762ad..aee0b9e19e 100644 --- a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # other coin-or projects expect instead of -modextrapaths = {'CPATH': 'include/coin'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/coin'} moduleclass = "math" diff --git a/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb index 42da9feba7..1b666a2023 100644 --- a/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ('binutils', '2.35'), ] -modextrapaths = {'CPATH': 'include/cpu_features'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/cpu_features'} sanity_check_paths = { 'files': ['bin/list_cpu_features', 'lib/libcpu_features.a'], diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb index da19daca51..6a9fc591e5 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb @@ -37,7 +37,7 @@ dependencies = [ ('Ghostscript', '9.53.3'), ] -modextrapaths = {'CPATH': ['include/GraphicsMagick']} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: ['include/GraphicsMagick']} sanity_check_paths = { 'files': ['bin/gm', 'lib/libGraphicsMagick.a', 'lib/libGraphicsMagick++.a', diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb index 91e084fc23..6b70706ce3 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb @@ -46,7 +46,7 @@ configopts = [ local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", ] -modextrapaths = {'CPATH': 'include/hdf'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/hdf'} sanity_check_paths = { 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb index 45e2b96a71..d5418f668d 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb @@ -35,6 +35,6 @@ sanity_check_paths = { 'dirs': [] } -modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/%(namelower)s-%(version)s'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb index 6a5a37d6d6..8ee634ca4f 100644 --- a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb @@ -33,6 +33,6 @@ sanity_check_paths = { sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] -modextrapaths = {'CPATH': 'include/jxrlib'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/jxrlib'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb index 634267b115..dabbb48b3e 100644 --- a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ('binutils', '2.35'), ] -modextrapaths = {'CPATH': 'include/libelf'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/libelf'} sanity_check_paths = { 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb index 9752901816..7b3c578596 100644 --- a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb @@ -23,6 +23,6 @@ sanity_check_paths = { 'dirs': ['include/tirpc', 'lib'], } -modextrapaths = {'CPATH': 'include/tirpc'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/tirpc'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb index a7fe767d11..22c8a33e99 100644 --- a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb @@ -26,7 +26,7 @@ sanity_check_paths = { } modextrapaths = { - 'CPATH': ['include/mariadb'], + MODULE_LOAD_ENV_HEADERS: ['include/mariadb'], 'LD_LIBRARY_PATH': ['lib/mariadb'], 'LIBRARY_PATH': ['lib/mariadb'], } diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 110f64221c..ce9b317be6 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -51,6 +51,6 @@ sanity_check_commands = [ "nss-config --version", ] -modextrapaths = {'CPATH': 'include/nss'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/nss'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb index 6b7abcdbec..f41e73a22d 100644 --- a/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb @@ -45,6 +45,6 @@ sanity_check_paths = { } # other coin-or projects expect instead of -modextrapaths = {'CPATH': 'include/coin'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/coin'} moduleclass = "math" diff --git a/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb index 1924ee814f..39abe70edb 100644 --- a/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb @@ -35,7 +35,7 @@ sanity_check_commands = ["funitproc --help"] modextrapaths = { 'PATH': ['PFUNIT-%(version_major_minor)s/bin'], - 'CPATH': [ + MODULE_LOAD_ENV_HEADERS: [ 'FARGPARSE-%s/include' % local_fargparse_major_minor_version, 'GFTL-%s/include' % local_gftl_major_minor_version, 'GFTL_SHARED-%s/include' % local_gftl_shared_major_minor_version, diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb index aa41fa1532..363c6c51c8 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ sanity_check_paths = { } modextrapaths = { - 'CPATH': ['qhull/include'], + MODULE_LOAD_ENV_HEADERS: ['qhull/include'], } maxparallel = 1 diff --git a/easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb index 038094f39e..3d6b004f1f 100644 --- a/easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb @@ -26,6 +26,6 @@ sanity_check_paths = { sanity_check_commands = ["spoa --help"] -modextrapaths = {'CPATH': 'include/%(namelower)s'} +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/%(namelower)s'} moduleclass = 'bio' From d8f6e3f9d74c5a5866c169d198ee1a4c23072366 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 2 Mar 2025 19:05:14 +0100 Subject: [PATCH 2332/2365] add missing Doxygen build dependency for bcl2fastq2 --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb index b6a06a8326..85c6e58941 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -28,6 +28,7 @@ checksums = [ builddependencies = [ ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), ] dependencies = [ From 7525b08aa5b7ebc94f224e6c0be7b5d47e0914b5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 5 Mar 2025 20:15:12 +0000 Subject: [PATCH 2333/2365] add `keepsymlinks = False` to NSS --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index ce9b317be6..2af20719c4 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -40,6 +40,7 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd # buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] +keepsymlinks = False sanity_check_paths = { 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], From 9c677515731b4d4d98a1401a5ba287cc80e49cf1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 5 Mar 2025 20:24:02 +0000 Subject: [PATCH 2334/2365] add a comment --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 2af20719c4..7ff8ade27f 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -40,6 +40,7 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd # buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] +# symlinks in bin/ would point to outside of installation directory, so can't keep them keepsymlinks = False sanity_check_paths = { From 52f79f568c8e31d90889dc4f60c471b2106ffe81 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 11 Mar 2025 16:44:48 +0100 Subject: [PATCH 2335/2365] switch XML-LibXML to PerlBundle --- .../XML-LibXML-2.0206-GCCcore-10.2.0.eb | 19 ++++++------------- 1 file changed, 6 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb index 62cc7c77d1..0eb8cb7f17 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PerlBundle' name = 'XML-LibXML' version = '2.0206' @@ -18,15 +18,17 @@ dependencies = [ ('libxml2', '2.9.10'), ] -exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") - exts_list = [ ('File::chdir', '0.1010', { 'source_tmpl': 'File-chdir-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['efc121f40bd7a0f62f8ec9b8bc70f7f5409d81cd705e37008596c8efc4452b01'], }), + ('FFI::CheckLib', '0.31', { + 'source_tmpl': 'FFI-CheckLib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['04d885fc377d44896e5ea1c4ec310f979bb04f2f18658a7e7a4d509f7e80bb80'], + }), ('Alien::Base', '2.38', { 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], @@ -44,13 +46,4 @@ exts_list = [ }), ] -modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', -} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], -} - moduleclass = 'data' From 141b61cd27874344ecc727c6eb90566f47b47357 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 13 Mar 2025 02:30:51 +0100 Subject: [PATCH 2336/2365] add Test2::V0 extension to XML-LibXML v2.0206 and v2.0207 --- .../x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb index 0eb8cb7f17..5e7e4c4dd2 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb @@ -24,6 +24,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['efc121f40bd7a0f62f8ec9b8bc70f7f5409d81cd705e37008596c8efc4452b01'], }), + ('Test2::V0', '1.302209', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['dde1a388b94e178808039361f6393c7195f72518c39967a7a3582299b8c39e3e'], + }), ('FFI::CheckLib', '0.31', { 'source_tmpl': 'FFI-CheckLib-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], From a3b328e157002979cafb8e9ff6d4708bfb63a3fd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 13 Mar 2025 11:54:00 +0100 Subject: [PATCH 2337/2365] add Term::Table extension to XML-LibXML v2.0206 and v2.0207 --- .../x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb index 5e7e4c4dd2..f290b9d2c9 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb @@ -24,6 +24,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['efc121f40bd7a0f62f8ec9b8bc70f7f5409d81cd705e37008596c8efc4452b01'], }), + ('Term::Table', '0.024', { + 'source_tmpl': 'Term-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['52288538c3b0514bcd2b61f645686c256619e56a421ae992e2b76d31927c4ece'], + }), ('Test2::V0', '1.302209', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], From 56d679c4e6740bb08442723a496b62ecf7b518d2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 13 Mar 2025 16:42:40 +0100 Subject: [PATCH 2338/2365] update download URLs for MPICH v3.x --- easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb index 9c3d7a9f59..0b28d5921b 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb @@ -7,7 +7,7 @@ of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://www.mpich.org/static/tarballs/%(version)s'] +source_urls = ['https://www.mpich.org/static/downloads/%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['4bfaf8837a54771d3e4922c84071ef80ffebddbb6971a006038d91ee7ef959b9'] From 0d12f5f5855f6c9bce587e2c866caacea7916846 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 15 Mar 2025 11:10:18 +0100 Subject: [PATCH 2339/2365] disable keepsymlinks in libStatGen --- .../easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb index 6cb6951226..06c1b1a902 100644 --- a/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb @@ -21,6 +21,7 @@ dependencies = [('zlib', '1.2.11')] runtest = 'test' +keepsymlinks = False files_to_copy = [ (['libStatGen.a'], 'lib'), ('include'), From 12e8ecaabf19be45835866df5a1dad1582e88c71 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 15 Mar 2025 18:52:02 +0100 Subject: [PATCH 2340/2365] make CMake a runtime dependency of gemmi --- .../g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb index de4750866d..e753b9bd2b 100644 --- a/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb @@ -20,24 +20,25 @@ that use CIF files (we have the fastest open-source CIF parser). toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'opt': True} +github_account = 'project-gemmi' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['af462dbb3a2a144b1437700637e78c0365a5273dc5bffadeea80f73765ab15c7'] -github_account = 'project-gemmi' - -runtest = 'cpptest ftest ftest_grid test' +builddependencies = [ + ('pybind11', '2.6.0'), + ('binutils', '2.35') +] +dependencies = [ + ('Python', '3.8.6'), + ('CMake', '3.18.4'), # cmake needed to import gemmi +] configopts = '-DUSE_PYTHON=1 ' configopts += '-DUSE_FORTRAN=1 ' configopts += '-DPYTHON_INSTALL_DIR=%(installdir)s/lib/python%(pyshortver)s/site-packages ' -builddependencies = [ - ('pybind11', '2.6.0'), - ('CMake', '3.18.4'), - ('binutils', '2.35') -] -dependencies = [('Python', '3.8.6')] +runtest = 'cpptest ftest ftest_grid test' sanity_check_paths = { 'files': ['bin/gemmi'], From 5fadc644eba7a4d5c701d5ee081ae16f7b996119 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 15 Mar 2025 19:51:21 +0100 Subject: [PATCH 2341/2365] remove default keepsymlink = True option from easyconfigs --- .../easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb index 76091ce5f2..eb17b50729 100644 --- a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb +++ b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb @@ -19,8 +19,6 @@ Required download: {' '.join(sources)}""" dependencies = [('libGLU', '9.0.1')] -keepsymlinks = True - sanity_check_paths = { 'files': [], 'dirs': ['atomicdata', 'bin', 'examples'], From 6c98002c0c8d4b22219f7b46b6dd654c344f0c86 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 15 Mar 2025 23:12:59 +0100 Subject: [PATCH 2342/2365] switch to .tar.xz archive and add checksums for git sources of GenomeWorks v2021.02.2 --- .../GenomeWorks-2021.02.2-fosscuda-2020b.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index c33ec23288..189014fee4 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} toolchainopts = {'pic': True} sources = [{ - 'filename': SOURCE_TAR_GZ, + 'filename': SOURCE_TAR_XZ, 'git_config': { 'url': 'https://github.com/clara-parabricks', 'repo_name': name, @@ -20,8 +20,7 @@ sources = [{ 'recursive': True, }, }] -# no checksum for source tarball because it's created locally via 'git clone' -checksums = [None] +checksums = ['ac3946d7172853efe3260339e7edc430bbbd585ed490c7f1ad9f7644446a5ae6'] builddependencies = [ ('CMake', '3.18.4'), @@ -64,9 +63,8 @@ exts_list = [ 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], }), ('genomeworks', version, { - 'sources': ['GenomeWorks-%(version)s.tar.gz'], - # no checksum for source tarball because it's created locally via 'git clone' - 'checksums': [None], + 'sources': ['GenomeWorks-%(version)s.tar.xz'], + 'checksums': ['ac3946d7172853efe3260339e7edc430bbbd585ed490c7f1ad9f7644446a5ae6'], 'start_dir': 'pygenomeworks', 'preinstallopts': local_genomeworks_preinstallopts, }), From a55b398589691a91f1f37a171967ff600a478828 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 15 Mar 2025 23:32:59 +0100 Subject: [PATCH 2343/2365] switch to .tar.xz archive and add checksums for git sources of NewHybrids v1.1_Beta3 --- .../n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb index 8f96c2cc11..ed75c66e78 100644 --- a/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb @@ -13,7 +13,7 @@ individuals fall into each of a set of user-defined hybrid categories.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} sources = [{ - 'filename': SOURCE_TAR_GZ, + 'filename': SOURCE_TAR_XZ, 'git_config': { 'url': 'https://github.com/eriqande', 'repo_name': 'newhybrids', @@ -21,7 +21,7 @@ sources = [{ 'recursive': True, } }] -checksums = [None] +checksums = ['cdb3f922bfb63a740ac0e56af77b15cf83a111e40dec3a12bb9d4bc0464c8520'] extract_sources = True From 264e199aaf6fd4c48d051f21216c75839392befe Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 16 Mar 2025 00:12:24 +0100 Subject: [PATCH 2344/2365] switch to .tar.xz archive and add checksums for git sources of PyTorch v1.8.1 and v1.9.0 --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 4 ++-- .../easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 4 ++-- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 4 ++-- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 4 ++-- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index b93b0e8242..20131a617e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -8,7 +8,7 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2020b'} sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', + 'filename': SOURCE_TAR_XZ, 'git_config': { 'url': 'https://github.com/pytorch', 'repo_name': 'pytorch', @@ -31,7 +31,7 @@ patches = [ 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '2a45d5c0344dc71ec998b5a86f62826dd0c5ac6b9a9084ce6dfb606ea2442c50', # PyTorch-1.8.1.tar.xz # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index 90e96f96e0..dc9f7ac60e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -8,7 +8,7 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', + 'filename': SOURCE_TAR_XZ, 'git_config': { 'url': 'https://github.com/pytorch', 'repo_name': 'pytorch', @@ -40,7 +40,7 @@ patches = [ 'PyTorch-1.8.1_fix_test_collect_shards.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '2a45d5c0344dc71ec998b5a86f62826dd0c5ac6b9a9084ce6dfb606ea2442c50', # PyTorch-1.8.1.tar.xz # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 000f5a2c4f..4576b15fb6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -8,7 +8,7 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2020b'} sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', + 'filename': SOURCE_TAR_XZ, 'git_config': { 'url': 'https://github.com/pytorch', 'repo_name': 'pytorch', @@ -32,7 +32,7 @@ patches = [ 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '6f9bc441bc7a3627dd9eba55121734ce69e17622da8b2b34b9fad2a50d277ff6', # PyTorch-1.9.0.tar.xz # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index 32f09e64e7..9911b4ab5f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -9,7 +9,7 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', + 'filename': SOURCE_TAR_XZ, 'git_config': { 'url': 'https://github.com/pytorch', 'repo_name': 'pytorch', @@ -42,7 +42,7 @@ patches = [ 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '6f9bc441bc7a3627dd9eba55121734ce69e17622da8b2b34b9fad2a50d277ff6', # PyTorch-1.9.0.tar.xz # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index a1aad90e3f..3f3661e997 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -8,7 +8,7 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', + 'filename': SOURCE_TAR_XZ, 'git_config': { 'url': 'https://github.com/pytorch', 'repo_name': 'pytorch', @@ -41,7 +41,7 @@ patches = [ 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '6f9bc441bc7a3627dd9eba55121734ce69e17622da8b2b34b9fad2a50d277ff6', # PyTorch-1.9.0.tar.xz # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch From f284cc76979f6022314e9d526015721a3ab49308 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 16 Mar 2025 00:30:30 +0100 Subject: [PATCH 2345/2365] switch to .tar.xz archive and add checksums for git sources of Sambamba v0.8.x --- easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb index 6198ea51bd..5c67c33ba0 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/biod/sambamba/archive/'] sources = [{ - 'filename': SOURCE_TAR_GZ, + 'filename': SOURCE_TAR_XZ, 'git_config': { 'url': 'https://github.com/biod', 'repo_name': 'sambamba', @@ -21,7 +21,7 @@ sources = [{ 'recursive': True, } }] -checksums = [None] +checksums = ['4a00d072ffc1d077fd8cd54294eea5ae0e890eedbaaa5b16b54fffa758caafce'] builddependencies = [ ('LDC', '1.25.1'), From 99f1d7aa91070552845dedfc8be647056a6f1d2a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 16 Mar 2025 00:34:50 +0100 Subject: [PATCH 2346/2365] switch to .tar.xz archive and add checksums for git sources of SeuratData v20210514 --- .../s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb index bc92c7305e..1301b837a6 100644 --- a/easybuild/easyconfigs/s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb @@ -12,14 +12,14 @@ package and data management systems.""" toolchain = {'name': 'foss', 'version': '2020b'} sources = [{ - 'filename': SOURCE_TAR_GZ, + 'filename': SOURCE_TAR_XZ, 'git_config': { 'url': 'https://github.com/satijalab', 'repo_name': 'seurat-data', 'commit': local_commit, }, }] -checksums = [None] +checksums = ['7bec7540f634b39089ba457b32784bb5236dfad0935937f8155240201ab862bd'] dependencies = [('R', '4.0.3')] From d13d93c3c1e6e3744289e897f99c32aa54b0363f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 16 Mar 2025 00:53:58 +0100 Subject: [PATCH 2347/2365] switch to .tar.xz archive and add checksums for git sources of SeuratWrappers --- .../SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb index badc4022cc..b7a771c9cb 100644 --- a/easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb @@ -11,14 +11,14 @@ description = "SeuratWrappers is a collection of community-provided methods and toolchain = {'name': 'foss', 'version': '2020b'} sources = [{ - 'filename': SOURCE_TAR_GZ, + 'filename': SOURCE_TAR_XZ, 'git_config': { 'url': 'https://github.com/satijalab', 'repo_name': 'seurat-wrappers', 'commit': local_commit, }, }] -checksums = [None] +checksums = ['01d1bfef64cd4f5b3c209a431ecc475349d4dec513318263ddb0354cd37ca47e'] dependencies = [ ('R', '4.0.3'), From 20f24fd4a19e4df860da23f2d96ad86e5b65fb3d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 16 Mar 2025 11:27:04 +0100 Subject: [PATCH 2348/2365] replace source URLs of Mesa to new location in archive.mesa3d.org --- easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb index 2c63a42feb..352626800c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb @@ -19,11 +19,8 @@ description = """Mesa is an open-source implementation of the OpenGL specificati toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [ - 'https://mesa.freedesktop.org/archive/', - 'https://mesa.freedesktop.org/archive/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', + 'https://archive.mesa3d.org/', + 'https://archive.mesa3d.org/older-versions/%(version_major)s.x/', ] sources = [SOURCELOWER_TAR_XZ] patches = ['%(name)s-20.0.2-match-swrast-loosely.patch'] From 7a8e2f2284a81783ad0d021277d108778210cd04 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 16 Mar 2025 12:16:01 +0100 Subject: [PATCH 2349/2365] use same sources definition for main build and extension build of GenomeWorks v2021.02.2 --- .../g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb index 189014fee4..ee75208982 100644 --- a/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -63,8 +63,8 @@ exts_list = [ 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], }), ('genomeworks', version, { - 'sources': ['GenomeWorks-%(version)s.tar.xz'], - 'checksums': ['ac3946d7172853efe3260339e7edc430bbbd585ed490c7f1ad9f7644446a5ae6'], + 'sources': sources, + 'checksums': checksums, 'start_dir': 'pygenomeworks', 'preinstallopts': local_genomeworks_preinstallopts, }), From 11fca487aedd5fae63da625c537a4a73c30ce362 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Mar 2025 00:54:24 +0100 Subject: [PATCH 2350/2365] replace homepage and sources og ParMETIS with new home at https://karypis.github.io --- .../easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb | 6 +++--- .../easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb index f74f7c6ef0..b7216ae5a6 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb @@ -4,7 +4,7 @@ name = 'ParMETIS' version = '4.0.3' -homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +homepage = 'https://karypis.github.io/glaros/projects/gp.html' description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and @@ -15,8 +15,8 @@ toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'usempi': True, 'pic': True} source_urls = [ - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', + 'https://karypis.github.io/glaros/files/sw/parmetis', + 'https://karypis.github.io/glaros/files/sw/parmetis/OLD', ] sources = [SOURCELOWER_TAR_GZ] checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb index 8cc997b562..5e75abae96 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb @@ -1,7 +1,7 @@ name = 'ParMETIS' version = '4.0.3' -homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +homepage = 'https://karypis.github.io/glaros/projects/gp.html' description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and @@ -12,8 +12,8 @@ toolchain = {'name': 'iimpi', 'version': '2020b'} toolchainopts = {'usempi': True, 'pic': True} source_urls = [ - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', + 'https://karypis.github.io/glaros/files/sw/parmetis', + 'https://karypis.github.io/glaros/files/sw/parmetis/OLD', ] sources = [SOURCELOWER_TAR_GZ] checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] From b308fdb0fa3913fbe6efa7e34daeec54fecc0770 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Mar 2025 00:58:46 +0100 Subject: [PATCH 2351/2365] replace homepage and sources of METIS with new home at https://karypis.github.io --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb index 7c20746615..6216f2aace 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb @@ -1,7 +1,7 @@ name = 'METIS' version = '5.1.0' -homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +homepage = 'https://karypis.github.io/glaros/projects/gp.html' description = """ METIS is a set of serial programs for partitioning graphs, partitioning @@ -15,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} source_urls = [ - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', + 'https://karypis.github.io/glaros/files/sw/metis', + 'https://karypis.github.io/glaros/files/sw/metis/OLD', ] sources = [SOURCELOWER_TAR_GZ] From 834a3def200b924d1c9b77ab4a5693af413589f3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Mar 2025 01:59:13 +0100 Subject: [PATCH 2352/2365] update homepage and sources of MUMPS with new home at https://mumps-solver.org --- easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb | 4 ++-- .../easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb index 771db93b9f..97ac31bba8 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb @@ -2,13 +2,13 @@ name = 'MUMPS' version = '5.3.5' versionsuffix = '-metis' -homepage = 'https://graal.ens-lyon.fr/MUMPS/' +homepage = 'https://mumps-solver.org' description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] +source_urls = ['https://mumps-solver.org'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb index aa6dcc6644..a43fb4fc4d 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -2,13 +2,13 @@ name = 'MUMPS' version = '5.3.5' versionsuffix = '-metis' -homepage = 'https://graal.ens-lyon.fr/MUMPS/' +homepage = 'https://mumps-solver.org' description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] +source_urls = ['https://mumps-solver.org'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD From cd750a7a5eb5686b9dc09410fd6059dbaa53ca5f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Mar 2025 02:29:19 +0100 Subject: [PATCH 2353/2365] switch webclu.bio.wzw.tum.de to HTTPS in VMD easyconfigs --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb | 2 +- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb index b170a6dc5f..26e658c5d6 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', - 'http://webclu.bio.wzw.tum.de/stride/' + 'https://webclu.bio.wzw.tum.de/stride/', ] sources = [ 'vmd-%(version)s.src.tar.gz', diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb index 6a7845eece..9037761dcb 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = [ 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', - 'http://webclu.bio.wzw.tum.de/stride/' + 'https://webclu.bio.wzw.tum.de/stride/', ] sources = [ 'vmd-%(version)s.src.tar.gz', From c1773e98439d31fe98ab2f14fce9aad8fc3c72de Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Mar 2025 10:12:54 +0100 Subject: [PATCH 2354/2365] add ftp.mcs.anl.gov as mirror of MUMPS sources --- .../easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb | 5 ++++- .../easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb index 97ac31bba8..7e85bf5569 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb @@ -8,7 +8,10 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['https://mumps-solver.org'] +source_urls = [ + 'https://mumps-solver.org', + 'https://ftp.mcs.anl.gov/pub/petsc/externalpackages', # mirror +] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb index a43fb4fc4d..8b3508f0a5 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -8,7 +8,10 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['https://mumps-solver.org'] +source_urls = [ + 'https://mumps-solver.org', + 'https://ftp.mcs.anl.gov/pub/petsc/externalpackages', # mirror +] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD From ca7d5aecaccf7f62d7b1dde4d27b68808579ebbd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Mar 2025 09:29:51 +0100 Subject: [PATCH 2355/2365] dance around problem with resolving %(pyshortver)s template in Mako easyconfig using multi_deps --- easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb index 8c91fddf7e..79f314e1fb 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb @@ -14,9 +14,11 @@ checksums = ['8195c8c1400ceb53496064314c6736719c6f25e7479cd24c77be3d9361cddc27'] builddependencies = [('binutils', '2.35')] multi_deps = {'Python': ['3.8.6', '2.7.18']} +enhance_sanity_check = True + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], + 'dirs': [], } moduleclass = 'devel' From f85c10a323980ee0a6be1d7af58fd5a99177483a Mon Sep 17 00:00:00 2001 From: Wes Hinsley Date: Thu, 20 Mar 2025 10:37:58 +0000 Subject: [PATCH 2356/2365] Update URLs for libGLU --- easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb index cea272ad1b..9f77d11e01 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libGLU' version = '9.0.1' -homepage = 'https://mesa.freedesktop.org/archive/glu/' +homepage = 'https://gitlab.freedesktop.org/mesa/glu' description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +source_urls = ['https://archive.mesa3d.org/glu'] sources = ['glu-%(version)s.tar.gz'] checksums = ['f6f484cfcd51e489afe88031afdea1e173aa652697e4c19ddbcb8260579a10f7'] From 167f5bcb149147d1c1c1125883136da20042c1e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Apr 2025 17:38:42 +0200 Subject: [PATCH 2357/2365] use HTTP rather than FTP in source URLs of 'file' easyconfigs --- easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb index 1e5eec58ab..969d9cb3f9 100644 --- a/easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/file/file-5.39-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ description = """The file command is 'a file type guesser', that is, a command-l toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = ['ftp://ftp.astron.com/pub/file/'] +source_urls = ['http://ftp.astron.com/pub/file/'] sources = [SOURCE_TAR_GZ] checksums = ['f05d286a76d9556243d0cb05814929c2ecf3a5ba07963f8f70bfaaa70517fad1'] From 78a3ab03d5e8b5ee44a515e2c525ca6f22cc46f8 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 10 Apr 2025 16:51:35 +0100 Subject: [PATCH 2358/2365] Ensure Infernal is built with MPI enabled, and drop toolchain to gompi --- .../i/Infernal/Infernal-1.1.4-gompi-2020b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2020b.eb diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2020b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2020b.eb new file mode 100644 index 0000000000..dbd97d57ca --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2020b.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# Updated:: Denis Kristak (INUITS) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.4" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc'] + +# MPI is disabled by default +configopts = '--enable-mpi' + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' From 6c009c79b364042d0de4d63c76da4ab8514bdb16 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 10 Apr 2025 16:51:35 +0100 Subject: [PATCH 2359/2365] Ensure Infernal is built with MPI enabled, and drop toolchain to gompi From 2c8fbe854ffd90eb2326188ec041c7c5d24177e2 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Fri, 11 Apr 2025 10:25:36 +0100 Subject: [PATCH 2360/2365] fix toolchain --- easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2020b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2020b.eb index dbd97d57ca..3cf3368886 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-gompi-2020b.eb @@ -20,7 +20,7 @@ homepage = 'http://eddylab.org/infernal/' description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.""" -toolchain = {'name': 'foss', 'version': '2020b'} +toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'pic': True} source_urls = ['http://eddylab.org/%(namelower)s'] From 67551b954d65115c1d0355c634ad0bf20e744ef3 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 23 Apr 2025 13:46:56 +0200 Subject: [PATCH 2361/2365] fix --sanity-check-only and --module only for minimap2 --- .../easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb index 8ba21e5c0f..abd40a4d87 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb @@ -35,17 +35,18 @@ files_to_copy = [ (['lib%(name)s.a'], 'lib'), (['*.h'], 'include'), 'LICENSE.txt', 'NEWS.md', 'README.md', - (['%(name)s.1'], 'share/man/man1') + (['%(name)s.1'], 'share/man/man1'), + (['test/MT-human.fa', 'test/MT-orang.fa'], 'test'), ] sanity_check_paths = { 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], - 'dirs': ['include'] + 'dirs': ['include', 'test'] } sanity_check_commands = [ "minimap2 --help", - "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", + "cd %(installdir)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", ] moduleclass = 'bio' From 056ebe2dc6fdaadc69e16d57a97baed758d844ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 26 May 2025 17:51:19 +0200 Subject: [PATCH 2362/2365] Archive 2020b --- 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easybuild/easyconfigs/{ => __archive__}/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/pocl/pocl-1.6-iccifort-2020.4.304.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/SWAT+/SWAT+-60.5.1-iccifort-2020.4.304.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb (100%) 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b/easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb similarity index 100% rename from easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb rename to easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb similarity index 100% rename from easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb rename to easybuild/easyconfigs/__archive__/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb similarity index 100% rename from easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb rename to easybuild/easyconfigs/__archive__/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb similarity index 100% rename from easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb rename to easybuild/easyconfigs/__archive__/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb From dbc9f49d91ccbbe70275b0afdaea22cf861f7525 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 26 May 2025 19:49:29 +0200 Subject: [PATCH 2365/2365] Archive yet more things connected to 2020b age toolchain --- .../easyconfigs/{ => __archive__}/h/HPL/HPL-2.3-intel-2020.12.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/iimpi/iimpi-2020.12.eb | 0 .../{ => __archive__}/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb | 0 .../{ => __archive__}/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb | 0 .../i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb | 0 .../i/intel-compilers/intel-compilers-2021.1.2.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/intel/intel-2020.12.eb | 0 easybuild/easyconfigs/{ => __archive__}/n/NVHPC/NVHPC-21.2.eb | 0 .../o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 0 .../{ => __archive__}/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb | 0 10 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.3-intel-2020.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iimpi/iimpi-2020.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/intel-compilers/intel-compilers-2021.1.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/intel/intel-2020.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/NVHPC/NVHPC-21.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb (100%) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020.12.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intel-2020.12.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020.12.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intel-2020.12.eb diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2020.12.eb b/easybuild/easyconfigs/__archive__/i/iimpi/iimpi-2020.12.eb similarity index 100% rename from easybuild/easyconfigs/i/iimpi/iimpi-2020.12.eb rename to easybuild/easyconfigs/__archive__/i/iimpi/iimpi-2020.12.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb similarity index 100% rename from easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb rename to easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb similarity index 100% rename from easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb rename to easybuild/easyconfigs/__archive__/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb diff --git a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/__archive__/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb similarity index 100% rename from easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb rename to easybuild/easyconfigs/__archive__/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb 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