diff --git a/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.4.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.4.1-foss-2020b.eb new file mode 100644 index 0000000000..57583831e0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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$EBROOTWANNIER90/lib -lwannier" && ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb new file mode 100644 index 0000000000..1cf3882b38 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.4.1-intel-2020b.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.4.1' + +homepage = 'https://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ec74133ef9d247cb6ad44c205675694919cf36d7f1682a9b85cae8bdecdc22a8'] + +builddependencies = [ + ('Python', '3.8.6'), +] +dependencies = [ + ('libxc', '4.3.4'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('HDF5', '1.10.7'), + ('Wannier90', '3.1.0'), +] + +# Ensure MPI with intel wrappers. +configopts = '--with-mpi="yes" --enable-openmp="no" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# BLAS/Lapack from MKL +configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb new file mode 100644 index 0000000000..0c83158cf8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'ABRA2' +version = '2.23' + +homepage = 'https://github.com/mozack/abra2' +description = "Assembly Based ReAligner" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/mozack/abra2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ABRA2-2.22_fix-Makefile.patch'] +checksums = [ + '3993f66a493070ee49df2865b6786a45a0cf6c379bae83e94b8339abbe673289', # v2.23.tar.gz + '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch +] + +builddependencies = [('Maven', '3.6.3', '', SYSTEM)] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('BWA', '0.7.17'), +] + +maxparallel = 1 + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' +buildopts += '&& make standalone CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +files_to_copy = [ + (['abra'], 'bin'), + (['target/libAbra.%s' % SHLIB_EXT], 'lib'), + 'target/abra2-%(version)s-jar-with-dependencies.jar', +] + +postinstallcmds = ["cd %(installdir)s && mv abra2-%(version)s-jar-with-dependencies.jar abra2-%(version)s.jar"] + +sanity_check_paths = { + 'files': ['abra2-%(version)s.jar', 'bin/abra', 'lib/libAbra.%s' % SHLIB_EXT], + 'dirs': [], +} + +# required to work around localization bug, see https://github.com/mozack/abra2/issues/25 +modextravars = {'LC_ALL': 'en_US.UTF-8'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-2.2.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-2.2.5-foss-2020b.eb new file mode 100644 index 0000000000..71ce82f694 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-2.2.5-foss-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '2.2.5' + +homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['38e886f455074c76b32dd549e94cc345f46cb1d33ab11ad3e8e1f5214fc65521'] + +dependencies = [ + ('Boost', '1.74.0'), + ('sparsehash', '2.0.4'), + ('SQLite', '3.33.0'), +] + +configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error=deprecated-copy"' + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/ACTC/ACTC-1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a82ddd0362 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = {MODULE_LOAD_ENV_HEADERS: 'include/ac'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb b/easybuild/easyconfigs/__archive__/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb new file mode 100644 index 0000000000..1bce2a99d5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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_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'}, + # {'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' diff --git a/easybuild/easyconfigs/__archive__/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb b/easybuild/easyconfigs/__archive__/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb new file mode 100644 index 0000000000..176bd70202 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), + ('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/__archive__/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb b/easybuild/easyconfigs/__archive__/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb new file mode 100644 index 0000000000..eb17b50729 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb @@ -0,0 +1,43 @@ +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'] +download_instructions = f"""{name} requires manual download from {homepage} +Required download: {' '.join(sources)}""" + +dependencies = [('libGLU', '9.0.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +modextrapaths = { + 'AMSHOME': '', + 'AMSBIN': 'bin', + '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 +""" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb new file mode 100644 index 0000000000..740009f42a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM)] + +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/__archive__/a/AOCC/AOCC-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/AOCC/AOCC-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2ff631e5f7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/a/AOCC/AOCC-3.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/AOCC/AOCC-3.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..18edf3ece0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..de0d6d8e54 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +## +# 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'} + +# 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'] + +clangversion = '12.0.0' + +dependencies = [ + ('binutils', '2.35'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..008bcc0a9d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AOMP/AOMP-13.0-2-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Jorgen 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 = ['AOMP-%(version)s_remove_hardcoded_paths.patch'] +checksums = [ + # aomp-13.0-2.tar.gz: + '0256a84aefcbf7c49112f068321b84e0620f4c43a9d490c64d820e40658e0d67', + # AOMP-13.0-2_remove_hardcoded_paths.patch: + 'ec41ffcec63d079b6a73c93bea29e0b8d77ca7b059725aa1d47c334f7e476ff0', +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), + ('elfutils', '0.183'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.35'), + ('libffi', '3.3'), + ('ncurses', '6.2'), + ('numactl', '2.0.13'), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..418c3a32ed --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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"], +} + +maxparallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/APR/APR-1.7.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/APR/APR-1.7.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c3a8371d34 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..8c7793c01b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.2-foss-2020b-ASE-3.21.1.eb @@ -0,0 +1,33 @@ +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} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b6c03c790ba4c9f0d231659078c26ce8193fa21314bf2fe4adaa7899d5cd9dbe'] + +builddependencies = [ + ('pkgconfig', '1.5.1', '-python'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('ASE', _aseversion), + ('kim-api', '2.2.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..9df173cbc5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.2-intel-2020b-ASE-3.21.1.eb @@ -0,0 +1,36 @@ +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} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b6c03c790ba4c9f0d231659078c26ce8193fa21314bf2fe4adaa7899d5cd9dbe'] + +builddependencies = [ + ('pkgconfig', '1.5.1', '-python'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('ASE', _aseversion), + ('kim-api', '2.2.1'), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..a11acd1dc2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.7-foss-2020b-ASE-3.21.1.eb @@ -0,0 +1,33 @@ +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'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..46212bd615 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASAP3/ASAP3-3.12.7-intel-2020b-ASE-3.21.1.eb @@ -0,0 +1,36 @@ +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'), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.20.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.20.1-foss-2020b.eb new file mode 100644 index 0000000000..061976b5e3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.20.1-foss-2020b.eb @@ -0,0 +1,41 @@ +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'), + ('Flask', '1.1.2'), + ('matplotlib', '3.3.3'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional +] + +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/__archive__/a/ASE/ASE-3.20.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.20.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..cff9594840 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.20.1-fosscuda-2020b.eb @@ -0,0 +1,41 @@ +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 +] + +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/__archive__/a/ASE/ASE-3.20.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.20.1-intel-2020b.eb new file mode 100644 index 0000000000..28f70c828d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.20.1-intel-2020b.eb @@ -0,0 +1,45 @@ +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'), + ('Flask', '1.1.2'), + ('matplotlib', '3.3.3'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional +] + +# 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 = [ + ('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/__archive__/a/ASE/ASE-3.21.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.21.1-foss-2020b.eb new file mode 100644 index 0000000000..341a4a53ba --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.21.1-foss-2020b.eb @@ -0,0 +1,41 @@ +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'), + ('Flask', '1.1.2'), + ('matplotlib', '3.3.3'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional +] + +exts_list = [ + ('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/__archive__/a/ASE/ASE-3.21.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.21.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..60e79afad3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.21.1-fosscuda-2020b.eb @@ -0,0 +1,41 @@ +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'), + ('Flask', '1.1.2'), + ('matplotlib', '3.3.3'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional +] + +exts_list = [ + ('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/__archive__/a/ASE/ASE-3.21.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.21.1-intel-2020b.eb new file mode 100644 index 0000000000..485206e49a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.21.1-intel-2020b.eb @@ -0,0 +1,45 @@ +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'), + ('Flask', '1.1.2'), + ('matplotlib', '3.3.3'), + ('Tkinter', '%(pyver)s'), # needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional +] + +# 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 = [ + ('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/__archive__/a/ASE/ASE-3.22.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.22.0-foss-2020b.eb new file mode 100644 index 0000000000..aee9f6b2eb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.22.0-foss-2020b.eb @@ -0,0 +1,44 @@ +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'), + ('Flask', '1.1.2'), + ('matplotlib', '3.3.3'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional +] + +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/__archive__/a/ASE/ASE-3.22.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.22.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..3321ef3e8d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.22.0-fosscuda-2020b.eb @@ -0,0 +1,44 @@ +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 +] + +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/__archive__/a/ASE/ASE-3.22.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.22.0-intel-2020b.eb new file mode 100644 index 0000000000..2338c47460 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.22.0-intel-2020b.eb @@ -0,0 +1,44 @@ +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'), + ('Flask', '1.1.2'), + ('matplotlib', '3.3.3'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional +] + +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/__archive__/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..eb70f8215e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = "--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/__archive__/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb new file mode 100644 index 0000000000..aef949181c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb @@ -0,0 +1,62 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.4.0' + +homepage = 'https://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 + 'e74023f28ee3e76590f4534d195c313b88b66a92ec779da184d30d056fc8e052', # 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'), + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +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/__archive__/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..310e4f767d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb new file mode 100644 index 0000000000..f6ee200cfd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -0,0 +1,174 @@ +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 = [ + # 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-%(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', + }), +] + +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'", +] + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..75db88dd0b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb @@ -0,0 +1,181 @@ +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/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-%(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', + }), +] + +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'", +] + +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' diff --git a/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb new file mode 100644 index 0000000000..66824433a6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb @@ -0,0 +1,176 @@ +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', + }), +] + +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'", +] + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..39b1a7c019 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb @@ -0,0 +1,180 @@ +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', + }), +] + +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'", +] + +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' diff --git a/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..d90fa11e46 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -0,0 +1,186 @@ +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 +] +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-2.1.0_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', + 'AlphaFold-2.0.1_relax_gpu.patch', + 'AlphaFold-2.1_fix-alphafold-tests.patch', + ], + 'checksums': [ + '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.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 + '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch + # AlphaFold-2.1_fix-alphafold-tests.patch + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', + ], + 'start_dir': 'alphafold-%(version)s', + }), +] + +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'", +] + +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' diff --git a/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..8f4a0548ff --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,182 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.2' +local_tf_version = '2.5.0' +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" + +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', + 'AlphaFold-2.1_fix-alphafold-tests.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 + # AlphaFold-2.1_fix-alphafold-tests.patch + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', + ], + 'start_dir': 'alphafold-%(version)s', + }), +] + +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'", +] + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +modextravars = { + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..7ecc3335ca --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,188 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.2' +local_tf_version = '2.5.0' +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" + +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', + 'AlphaFold-2.1_fix-alphafold-tests.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 + # AlphaFold-2.1_fix-alphafold-tests.patch + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', + ], + 'start_dir': 'alphafold-%(version)s', + }), +] + +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'", +] + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +modextravars = { + # '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' diff --git a/easybuild/easyconfigs/__archive__/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb new file mode 100644 index 0000000000..6135637a22 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -0,0 +1,80 @@ +# 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'} + +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'), +] + +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_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/__archive__/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..3cdf5fa98f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb @@ -0,0 +1,80 @@ +# 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'), +] + +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_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/__archive__/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb new file mode 100644 index 0000000000..3e43c7245a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb @@ -0,0 +1,93 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 21 +# 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 = 'https://ambermd.org/' +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, + {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'} +] +patches = [ + {'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 + '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', +] +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'), + ('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' diff --git a/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb new file mode 100644 index 0000000000..a3ba577980 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb @@ -0,0 +1,66 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 21 +# 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 = 'https://ambermd.org/' +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', + 'AmberTools-20_fix_xblas_missing_make_dependency.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', + # 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'), + ('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', SYSTEM), +] + +# Some CUDA tests differs from expected results +runtest = False + +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..09c556f1fb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +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'] + +builddependencies = [ + ('binutils', '2.35'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-10.5.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-10.5.3-foss-2020b.eb new file mode 100644 index 0000000000..8bc6b53c4d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..05191b206c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb @@ -0,0 +1,48 @@ +# 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'), + ('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'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [('%(namelower)s', '-h')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-foss-2020b.eb new file mode 100644 index 0000000000..c5b59f6ec8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -0,0 +1,63 @@ +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 = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +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'), + ('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'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/python/development.html +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-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_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] + +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.dataset'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..03b39ad84d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -0,0 +1,66 @@ +# 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 = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +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'), + ('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'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-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=$TMPDIR && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " +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] + +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.dataset'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-intel-2020b.eb new file mode 100644 index 0000000000..381b36a6c1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -0,0 +1,63 @@ +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 = ['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 = [ + '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'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-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_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] + +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.dataset'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb new file mode 100644 index 0000000000..41b7744f93 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/ArviZ/ArviZ-0.11.1-intel-2020b.eb @@ -0,0 +1,23 @@ +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'} + +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'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb new file mode 100644 index 0000000000..537b89a6a6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb @@ -0,0 +1,36 @@ +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'), +] + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('anndata', '0.7.6', { + 'checksums': ['a3cc67bba9a4cd4b5984aec64c4f577c2d5a4695f4064027f8e6a9dac1f508b2'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('autogenes', version, { + 'checksums': ['8daa6e9aa97c7ddf45ab0906307a4875a25bd99301be0838bb17e313d837446a'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/Autoconf-archive/Autoconf-archive-2021.02.19-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/a/Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c5f974ed99 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..94d0fe0023 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['b2f361094b410b4acbf4efba7337bdb786335ca09eb2518635a09fb7319ca5c1'] + +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/__archive__/a/Autotools/Autotools-20200321-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20200321-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..748c84f8d6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/__archive__/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..d913618d8b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb @@ -0,0 +1,37 @@ +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 + '7aa081d6543bbec7024e2f4f166b9ea6ba62624fae465db04d231cce207b9b21', + '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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/__archive__/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..50fd79899c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb @@ -0,0 +1,35 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/__archive__/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..86f067f3ce --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb @@ -0,0 +1,35 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/a/ack/ack-3.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/ack/ack-3.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d532200154 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ea9607c100 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e679e46298 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['https://www.alsa-project.org/files/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' diff --git a/easybuild/easyconfigs/__archive__/a/angsd/angsd-0.935-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/angsd/angsd-0.935-GCC-10.2.0.eb new file mode 100644 index 0000000000..35882a6104 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb new file mode 100644 index 0000000000..cf6d8de85b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -0,0 +1,98 @@ +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', '3.8.31'), + ('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', '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"', + }), +] + +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 + ], + # 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': [ + # antismash/databases subdirectory is only populated when postinstallcmds above are commented out + # 'lib/python%(pyshortver)s/site-packages/antismash/databases', + ], +} + +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", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb new file mode 100644 index 0000000000..c69a7b6bb5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb @@ -0,0 +1,80 @@ +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', + }), +] + +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", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..52f8445081 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# Updated by: 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/__archive__/a/apex/apex-20210420-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/a/apex/apex-20210420-fosscuda-2020b.eb new file mode 100644 index 0000000000..d4aefdb6d5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/apex/apex-20210420-fosscuda-2020b.eb @@ -0,0 +1,28 @@ +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'), +] + +installopts = "--no-cache-dir --global-option='--cpp_ext' --global-option='--cuda_ext' --global-option='--pyprof'" + +sanity_check_commands = ["python -c 'from apex import amp'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7b486d4f4a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +## +# 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')] + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/argtable/argtable-2.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/argtable/argtable-2.13-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bf680a03bd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = 'https://argtable.sourceforge.io/' +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' diff --git a/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb new file mode 100644 index 0000000000..6a206a117b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.8.0-foss-2020b.eb @@ -0,0 +1,38 @@ +## +# 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' diff --git a/easybuild/easyconfigs/__archive__/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb new file mode 100644 index 0000000000..ac69d69016 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -0,0 +1,88 @@ +# 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'), + ('minimap2', '2.18'), + ('SAMtools', '1.11'), + ('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', '', SYSTEM), + ('gotree', '0.4.0', '', SYSTEM), + ('rampart', '1.2.0'), + ('libdeflate', '1.7'), + ('nanopolish', '0.13.3'), + ('seqtk', '1.3'), + ('BCFtools', '1.11'), + ('tqdm', '4.56.2'), +] + +exts_list = [ + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('PyVCF', '0.6.8', { + 'modulename': 'vcf', + 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], + }), + ('fieldbioinformatics', '1.2.1', { + 'modulename': 'artic', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], + 'checksums': ['74b5fdb18dca57e73fbe872c5c4e25c110e7826fac7a062f0eb0a5453e4e7b20'], + }), +] + +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_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], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'artic -v', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.2.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.2.1-foss-2020b.eb new file mode 100644 index 0000000000..05cea4d686 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.2.1-foss-2020b.eb @@ -0,0 +1,36 @@ +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'), +] + +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/__archive__/a/astropy/astropy-4.2.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.2.1-intel-2020b.eb new file mode 100644 index 0000000000..3f8dd88d7d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.2.1-intel-2020b.eb @@ -0,0 +1,36 @@ +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'), +] + +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/__archive__/a/astropy/astropy-4.2.1-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.2.1-intelcuda-2020b.eb new file mode 100644 index 0000000000..296cbb27dc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.2.1-intelcuda-2020b.eb @@ -0,0 +1,36 @@ +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': 'intelcuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +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/__archive__/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..18f70fd3f8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +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'), +] + +# Hard disable Dbus broker detection +preconfigopts = "sed -i s/'dbus_broker.found()'/false/ ../*/bus/meson.build &&" +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-38.90-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-38.90-GCC-10.2.0.eb new file mode 100644 index 0000000000..d0f16e3b3b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM)] + +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' diff --git a/easybuild/easyconfigs/__archive__/b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/BCFtools/BCFtools-1.11-GCC-10.2.0.eb new file mode 100644 index 0000000000..c0e967c4db --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/BCFtools/BCFtools-1.12-GCC-10.2.0.eb new file mode 100644 index 0000000000..087e109afd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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=$EBROOTHTSLIB --enable-libgsl" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['libexec/bcftools'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BEDTools/BEDTools-2.30.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/BEDTools/BEDTools-2.30.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..ba9d1d085d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BEDTools/BEDTools-2.30.0-GCC-10.2.0.eb @@ -0,0 +1,43 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.30.0' + +homepage = "https://bedtools.readthedocs.io/" +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8'] + +builddependencies = [('Python', '3.8.6')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.1'), +] + +buildopts = 'CXX="$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/__archive__/b/BEDTools/BEDTools-2.30.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/b/BEDTools/BEDTools-2.30.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..4564f1bb57 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..0de4a51f65 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BEEF/BEEF-0.1.1-iccifort-2020.4.304.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'BEEF' +version = '0.1.1' + +homepage = 'https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software' +description = """BEEF is a library-based implementation of the Bayesian +Error Estimation Functional, suitable for linking against by Fortran- +or C-based DFT codes. A description of BEEF can be found at +http://dx.doi.org/10.1103/PhysRevB.85.235149.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://confluence.slac.stanford.edu/download/attachments/146704476/'] +sources = ['libbeef-%(version)s.tar.gz'] +checksums = ['b6af622b74a4e55d637d8cd5027cfa850cf22fec53981c5732de5c40cc0a938a'] + +configopts = 'CC="$CC"' + +sanity_check_paths = { + 'files': ['bin/bee', 'lib/libbeef.a'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.11.0-gompi-2020b.eb new file mode 100644 index 0000000000..27565c0c39 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), + ('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" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-0.8.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9917d88d4a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb b/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb new file mode 100644 index 0000000000..767f214dca --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb @@ -0,0 +1,51 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '3.0.1' +versionsuffix = '-amd' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' +description = """AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/amd/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-0.8.1_enable_ppc_autodetect.patch', + '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', +] +checksums = [ + 'dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e', # 3.0.1.tar.gz + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', + # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch + '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', +] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +# Build Serial and multithreaded library +configopts = ['--enable-cblas --enable-shared CC="$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 = {MODULE_LOAD_ENV_HEADERS: 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb new file mode 100644 index 0000000000..84d5b402f5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb @@ -0,0 +1,50 @@ +# 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'), +] + +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/__archive__/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb new file mode 100644 index 0000000000..2c8f327027 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BUSCO/BUSCO-5.0.0-foss-2020b.eb @@ -0,0 +1,50 @@ +# 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'), +] + +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/__archive__/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb new file mode 100644 index 0000000000..0a751183af --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BUSCO/BUSCO-5.1.2-foss-2020b.eb @@ -0,0 +1,50 @@ +# 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'), +] + +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/__archive__/b/BWA/BWA-0.7.17-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.17-GCC-10.2.0.eb new file mode 100644 index 0000000000..b6825ba6a8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.17-GCC-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 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'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.17-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.17-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..d3c453af6d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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="$CFLAGS -fcommon" && ' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bader/Bader-1.04-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/b/Bader/Bader-1.04-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..51520b0c75 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Bader/Bader-1.04-iccifort-2020.4.304.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'Bader' +version = '1.04' + +homepage = 'http://theory.cm.utexas.edu/henkelman/code/bader/' +description = "A fast algorithm for doing Bader's analysis on a charge density grid." + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] +sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f20a0a021157d911bea06666911763b737c4ff38b39e793b8560f940fe391b8e'] + +buildopts = '-f makefile.lnx_ifort FFLAGS="$FFLAGS" LINK="-static-intel"' +maxparallel = 1 + +files_to_copy = [(['bader'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bader'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s -h"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..832de6cddb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.5.1-GCC-10.2.0.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'CMakeMake' + +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')] + +sanity_check_paths = { + 'files': ['bin/bamtools', 'include/bamtools/shared/bamtools_global.h', 'lib/libbamtools.a'], + 'dirs': ['include/bamtools/api', 'lib/pkgconfig'], +} + +sanity_check_commands = ["bamtools --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..7e8593030c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.5.1-iccifort-2020.4.304.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'CMakeMake' + +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} + +# 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'), + ('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'], +} + +sanity_check_commands = ["bamtools --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3c49531cee --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '11', '', SYSTEM)] + +runtest = True +testopts = ' '.join([ + '--', + '//examples/cpp:hello-success_test', + '//examples/py/...', + '//examples/py_native:test', + '//examples/shell/...', +]) + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f540819325 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM)] + +runtest = True +testopts = ' '.join([ + '--', + '//examples/cpp:hello-success_test', + '//examples/py/...', + '//examples/py_native:test', + '//examples/shell/...', +]) + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/Beast/Beast-1.10.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Beast/Beast-1.10.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..799b63b5ea --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/b/Beast/Beast-2.6.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Beast/Beast-2.6.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..9c383f87b5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..05cf100235 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb new file mode 100644 index 0000000000..e40828947d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb new file mode 100644 index 0000000000..124fad4ecb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb @@ -0,0 +1,32 @@ +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'), +] + +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..124e6f8875 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8e7eb5871f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/BioPerl/BioPerl-1.7.8-GCCcore-10.2.0.eb @@ -0,0 +1,54 @@ +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_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' diff --git a/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..870a0d3e85 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.76-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,39 @@ +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), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-foss-2020b.eb b/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-foss-2020b.eb new file mode 100644 index 0000000000..9b3f063cb1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-foss-2020b.eb @@ -0,0 +1,38 @@ +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'), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-fosscuda-2020b.eb new file mode 100644 index 0000000000..7d0f43fd2f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-fosscuda-2020b.eb @@ -0,0 +1,38 @@ +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'), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-intel-2020b.eb b/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-intel-2020b.eb new file mode 100644 index 0000000000..15fb03b774 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-intel-2020b.eb @@ -0,0 +1,38 @@ +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'), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7924ce6969 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), +] + + +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/__archive__/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8edc3c84d8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), +] + + +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/__archive__/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8dfa22d145 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +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'] +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')] + +sanity_check_paths = { + 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], + 'dirs': ['include/blitz/array', 'include/blitz/meta', + 'include/random', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/b/Blosc/Blosc-1.21.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Blosc/Blosc-1.21.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7ff2a0c648 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d41c44db0f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb new file mode 100644 index 0000000000..04ce4f3028 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Bonito/Bonito-0.3.8-fosscuda-2020b.eb @@ -0,0 +1,113 @@ +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'), +] + +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_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/__archive__/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..f2b748f8d3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Bonito/Bonito-0.4.0-fosscuda-2020b.eb @@ -0,0 +1,122 @@ +# 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'), + ('ont-fast5-api', '3.3.0'), +] + +# 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 +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 && " + +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'], + }), + ('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', { + 'checksums': ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'], + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'preinstallopts': local_bonito_preinstallopts, + 'checksums': ['429310d56e2d7dabd91a9a9c972504a0aa2b6d6469563b14d4aae30adfe9a87e'], + }), +] + +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/__archive__/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Boost.Python/Boost.Python-1.74.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..9ca9d5f851 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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://archives.boost.io/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/__archive__/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.74.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..164df10bb3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +## +# Authors:: Denis Kristak +## +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://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 = [ + 'afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5', # boost_1_74_0.tar.gz + # Boost-1.74.0-library_version_type_serialization.patch + 'ee61e889ce9473ad82b69c9a8cbe1bf9650d633b74fdf7e4f4a4825aa990feca', +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('zstd', '1.4.5'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..088daf7c7f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb @@ -0,0 +1,33 @@ +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://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 = [ + 'afff36d392885120bcac079148c177d1f6f7730ec3d47233aa51b0afa4db94a5', # boost_1_74_0.tar.gz + # Boost-1.74.0-library_version_type_serialization.patch + 'ee61e889ce9473ad82b69c9a8cbe1bf9650d633b74fdf7e4f4a4825aa990feca', +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('zstd', '1.4.5'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/Bowtie/Bowtie-1.3.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Bowtie/Bowtie-1.3.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..8b2978402e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..2a3ee99cd4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..382bedd030 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +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'), +] + +options = {'modulename': 'brotli'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8626bb2733 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 +] + +builddependencies = [ + ('binutils', '2.35'), + ('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': [], +} + +sanity_check_commands = ["brotli --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8de6003c4d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('Brotli', '1.0.9'), +] + +# 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 libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..719cac72c8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/b/barrnap/barrnap-0.9-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/b/barrnap/barrnap-0.9-gompi-2020b.eb new file mode 100644 index 0000000000..42ca6abb5e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb new file mode 100644 index 0000000000..3ca36911d1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb @@ -0,0 +1,38 @@ +# 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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..85c6e58941 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +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, '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-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 + '7908c268c213a6cfeafe05afcd5d3b34098241b6ab0a62c11ea47664cd0a63c5', # bcl2fastq2-2.20.0-fix-cmake-target-libs.patch + '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1', # bcl2fastq2-2.20.0-find-boost.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), +] + +start_dir = 'src' + +# check versions of libxml2 and libxslt from EB +local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' +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 += 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 ' +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'], + 'dirs': ['lib'], +} + +sanity_check_commands = ["bcl2fastq --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/bcolz/bcolz-1.2.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/b/bcolz/bcolz-1.2.1-foss-2020b.eb new file mode 100644 index 0000000000..a3f3693c43 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/bcolz/bcolz-1.2.1-foss-2020b.eb @@ -0,0 +1,40 @@ +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'), +] + +preinstallopts = "BLOSC_DIR=$EBROOTBLOSC" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import bcolz; bcolz.test()'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..e676c19b2a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), + ('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/__archive__/b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..460afd5c0d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.35-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..43435891a6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.35-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +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] +# 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. +sources = ["%(name)s-%(version)s.2.tar.gz"] +patches = ['binutils-2.34-readd-avx512-vmovd.patch'] +checksums = [ + 'f484f61c81aa679df84d358d9818d5bf3e71fd227303f234f72b24420d98d3cd', # binutils-2.35.2.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, '', SYSTEM) +] + +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 + +# 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' diff --git a/easybuild/easyconfigs/__archive__/b/bmtagger/bmtagger-3.101-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/b/bmtagger/bmtagger-3.101-gompi-2020b.eb new file mode 100644 index 0000000000..afe9d05064 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/b/bokeh/bokeh-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-foss-2020b.eb new file mode 100644 index 0000000000..2fa54376e2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-foss-2020b.eb @@ -0,0 +1,35 @@ +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'), +] + +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"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..b51d9f9d43 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-fosscuda-2020b.eb @@ -0,0 +1,35 @@ +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'), +] + +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"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-intel-2020b.eb b/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-intel-2020b.eb new file mode 100644 index 0000000000..706ee596f5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-intel-2020b.eb @@ -0,0 +1,35 @@ +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'), + ('typing-extensions', '3.7.4.3'), +] + +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"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb new file mode 100644 index 0000000000..f96cc03618 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb @@ -0,0 +1,35 @@ +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'), +] + +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"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/bpytop/bpytop-1.0.60-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/bpytop/bpytop-1.0.60-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cbc86c851a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..67f22a6705 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/bsddb3/bsddb3-6.2.9-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['70d05ec8dc568f42e70fc919a442e0daadc2a905a1cfb7ca77f549d49d6e7801'] + +osdependencies = [('libdb-dev', 'libdb-devel')] + +builddependencies = [('binutils', '2.35')] +dependencies = [('Python', '3.8.6')] + +# Need to unset LIBS or pip install crashes. +preinstallopts = 'unset LIBS && ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-foss-2020b.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-foss-2020b.eb new file mode 100644 index 0000000000..8a480f0a78 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/b/buildenv/buildenv-default-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-fosscuda-2020b.eb new file mode 100644 index 0000000000..cf4d4b054b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/b/buildenv/buildenv-default-intel-2020b.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-intel-2020b.eb new file mode 100644 index 0000000000..227c38508d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/b/buildenv/buildenv-default-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-intelcuda-2020b.eb new file mode 100644 index 0000000000..2670ea6735 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..91da342e8f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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': {'paths': '', 'delimiter': ' '}} + +sanity_check_paths = { + 'files': ['button.tcl'], + 'dirs': ['BWman'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4e0873a1c5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..2f7bc2e4c9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Max Voit + +easyblock = 'MakeCp' + +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, 'cstd': 'c++11'} + +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 $CXXFLAGS -o" ' +with_configure = True +files_to_copy = ['bin', 'examples'] +postinstallcmds = ['chmod -x %(installdir)s/examples/*.txt'] + +sanity_check_paths = { + 'files': ['bin/cafe5'], + 'dirs': ['examples'], +} + +sanity_check_commands = ['cafe5 --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb new file mode 100644 index 0000000000..8ce474d08a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CAMPARI/CAMPARI-4.0-intel-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'CAMPARI' +version = '4.0' +_date = '12202020' + +homepage = 'http://campari.sourceforge.net/V4/index.html' +description = """ +CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological +relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte +Carlo and molecular dynamics in seamless fashion.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['campari_v%s_%s.zip' % (version.split('.')[0], _date)] +checksums = ['bc627fb286b5461a5c68aa3e1a551ecd81016495163685800163c734f7c4f1bd'] + +dependencies = [ + ('netCDF-Fortran', '4.5.3'), + ('libtirpc', '1.3.1'), +] + +start_dir = 'source' + +configopts = '--enable-mpi=auto LIBS="$LIBS $LIBFFT -ltirpc"' + +buildopts = 'all LIBS="$LIBS $LIBFFT -ltirpc"' + +maxparallel = 10 + +postinstallcmds = ['cp -a %(builddir)s/campari/{data,doc,examples,params,tools,LICENSE} %(installdir)s/'] + +_binaries = ['campari', 'campari_mpi', 'campari_mpi_threads', 'campari_threads', 'camp_ncminer', 'camp_ncminer_threads'] +_libraries = ['lcampari.a', 'lcampari_mpi.a', 'lcampari_mpi_threads.a', 'lcampari_threads.a', 'libxdrf.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/%s' % x for x in _libraries], + 'dirs': [], +} + +sanity_check_commands = ['campari -h | grep "USAGE: CAMPARI"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..0277630cc1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CD-HIT/CD-HIT-4.8.1-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.32.0'), + ('zlib', '1.2.11'), +] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb new file mode 100644 index 0000000000..11fc1a9fd9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'CDBtools' +version = '0.99' + +homepage = 'http://compbio.dfci.harvard.edu/tgi' +description = "CDB (Constant DataBase) indexing and retrieval tools for FASTA files" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta'] +sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c'] + +buildopts = 'CC="$CXX" DBGFLAGS="$CXXFLAGS"' + +files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cdbfasta', 'bin/cdbyank'], + 'dirs': [], +} + +sanity_check_commands = [ + "cdbfasta -v", + "cdbyank -v", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CDO/CDO-1.9.10-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/c/CDO/CDO-1.9.10-gompi-2020b.eb new file mode 100644 index 0000000000..1821dbe769 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CDO/CDO-1.9.10-gompi-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.9.10' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/24638/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc39c89bbb481d7b3945a06c56a8492047235f46ac363c4f0d980fccdde6677e'] + +dependencies = [ + ('HDF5', '1.10.7'), + ('netCDF', '4.7.4'), + ('YAXT', '0.9.0'), + ('ecCodes', '2.20.0'), +] + +configopts = "--with-hdf5=$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' diff --git a/easybuild/easyconfigs/__archive__/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..508660721a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/c/CGAL/CGAL-5.2-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-5.2-gompi-2020b.eb new file mode 100644 index 0000000000..0ee32908a0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-5.2-gompi-2020b.eb @@ -0,0 +1,37 @@ +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 -DWITH_GMPXX=ON" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb new file mode 100644 index 0000000000..262fe6aad5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb @@ -0,0 +1,27 @@ +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] +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +builddependencies = [ + ('Cython', '3.0a5'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb new file mode 100644 index 0000000000..2b683aad14 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -0,0 +1,27 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +builddependencies = [ + ('Cython', '3.0a5'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb new file mode 100644 index 0000000000..8ba151985f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb @@ -0,0 +1,27 @@ +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') +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb new file mode 100644 index 0000000000..376242695f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb @@ -0,0 +1,27 @@ +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') +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..4638c0d32a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,39 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8261ee884f6d895131ce681d5eda6554376e973851a9de4dc50e2b3e242ccc80'] + +dependencies = [ + ('Python', '2.7.18'), + ('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'), + ('BEDTools', '2.30.0'), + ('Kent_tools', '411'), + ('STAR', '2.7.6a'), + ('BWA', '0.7.17'), + ('segemehl', '0.3.4'), + ('Pysam', '0.16.0.1', versionsuffix), + ('pybedtools', '0.8.2', versionsuffix), +] + +options = {'modulename': 'circ2'} + +sanity_check_paths = { + 'files': ['bin/CIRCexplorer2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["CIRCexplorer2 denovo --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb new file mode 100644 index 0000000000..4bba2206c3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb @@ -0,0 +1,49 @@ +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', '1.11'), + ('Biopython', '1.78'), + ('pyspoa', '0.0.8'), + ('python-Levenshtein', '0.12.1'), +] + +exts_list = [ + ('mappy', '2.17', { + 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], + }), + ('bwapy', '0.1.4', { + 'checksums': ['fcdad0c7311753d550b3a3aefbc2619380e7e35e7aeaa386fd491cba47e71824'], + }), + (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', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CLHEP/CLHEP-2.4.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CLHEP/CLHEP-2.4.4.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..190ed762b8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..adcb0b84ea --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +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'), + ('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'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..16e8766c69 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..b8f169bcc8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CNVkit/CNVkit-0.9.8-foss-2020b-R-4.0.3.eb @@ -0,0 +1,52 @@ +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'), + ('pyfaidx', '0.5.9.5'), + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +exts_list = [ + ('reportlab', '3.5.66', { + 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], + }), + ('pomegranate', '0.13.5', { + 'checksums': ['b1b803fa18c8a8ca4a8fd2824573914bbff7574e3dc6be770ab68efd00503341'], + }), + (name, version, { + 'postinstallcmds': ["cd test/ && make"], + 'modulename': 'cnvlib', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/etal/cnvkit/archive/'], + 'checksums': ['57e3081fd12c402abbc448851fda741795f23e68416c2564d9c09930bd56eef8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cnvkit.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cnvkit.py --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..c5d5cf7a6d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,41 @@ +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', SYSTEM), + ('Pysam', '0.16.0.1', versionsuffix), + ('SAMtools', '1.11'), + ('scikit-learn', '0.20.4', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/concoct'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["concoct --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-5.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-5.1-foss-2020b.eb new file mode 100644 index 0000000000..8bc41a594e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-foss-2020b-psmp.eb new file mode 100644 index 0000000000..ce2ab7909a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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, 'openmp': 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' diff --git a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-foss-2020b.eb new file mode 100644 index 0000000000..742f3d1372 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-intel-2020b.eb new file mode 100644 index 0000000000..ee964e56ae --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-8.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-8.1-foss-2020b.eb new file mode 100644 index 0000000000..de7450f83b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb new file mode 100644 index 0000000000..52537f135f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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-%(version)s_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'), # provides naturalsort R package + ('Perl', '5.32.0'), + ('NGS', '2.10.9'), + ('Pysam', '0.16.0.1'), + ('Excel-Writer-XLSX', '1.09'), + ('pysamstats', '1.1.2'), + ('ABRA2', '2.23'), + ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), + ('SAMtools', '1.11'), + ('BEDTools', '2.30.0'), + ('FLASH', '2.2.00'), + ('Archive-Zip', '1.68'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..743acb941e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,59 @@ +# 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_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_v2.1.2.fastq.gz +] + +dependencies = [ + ('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', SYSTEM), + ('FLASH', '2.2.00'), + ('SAMtools', '1.11'), + ('Bowtie2', '2.4.2'), + ('Seaborn', '0.9.1', '-Python-%(pyver)s'), +] + +# 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, +] + +options = {'modulename': name} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb new file mode 100644 index 0000000000..4659d76481 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb @@ -0,0 +1,58 @@ +# 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', '', SYSTEM), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', SYSTEM), + ('FLASH', '2.2.00'), + ('SAMtools', '1.11'), + ('Bowtie2', '2.4.2'), + ('Seaborn', '0.11.1'), +] + +# 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, +] + +options = {'modulename': name} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CSB/CSB-1.2.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/CSB/CSB-1.2.5-foss-2020b.eb new file mode 100644 index 0000000000..452e52e64c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CSB/CSB-1.2.5-foss-2020b.eb @@ -0,0 +1,43 @@ +# 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'] + +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' diff --git a/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..02cea32f4a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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, '', SYSTEM)] + +altroot = 'CUDAcore' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..60c8e70673 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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, '', SYSTEM)] + +altroot = 'CUDAcore' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb new file mode 100644 index 0000000000..2192fdc7fa --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb @@ -0,0 +1,36 @@ +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/c/CapnProto/CapnProto-0.9.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CapnProto/CapnProto-0.9.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5f3f76e2e2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb new file mode 100644 index 0000000000..cb726e86e4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb @@ -0,0 +1,47 @@ +# 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'), +] + +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/__archive__/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb new file mode 100644 index 0000000000..2135a8f521 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb @@ -0,0 +1,47 @@ +# 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'), +] + +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/__archive__/c/Catch2/Catch2-2.13.4.eb b/easybuild/easyconfigs/__archive__/c/Catch2/Catch2-2.13.4.eb new file mode 100644 index 0000000000..f1be3f1c7c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['e7eb70b3d0ac2ed7dcf14563ad808740c29e628edde99e973adad373a2b5e4df'] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/c/Catch2/Catch2-2.13.9.eb b/easybuild/easyconfigs/__archive__/c/Catch2/Catch2-2.13.9.eb new file mode 100644 index 0000000000..23d28166d6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/Cbc/Cbc-2.10.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/Cbc/Cbc-2.10.5-foss-2020b.eb new file mode 100644 index 0000000000..26a9185dc8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' % (x, SHLIB_EXT) for x in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/__archive__/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb new file mode 100644 index 0000000000..200d507153 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb @@ -0,0 +1,44 @@ +# 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'), +] + +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/__archive__/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..007fb40d94 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb @@ -0,0 +1,44 @@ +# 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'), +] + +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/__archive__/c/Centrifuge/Centrifuge-1.0.4-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/c/Centrifuge/Centrifuge-1.0.4-gompi-2020b.eb new file mode 100644 index 0000000000..10d20754e0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/Cgl/Cgl-0.60.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/Cgl/Cgl-0.60.3-foss-2020b.eb new file mode 100644 index 0000000000..3a65e5ac28 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = {MODULE_LOAD_ENV_HEADERS: 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/__archive__/c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..afad4ef356 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/Check/Check-0.15.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/Check/Check-0.15.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..730f400e97 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..04f2236821 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,58 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +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', '', SYSTEM), + ('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), +] + +# 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"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6d6f037e9e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,74 @@ +## +# 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'), + ('libffi', '3.3'), + ('elfutils', '0.183'), +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +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/__archive__/c/Clang/Clang-11.0.1-gcccuda-2020b.eb b/easybuild/easyconfigs/__archive__/c/Clang/Clang-11.0.1-gcccuda-2020b.eb new file mode 100644 index 0000000000..d5b83b6bd5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/Clang/Clang-11.0.1-gcccuda-2020b.eb @@ -0,0 +1,74 @@ +## +# 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'), + ('libffi', '3.3'), + ('elfutils', '0.183'), +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +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/__archive__/c/Clp/Clp-1.17.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/Clp/Clp-1.17.6-foss-2020b.eb new file mode 100644 index 0000000000..ff0a3292b0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' % (x, SHLIB_EXT) for x in ['Clp', 'ClpSolver', 'OsiClp']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/__archive__/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..aee0b9e19e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = {MODULE_LOAD_ENV_HEADERS: 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/__archive__/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb new file mode 100644 index 0000000000..7f05717089 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..61e5d8e491 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..adec31e36e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb @@ -0,0 +1,40 @@ +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-%(cudaver)s', SYSTEM), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('cuTENSOR', '1.2.2.5', '-CUDA-%(cudaver)s', SYSTEM), +] + +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/*-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 + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/c/CubeGUI/CubeGUI-4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CubeGUI/CubeGUI-4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..99955038a6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/c/CubeLib/CubeLib-4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CubeLib/CubeLib-4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a669ee8b3f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CubeWriter/CubeWriter-4.4.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4b3c1d7de0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = [ + ('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.so'], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/c/CubeWriter/CubeWriter-4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/CubeWriter/CubeWriter-4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2d3fc4b8b4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/Cufflinks/Cufflinks-20190706-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/Cufflinks/Cufflinks-20190706-GCC-10.2.0.eb new file mode 100644 index 0000000000..af9650a7fd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8aa80047a4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/Cython/Cython-0.29.22-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# 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'} + +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')] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cython --version', +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b747ba9017 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# 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')] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cython --version', +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c745d57b96 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +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', '1.1.1h') +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +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' diff --git a/easybuild/easyconfigs/__archive__/c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0449c9cee8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/c/canu/canu-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/canu/canu-2.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1a81cacc46 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), + ('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' diff --git a/easybuild/easyconfigs/__archive__/c/carputils/carputils-20210513-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/carputils/carputils-20210513-foss-2020b.eb new file mode 100644 index 0000000000..82b0ce4901 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/carputils/carputils-20210513-foss-2020b.eb @@ -0,0 +1,70 @@ +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'), +] + +# 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"] + +modextravars = {'CARPUTILS_SETTINGS': '%(installdir)s/settings.yaml'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/ccache/ccache-4.2.1.eb b/easybuild/easyconfigs/__archive__/c/ccache/ccache-4.2.1.eb new file mode 100644 index 0000000000..c367614071 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/ccache/ccache-4.2.1.eb @@ -0,0 +1,42 @@ +# 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)), +] + +# 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'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb b/easybuild/easyconfigs/__archive__/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb new file mode 100644 index 0000000000..66f537471f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb @@ -0,0 +1,61 @@ +# author: Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +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_pyver = '3.8.6' +local_pyver_special = ''.join(local_pyver.split('.')[:2]) + +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, { + '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'], + # remove deps (they fail during sanity check, even though they are installed) + 'postinstallcmds': ["echo '' > %s" % local_metadata], + 'modulename': 'cctbx', + }), +] + +sanity_check_paths = { + 'files': ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cctbx_website'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb new file mode 100644 index 0000000000..ecf4c4cf84 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb @@ -0,0 +1,64 @@ +# 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'], + }), +] + +sanity_check_paths = { + "files": ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], + "dirs": ['lib/python%(pyshortver)s/site-packages/cctbx_website'], +} + +moduleclass = "lib" diff --git a/easybuild/easyconfigs/__archive__/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb new file mode 100644 index 0000000000..0d601f949a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -0,0 +1,124 @@ +# 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'), + ('flex', '2.6.4'), # needed by louvain +] + +dependencies = [ + ('Python', '3.8.6'), + ('Java', '11', '', SYSTEM), + ('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 && " + +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_urls': ['https://github.com/BayraktarLab/cell2location/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['b1d4fc0e1eb8292457793d6af8228189bd24dd87837b8f4435d0a0312ed20c6b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/loompy', 'bin/scanpy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/cicero/cicero-1.3.4.11-foss-2020b-R-4.0.3-Monocle3.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..be9c499a5a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +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'} + +builddependencies = { + ('binutils', '2.35'), +} + +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_paths = { + 'files': ['bin/configurable-http-proxy'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/c/coverage/coverage-5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/coverage/coverage-5.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..152f380e38 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/coverage/coverage-5.5-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ebe78fe9a0e874362175b02371bdfbee64d8edc42a044253ddf4ee7d3c15212c'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1b666a2023 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = {MODULE_LOAD_ENV_HEADERS: '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/__archive__/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..a7307e3a97 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'cryoDRGN' +version = '0.3.2' + +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 + 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'), + ('plotly.py', '4.14.3'), + ('scikit-learn', '0.23.2'), + ('matplotlib', '3.3.3'), + ('Seaborn', '0.11.1'), +] + +exts_list = [ + ('colorlover', '0.3.0', { + 'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'], + }), + ('cufflinks', '0.17.3', { + 'checksums': ['48c1b3406dc030004121966489eebc5518cea70fd4e3f16379b491328501a644'], + }), + ('pynndescent', '0.5.2', { + 'checksums': ['d9fd22210b8d64368376ff392e876fb72fe3cda282396cfa6a59440ab6600771'], + }), + ('umap-learn', '0.5.1', { + 'checksums': ['3e3e5e526109866012a9da79f423c922edc379c6cac9bf65ea08fbb9dd93ff3a'], + 'modulename': 'umap', + }), + (name.lower(), version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/zhonge/cryodrgn/archive'], + 'checksums': ['1efecc2a0add2392411076082c122039a490f5ddf3e01f1da38aea1a81592077'], + 'postinstallcmds': [ + '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', + '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' diff --git a/easybuild/easyconfigs/__archive__/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb new file mode 100644 index 0000000000..9f5fe72dfb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb @@ -0,0 +1,48 @@ +# 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] +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 = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5'), + ('LibTIFF', '4.1.0'), + ('GSL', '2.6'), + ('wxWidgets', '3.1.4'), +] + +configopts = '--enable-openmp ' + +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..ee0f8d906f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-1.18-GCC-10.2.0-Python-2.7.18.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 +# 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')] + +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 +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..754f14bd46 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +# 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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..df95ca0d5d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +# 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 = [ + ('pigz', '2.6'), + ('Python', '3.8.6'), + ('python-isal', '0.11.1'), +] + +exts_list = [ + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + ('dnaio', '0.5.2', { + 'checksums': ['549e1c6afa192a4bf79c112b57cc5e927b286ab9a3c2803d6577613a7e3ff180'], + }), + (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/__archive__/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/DB/DB-18.1.40-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c409d75484 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# 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'} + +# 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 + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +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/__archive__/d/DBD-mysql/DBD-mysql-4.050-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/DBD-mysql/DBD-mysql-4.050-GCC-10.2.0.eb new file mode 100644 index 0000000000..b9c2fcbe4a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3c7b085c1a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/%(arch)s-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b049fce156 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +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 = ['8078f5c25e34ab907ce06905d969dc8ef0ccbec367e1e1707c7ecf8460f4254e'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('expat', '2.2.9'), +] + +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 + ['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/__archive__/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bd4bec9dbd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/DFA/DFA-2.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +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'), +] + +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/__archive__/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..29e0a67ce6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = '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/grimme/de/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/__archive__/d/DIAMOND/DIAMOND-2.0.7-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/DIAMOND/DIAMOND-2.0.7-GCC-10.2.0.eb new file mode 100644 index 0000000000..e8a87219c1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/d/DL_POLY_4/DL_POLY_4-5.0.0-foss-2020b.eb new file mode 100644 index 0000000000..a6ef70157e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = "DL_POLY is a general purpose classical molecular dynamics (MD) simulation software" + +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/__archive__/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/d/DL_POLY_4/DL_POLY_4-5.0.0-intel-2020b.eb new file mode 100644 index 0000000000..77e8e8fecd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = "DL_POLY is a general purpose classical molecular dynamics (MD) simulation software" + +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' diff --git a/easybuild/easyconfigs/__archive__/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..43b7b86327 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -0,0 +1,69 @@ +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', '', SYSTEM), + ('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', '', SYSTEM), +] + +# 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'], + }), + ('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', { + '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'], + }), +] + +sanity_check_paths = { + 'files': ['bin/drop'], + 'dirs': [], +} + +sanity_check_commands = ['drop --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..d5ca4b706d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb @@ -0,0 +1,66 @@ +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', '', SYSTEM), + ('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', '', SYSTEM), +] + +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'], + }), +] + +sanity_check_paths = { + 'files': ['bin/drop'], + 'dirs': [], +} + +sanity_check_commands = ['drop --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/Delly/Delly-0.8.7-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/d/Delly/Delly-0.8.7-gompi-2020b.eb new file mode 100644 index 0000000000..a91dbfee3e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 PARALLEL=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/__archive__/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/__archive__/d/Demystify/Demystify-0.0.17-foss-2020b.eb new file mode 100644 index 0000000000..cfce3200f6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -0,0 +1,25 @@ +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'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..5187e2bd4d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/DendroPy/DendroPy-4.5.2-GCCcore-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 +# +# 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')] + +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"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e26ef6250b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/DendroPy/DendroPy-4.5.2-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +## +# 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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +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"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..1076bd462a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/DosageConvertor/DosageConvertor-1.0.4-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +# Includes some material from the BEAR Software team at the University of Birmingham. + +easyblock = 'CMakeMake' + +name = 'DosageConvertor' +version = '1.0.4' +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 + 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_hash] +checksums = ['3ee1f3ef23d7e7c04295a5fa43c3b59811cc8fe778f0f69c9759c2624ae3aa47'] + +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_hash, local_hash) +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..245da26746 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +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" + +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/d/dSFMT/dSFMT-2.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/dSFMT/dSFMT-2.2.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6e45821bd8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-foss-2020b.eb new file mode 100644 index 0000000000..37cfcc5fb3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-foss-2020b.eb @@ -0,0 +1,71 @@ +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'), +] + +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_check_commands = ["dask-scheduler --help"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..8ed1c35da2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-fosscuda-2020b.eb @@ -0,0 +1,69 @@ +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'), +] + +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'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-intel-2020b.eb new file mode 100644 index 0000000000..ecf8a22c9e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-intel-2020b.eb @@ -0,0 +1,71 @@ +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'), +] + +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_check_commands = ["dask-scheduler --help"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-intelcuda-2020b.eb new file mode 100644 index 0000000000..929025fe26 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dask/dask-2021.2.0-intelcuda-2020b.eb @@ -0,0 +1,69 @@ +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'), +] + +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'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/d/datamash/datamash-1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/datamash/datamash-1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cfb866c453 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb new file mode 100644 index 0000000000..e38a7cd686 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb @@ -0,0 +1,29 @@ +# 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'] + +dependencies = [ + ('Python', '3.8.6'), + ('pydicom', '2.1.2'), + ('NiBabel', '3.2.1'), +] + +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/__archive__/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..3ec515d54f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb @@ -0,0 +1,29 @@ +# 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'), +] + +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/__archive__/d/dill/dill-0.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/dill/dill-0.3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ab34d50b7f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dill/dill-0.3.3-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +# 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'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb new file mode 100644 index 0000000000..ec07bb12ae --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb @@ -0,0 +1,40 @@ +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'), + ('protobuf', '3.14.0'), + ('dm-tree', '0.1.5'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +# Bundled upb sets -Werror, failing on any warning. Disable for harmless warnings +buildopts = "--copt='-Wno-error=stringop-truncation'" + +options = {'modulename': 'reverb'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e444b966c7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dm-tree/dm-tree-0.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a951d2239111dfcc468071bc8ff792c7b1e3192cab5a3c94d33a8b2bda3127fa'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bazel', '3.7.2'), +] +dependencies = [('Python', '3.8.6')] + +options = {'modulename': 'tree'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ba6b262e5e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +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'), +] + +# 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/__archive__/d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb new file mode 100644 index 0000000000..e2c9c89b8c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb new file mode 100644 index 0000000000..c7a15bbfaf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -0,0 +1,51 @@ +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. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('CMake', '3.18.4'), +] + +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/__archive__/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb new file mode 100644 index 0000000000..a30e864c23 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -0,0 +1,64 @@ +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. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PETSc', '3.14.4'), + ('CMake', '3.18.4'), + ('dune-core', '2.8.0.post1'), + ('matplotlib', '3.3.3'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb new file mode 100644 index 0000000000..09a1107118 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/EIGENSOFT/EIGENSOFT-7.2.1-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 +# 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', + ('%(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 = [ + ('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', 'bin/ploteig'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL", "ploteig"]], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2020.11.001-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2020.11.001-foss-2020b.eb new file mode 100644 index 0000000000..73968dfba3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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.mpcdf.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/software/tarball-archive/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/__archive__/e/ELPA/ELPA-2020.11.001-intel-2020b.eb b/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2020.11.001-intel-2020b.eb new file mode 100644 index 0000000000..36d6628f6c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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.mpcdf.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/software/tarball-archive/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['15591f142eeaa98ab3201d27ca9ac328e21beabf0803b011a04183fcaf6efdde'] + +builddependencies = [ + ('Autotools', '20200321'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.8.6'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2021.05.002-intel-2020b.eb b/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2021.05.002-intel-2020b.eb new file mode 100644 index 0000000000..03bbb92844 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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.mpcdf.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/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 = [ + {'elpa-2021.05.002_bugfix.tar.gz': 'deabc48de5b9e4b2f073d749d335c8f354a7ce4245b643a23b7951cd6c90224b'}, + {'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' diff --git a/easybuild/easyconfigs/__archive__/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb new file mode 100644 index 0000000000..24ee50dfb9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 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/__archive__/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb new file mode 100644 index 0000000000..8e5e7166b3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 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/__archive__/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/__archive__/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb new file mode 100644 index 0000000000..68020a6e29 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -0,0 +1,46 @@ +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, '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', + '%(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 +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('ELPA', '2020.11.001'), + ('NTPoly', '2.5.1'), +] + +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb b/easybuild/easyconfigs/__archive__/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb new file mode 100644 index 0000000000..ff84be63e3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb @@ -0,0 +1,46 @@ +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] +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 +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('ELPA', '2020.11.001'), + ('NTPoly', '2.5.1'), +] + +build_internal_pexsi = True + +configopts = "-DENABLE_BSEPACK=ON" + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb new file mode 100644 index 0000000000..bc7a3b0e4f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +maxparallel = 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/__archive__/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb new file mode 100644 index 0000000000..80ff5c2bd6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '-PEXSI'), + ('spglib', '1.16.1'), + ('Wannier90', '3.1.0'), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb new file mode 100644 index 0000000000..10c5d31e52 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-8.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-8.0.1-foss-2020b.eb new file mode 100644 index 0000000000..8fc38d9f4e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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, '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('.'))] +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' diff --git a/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-8.0.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-8.0.1-intel-2020b.eb new file mode 100644 index 0000000000..dccfd612ef --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb new file mode 100644 index 0000000000..15711a15f0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/ESMPy/ESMPy-8.0.1-intel-2020b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'ESMPy' +version = '8.0.1' + +homepage = 'https://earthsystemmodeling.org/esmpy' +description = "Earth System Modeling Framework (ESMF) Python Interface" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['ESMF_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['9172fb73f3fe95c8188d889ee72fdadb4f978b1d969e1d8e401e8d106def1d84'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy, mpi4py + ('ESMF', version), +] + +start_dir = 'src/addon/ESMPy' + +# ESMPy's setup.py script doesn't support using "pip install" +use_pip = False + +buildopts = "--ESMFMKFILE=$EBROOTESMF/lib/esmf.mk" + +options = {'modulename': 'ESMF'} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/e/ETE/ETE-3.1.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/ETE/ETE-3.1.2-foss-2020b.eb new file mode 100644 index 0000000000..cb9b36ddf6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/ETE/ETE-3.1.2-foss-2020b.eb @@ -0,0 +1,29 @@ +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'), +] + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.3.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.3.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..37d76d4f48 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..749a4d82e8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..97fabdb318 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/e/EigenExa/EigenExa-2.11-intel-2020b.eb b/easybuild/easyconfigs/__archive__/e/EigenExa/EigenExa-2.11-intel-2020b.eb new file mode 100644 index 0000000000..510d8d37be --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/EigenExa/EigenExa-2.11-intel-2020b.eb @@ -0,0 +1,29 @@ +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'] + +builddependencies = [ + ('Autotools', '20200321') +] + +preconfigopts = './cleanup && ./bootstrap && ' + +maxparallel = 1 + +sanity_check_paths = { + 'files': ['lib/libEigenExa.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/e/Elk/Elk-7.0.12-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/Elk/Elk-7.0.12-foss-2020b.eb new file mode 100644 index 0000000000..551f52c847 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/Elk/Elk-7.0.12-foss-2020b.eb @@ -0,0 +1,62 @@ +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' + +maxparallel = 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': [] +} + +sanity_check_commands = ["elk | grep '^Elk code version %(version)s'"] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2c9a2063b3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/Emacs/Emacs-27.1-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# +# 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'), + ('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' diff --git a/easybuild/easyconfigs/__archive__/e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9bfb1e644e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb new file mode 100644 index 0000000000..cffa913c11 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -0,0 +1,33 @@ +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-%(version)s.tar.gz'] +checksums = ['d679c6ac19e93c32ab77594c793e41b948c7bb3873b600e70ad637d093dca187'] + +dependencies = [ + ('Perl', '5.32.0'), + ('Archive-Zip', '1.68'), +] + +options = {'modulename': 'Excel::Writer::XLSX'} + +sanity_check_paths = { + 'files': ['bin/extract_vba'], + '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"', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/Exonerate/Exonerate-2.4.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..360c6edd62 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 +maxparallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/e/Extrae/Extrae-3.8.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/e/Extrae/Extrae-3.8.0-gompi-2020b.eb new file mode 100644 index 0000000000..732bba271d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb new file mode 100644 index 0000000000..54cb9105d3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..c4dc7d4789 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -0,0 +1,55 @@ +# Written by Tom Strempel +# Modified by Ben Langenberg +easyblock = "CMakeMake" + +name = 'ecFlow' +version = '5.7.0' + +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 + 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', '', SYSTEM), +] + +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" && ' + +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" diff --git a/easybuild/easyconfigs/__archive__/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb new file mode 100644 index 0000000000..ad377b08e6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/eccodes-python/eccodes-python-1.1.0-foss-2020b.eb @@ -0,0 +1,24 @@ +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'), +] + +options = {'modulename': 'eccodes'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/e/edlib/edlib-1.3.9-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/edlib/edlib-1.3.9-GCC-10.2.0.eb new file mode 100644 index 0000000000..d28d60e6be --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/edlib/edlib-1.3.9-GCC-10.2.0.eb @@ -0,0 +1,18 @@ +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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb new file mode 100644 index 0000000000..02a167deba --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb @@ -0,0 +1,52 @@ +# 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 && " + +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' diff --git a/easybuild/easyconfigs/__archive__/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb new file mode 100644 index 0000000000..6cf33db466 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/eggnog-mapper/eggnog-mapper-2.1.4-foss-2020b.eb @@ -0,0 +1,52 @@ +# 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 = '2.1.4' + +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'] +checksums = ['c131043eb3cf5c8f32a4f088dabcbe0eae8fbb3680c2a6ac997c3bcd2fa5f0f2'] + +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 && " + +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' diff --git a/easybuild/easyconfigs/__archive__/e/einops/einops-0.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/einops/einops-0.3.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ff0614928b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/einops/einops-0.3.2-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +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'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e51ac2c864 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/elfutils/elfutils-0.183-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +# 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 = [ + ('M4', '1.4.18'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.35'), + ('bzip2', '1.0.8'), + ('libarchive', '3.4.3'), + ('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': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..73c40af988 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_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/__archive__/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..aa26265cbd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,21 @@ +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')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..262981fa95 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb @@ -0,0 +1,37 @@ +# 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'), +] + +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/__archive__/f/FDS/FDS-6.7.6-intel-2020b.eb b/easybuild/easyconfigs/__archive__/f/FDS/FDS-6.7.6-intel-2020b.eb new file mode 100644 index 0000000000..9b15ca6c7b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompi-2020b.eb new file mode 100644 index 0000000000..d866eed7b5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/f/FFTW/FFTW-3.3.8-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompic-2020b.eb new file mode 100644 index 0000000000..d536144165 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/f/FFTW/FFTW-3.3.8-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-iimpi-2020b.eb new file mode 100644 index 0000000000..e9ebf6b3f2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/f/FFTW/FFTW-3.3.8-intel-2020b.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-intel-2020b.eb new file mode 100644 index 0000000000..00efb3ab98 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-iomkl-2020b.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-iomkl-2020b.eb new file mode 100644 index 0000000000..a3012e1e59 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-iompi-2020b.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-iompi-2020b.eb new file mode 100644 index 0000000000..65082d495d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-iompi-2020b.eb @@ -0,0 +1,29 @@ +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 + +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/f/FFmpeg/FFmpeg-4.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FFmpeg/FFmpeg-4.3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..edbc0620c2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/f/FIGARO/FIGARO-1.1.2-intel-2020b.eb b/easybuild/easyconfigs/__archive__/f/FIGARO/FIGARO-1.1.2-intel-2020b.eb new file mode 100644 index 0000000000..e372c08053 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/__archive__/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb new file mode 100644 index 0000000000..c7a0866a3d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020b.eb @@ -0,0 +1,41 @@ +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/v%(version)s/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['a3b09ac4ec29c3d24750bf161c58abe6b9c2f86d56f046d2657be72daf63b673'] + +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=OFF' +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' diff --git a/easybuild/easyconfigs/__archive__/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c288ef191b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FLAC/FLAC-1.3.3-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +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': ['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' diff --git a/easybuild/easyconfigs/__archive__/f/FLASH/FLASH-2.2.00-foss-2020b.eb b/easybuild/easyconfigs/__archive__/f/FLASH/FLASH-2.2.00-foss-2020b.eb new file mode 100644 index 0000000000..68775a2c86 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FLASH/FLASH-2.2.00-foss-2020b.eb @@ -0,0 +1,34 @@ +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')] + +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' diff --git a/easybuild/easyconfigs/__archive__/f/FLTK/FLTK-1.3.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FLTK/FLTK-1.3.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6cf60f80c8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/f/FMM3D/FMM3D-20211018-foss-2020b.eb b/easybuild/easyconfigs/__archive__/f/FMM3D/FMM3D-20211018-foss-2020b.eb new file mode 100644 index 0000000000..6b34a42a98 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FMM3D/FMM3D-20211018-foss-2020b.eb @@ -0,0 +1,43 @@ +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", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d1e7b38c75 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,60 @@ +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'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Graphviz', '2.47.0', '-Java-11'), + ('BeautifulSoup', '4.9.3'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/f/FSON/FSON-1.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FSON/FSON-1.0.5-GCC-10.2.0.eb new file mode 100644 index 0000000000..c81063b3dd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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" diff --git a/easybuild/easyconfigs/__archive__/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6f17150fb6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/f/FabIO/FabIO-0.11.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/f/FabIO/FabIO-0.11.0-foss-2020b.eb new file mode 100644 index 0000000000..adfae3f450 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FabIO/FabIO-0.11.0-foss-2020b.eb @@ -0,0 +1,22 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1d2fcf58006c82548a16004e607d4518613d49e4a2f02a3797703eee2b39c6d8'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..72f3553560 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb @@ -0,0 +1,22 @@ +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'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/f/FastANI/FastANI-1.33-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FastANI/FastANI-1.33-GCC-10.2.0.eb new file mode 100644 index 0000000000..63f4cc6433 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/f/FastANI/FastANI-1.33-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/f/FastANI/FastANI-1.33-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..6fa29aa6ab --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..d835df6e32 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb @@ -0,0 +1,28 @@ +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 = [ + ('Autotools', '20200321'), +] + +preconfigopts = "autoreconf -if && " + +sanity_check_paths = { + 'files': ['bin/fastme'], + 'dirs': [] +} + +sanity_check_commands = ["fastme --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2d4bc28f2b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +# 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 = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.35')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)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': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/Filtlong/Filtlong-0.2.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..c1affd1cd7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' + +maxparallel = 1 + +dependencies = [ + ('zlib', '1.2.11'), +] + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ['bin/filtlong'], + 'dirs': [] +} + +sanity_check_commands = ["filtlong --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/Fiona/Fiona-1.8.20-foss-2020b.eb b/easybuild/easyconfigs/__archive__/f/Fiona/Fiona-1.8.20-foss-2020b.eb new file mode 100644 index 0000000000..187b08065d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/Fiona/Fiona-1.8.20-foss-2020b.eb @@ -0,0 +1,45 @@ +# 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'), +] + +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_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["fio --help"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/f/Fiona/Fiona-1.8.20-intel-2020b.eb b/easybuild/easyconfigs/__archive__/f/Fiona/Fiona-1.8.20-intel-2020b.eb new file mode 100644 index 0000000000..dbc0d641f9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/Fiona/Fiona-1.8.20-intel-2020b.eb @@ -0,0 +1,45 @@ +# 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'), +] + +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_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["fio --help"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ea736672a8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/Flask/Flask-1.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +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')] + +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' diff --git a/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.3-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..611a9d32df --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.3-GCC-10.2.0.eb @@ -0,0 +1,28 @@ +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')] + +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..9d58a9667a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.3-iccifort-2020.4.304.eb @@ -0,0 +1,25 @@ +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')] + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1b21dae3e0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +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'] + +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'] + +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/__archive__/f/FreeImage/FreeImage-3.18.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FreeImage/FreeImage-3.18.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6953a03baf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c0dd7325a8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# 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'), +] + +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/__archive__/f/fastahack/fastahack-1.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/fastahack/fastahack-1.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..73aaa73c4a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/f/fdict/fdict-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/fdict/fdict-0.8.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..bfae886c93 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/fdict/fdict-0.8.0-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +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'] + +buildopts = 'VENDOR="gnu" FFLAGS="$FFLAGS"' + +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'share'), +] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..1158369a84 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb @@ -0,0 +1,30 @@ +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'] + +buildopts = 'VENDOR="intel" FFLAGS="$FFLAGS" FPP="$FC -E -P"' + +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'share'), +] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/f/fermi-lite/fermi-lite-20190320-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/fermi-lite/fermi-lite-20190320-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5f7b29effc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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="$CFLAGS -fcommon"' + +files_to_copy = [ + (['fml-asm'], 'bin'), + (['*.a', '*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/fml'), + 'test', +] + +sanity_check_paths = { + 'files': ['bin/fml-asm', 'lib/libfml.a', 'lib/libfml.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/fftlib/fftlib-20170628-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/f/fftlib/fftlib-20170628-gompi-2020b.eb new file mode 100644 index 0000000000..8e08523b89 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/fftlib/fftlib-20170628-gompi-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'fftlib' +version = '20170628' +local_commit = '44c5fa0' + +homepage = 'https://github.com/flwende/fftlib' +description = """A library that intercepts FFTW calls and adds features on top of it. + In particular, it enables FFT plan reuse when there are multiple calls for the same geometry.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/flwende/fftlib/archive/'] +sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_ZIP}] +checksums = ['f73dffeaf5c2e6972a5bc67d11ec28390f9eda281a7cb47edc1ee2fe394ed057'] + +dependencies = [('FFTW', '3.3.8')] + +local_options = "-DFFTLIB_THREADSAFE " # use this when multiple threads access fftlib +# local_options += "-DFFTLIB_USE_MKL " # use symbols from MKL's fft library +# local_options += "-DFFTLIB_BYPASS " # bypass fftlib's internal logic +# local_options += "-DFFTLIB_OWN_LOCK " # use fftlib's reader/writer lock +# local_options += "-DFFTLIB_UNSAFE_OPT " # activate unsafe optimizations in fftlib +# local_options += "-DFFTLIB_DEBUG " # print debug messages (infos and warnings) +# local_options += "-DFFTLIB_WARNINGS_ONLY " # print warnings only +# local_options += "-DFFTLIB_COMPOSED_FFT " # split 3d FFT computation into 2d+1d FFT + +start_dir = 'src' + +maxparallel = 1 + +build_cmd = "$CXX $CXXFLAGS -I../include -I$EBROOTFFTW/include %s -c fftlib.cpp -o fftlib.o" % local_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' diff --git a/easybuild/easyconfigs/__archive__/f/file/file-5.39-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/file/file-5.39-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..969d9cb3f9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['http://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/__archive__/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5aafc94550 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 + '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f', # 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/__archive__/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..50c8a63725 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/flatbuffers-python/flatbuffers-python-1.12-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +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'), +] + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8f9764b10b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/flatbuffers/flatbuffers-1.12.0-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +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'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f9dd97bb26 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), +] + +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/__archive__/f/flook/flook-0.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/flook/flook-0.8.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..6e3b75a3c9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/flook/flook-0.8.1-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +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'] +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')] + +maxparallel = 1 + +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'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/f/flook/flook-0.8.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/f/flook/flook-0.8.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..7ef6dccb66 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/flook/flook-0.8.1-iccifort-2020.4.304.eb @@ -0,0 +1,36 @@ +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'] +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')] + +maxparallel = 1 + +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'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5e691036a5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/f/foss/foss-2020b.eb b/easybuild/easyconfigs/__archive__/f/foss/foss-2020b.eb new file mode 100644 index 0000000000..2b3e59acb6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '0.3.12', '', ('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/__archive__/f/fosscuda/fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/f/fosscuda/fosscuda-2020b.eb new file mode 100644 index 0000000000..89c986f17f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb new file mode 100644 index 0000000000..6cdb2634cf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb @@ -0,0 +1,62 @@ +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'} + +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'), +] + +# 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 ${LDFLAGS}"' + +postinstallcmds = [ + # add extra scripts + "cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s/", + # only make freebayes-parallel directly executable + "cd %(installdir)s/bin && ln -s ../scripts/freebayes-parallel", +] + +sanity_check_paths = { + 'files': ['bin/freebayes', 'bin/bamleftalign', 'bin/freebayes-parallel'], + 'dirs': ['scripts'], +} + +sanity_check_commands = ["freebayes --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..45d3fbdee6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/freeglut/freeglut-3.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.2.1' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['freeglut-3.2.1_gcc10_fix-1.patch'] +checksums = [ + 'd4000e02102acaf259998c870e25214739d1f16f67f99cb35e4f46841399da68', # freeglut-3.2.1.tar.gz + 'f278467e03348b87d9b4ae69f491e503ab80c6d82433cf7468eac89b7f859d37', # freeglut-3.2.1_gcc10_fix-1.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), +] + +configopts = ' -DX11_X11_LIB="$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' diff --git a/easybuild/easyconfigs/__archive__/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..841fd64593 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +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, + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] +checksums = ['9dfb4e11efd6e460a87b1991a64bc69344ee7dc219d9b29e7faabc1c168ce8b0'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('Brotli', '1.0.9'), +] + +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/__archive__/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb new file mode 100644 index 0000000000..fd3f68b440 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb @@ -0,0 +1,43 @@ +## +# 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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/f/fsom/fsom-20141119-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/fsom/fsom-20141119-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a298d8f099 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/fsom/fsom-20141119-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +# 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' +] +checksums = [ + '832ec7d0aff53e04fdb8bbaa5be2177de362afac6ed58a59a97abb7eef29cb60', # a6ef318.tar.gz + 'a6349a6462473f011260074eca6ad9826e3c6aeb20674b696c5848d10610cdd7', # fsom-20141119_build-libs.patch + '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639', # fsom-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/__archive__/f/futile/futile-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/f/futile/futile-1.8.3-foss-2020b.eb new file mode 100644 index 0000000000..36a7a5ac4e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/futile/futile-1.8.3-foss-2020b.eb @@ -0,0 +1,46 @@ +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 = {'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_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" + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libyaml', '0.2.5'), +] + +preconfigopts = 'export FCFLAGS="$FCLAGS -fallow-argument-mismatch" && ' + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + ['lib/libfutile-1.a', 'lib/libfutile-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/f/futile/futile-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/__archive__/f/futile/futile-1.8.3-intel-2020b.eb new file mode 100644 index 0000000000..2a39fe6802 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/f/futile/futile-1.8.3-intel-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +patches = [ + 'futile_index_bug.patch', + 'futile_intel_bug.patch', +] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '5ef5f8ad7644259da0d2d2bcb64c44b923cb64b1eedf03898d0da18228ea392f', # futile_index_bug.patch + 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch +] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libyaml', '0.2.5'), +] + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + ['lib/libfutile-1.a', 'lib/libfutile-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb b/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb new file mode 100644 index 0000000000..097bd00e48 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), + ('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/__archive__/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb new file mode 100644 index 0000000000..515f6cea9b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), + ('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' diff --git a/easybuild/easyconfigs/__archive__/g/GCC/GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GCC/GCC-10.2.0.eb new file mode 100644 index 0000000000..45f4144c99 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-10.2.0.eb new file mode 100644 index 0000000000..880ff3864f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-10.2.0.eb @@ -0,0 +1,76 @@ +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 + '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 +] +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', + 'newlib-3.3.0.tar.gz', + {'download_filename': '5f6f343.tar.gz', 'filename': 'nvptx-tools-20180301.tar.gz'}, +] +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', + '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 = [ + {'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 = [ + ('M4', '1.4.19'), + ('binutils', '2.35'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.2.1-foss-2020b.eb new file mode 100644 index 0000000000..8453e7a125 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -0,0 +1,63 @@ +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 +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +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'), + ('PCRE', '8.44'), + ('PROJ', '7.2.1'), + ('libgeotiff', '1.6.0'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('HDF', '4.2.15'), +] + +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' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +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/__archive__/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..183a5e05d0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb @@ -0,0 +1,63 @@ +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 +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +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'), + ('PCRE', '8.44'), + ('PROJ', '7.2.1'), + ('libgeotiff', '1.6.0'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('HDF', '4.2.15'), +] + +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' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +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/__archive__/g/GDAL/GDAL-3.2.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.2.1-intel-2020b.eb new file mode 100644 index 0000000000..b03dcaa460 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.2.1-intel-2020b.eb @@ -0,0 +1,69 @@ +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 +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +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'), + ('PCRE', '8.44'), + ('PROJ', '7.2.1'), + ('libgeotiff', '1.6.0'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('HDF', '4.2.15'), +] + +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' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +prebuildopts = "env LDSHARED='icc -shared' " + +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/__archive__/g/GDB/GDB-10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GDB/GDB-10.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0300093f74 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GDB/GDB-10.1-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +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'), + ('makeinfo', '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': [], +} + +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/__archive__/g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9386c09091 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/__archive__/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb new file mode 100644 index 0000000000..915d01b254 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['v%(version)s.tar.gz'] +checksums = ['cecc7dcc071107f77396f5553c9109790b6d2298ae29eb2dbbdd52b2a213e4ea'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CUDAcore', local_cudaversion, '', SYSTEM), # needed by GDRCopy binaries, which are tools for testing + ('Check', '0.15.2'), +] + +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'] + +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/__archive__/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/__archive__/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb new file mode 100644 index 0000000000..443bbdd4af --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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, '', SYSTEM), # needed by GDRCopy binaries, which are tools for testing + ('Check', '0.15.2'), +] + +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'] + +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/__archive__/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f6498b61ef --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), +] + +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'] + +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' diff --git a/easybuild/easyconfigs/__archive__/g/GEOS/GEOS-3.9.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GEOS/GEOS-3.9.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..70f364a942 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/GEOS/GEOS-3.9.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/g/GEOS/GEOS-3.9.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..757f093e12 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/GL2PS/GL2PS-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GL2PS/GL2PS-1.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..173f65d0fc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GLFW/GLFW-3.3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f3e6e7ecec --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..197298d43e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +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 && ' +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 &&' + +preinstallopts = 'cd src &&' + +maxparallel = 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" diff --git a/easybuild/easyconfigs/__archive__/g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GLM/GLM-0.9.9.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1249ce4888 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GLPK/GLPK-4.65-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1c4af51730 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..70f37bb9e8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = "--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/__archive__/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2e5b24b063 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' % (x, e) for x in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/GMT/GMT-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/g/GMT/GMT-6.2.0-foss-2020b.eb new file mode 100644 index 0000000000..51623405d1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb new file mode 100644 index 0000000000..a21d0dfe33 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb @@ -0,0 +1,47 @@ +# 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'} + +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'), + ('SciPy-bundle', '2020.11'), + ('XlsxWriter', '1.4.0'), + ('statsmodels', '0.12.1'), + ('pydot', '1.4.2'), +] + +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_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': ['data'], +} + +# 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", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c828437cf5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +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'), + ('pkg-config', '0.29.2'), + ('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/__archive__/g/GPAW/GPAW-20.10.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-20.10.0-foss-2020b.eb new file mode 100644 index 0000000000..d7eb16cc6f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-20.10.0-foss-2020b.eb @@ -0,0 +1,44 @@ +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} + +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 + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', + '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', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +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/__archive__/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-20.10.0-intel-2020b.eb new file mode 100644 index 0000000000..2c7b81fa3b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -0,0 +1,47 @@ +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} + +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 + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', + '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'), + ('ASE', '3.20.1'), + ('libxc', '4.3.4'), + ('GPAW-setups', '0.9.20000', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +# 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/__archive__/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..4ac79a96d8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb @@ -0,0 +1,44 @@ +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} + +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 + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('libxc', '4.3.4'), + ('libvdwxc', '0.4.0'), + ('GPAW-setups', '0.9.20000', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +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/__archive__/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb new file mode 100644 index 0000000000..40a999e312 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb @@ -0,0 +1,46 @@ +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} + +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 + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('libxc', '4.3.4'), + ('GPAW-setups', '0.9.20000', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +# 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/__archive__/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..6ee58a76a5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb @@ -0,0 +1,45 @@ +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 + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('libxc', '4.3.4'), + ('libvdwxc', '0.4.0'), + ('GPAW-setups', '0.9.20000', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +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/__archive__/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..c551cb07f2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -0,0 +1,45 @@ +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 + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', +] + +# 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', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +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/__archive__/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb b/easybuild/easyconfigs/__archive__/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb new file mode 100644 index 0000000000..6ce4b95009 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GPyOpt/GPyOpt-1.2.6-intel-2020b.eb @@ -0,0 +1,31 @@ +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'), +] + +exts_list = [ + ('paramz', '0.9.5', { + 'checksums': ['0917211c0f083f344e7f1bc997e0d713dbc147b6380bc19f606119394f820b9a'], + }), + ('GPy', '1.9.9', { + 'modulename': 'GPy', + 'checksums': ['04faf0c24eacc4dea60727c50a48a07ddf9b5751a3b73c382105e2a31657c7ed'], + }), + (name, version, { + 'modulename': 'GPyOpt', + 'checksums': ['e714daa035bb529a6db23c53665a762a4ab3456b9329c19ad3b03983f94c9b2a'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb new file mode 100644 index 0000000000..0bed20eb35 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GPyTorch/GPyTorch-1.3.0-foss-2020b.eb @@ -0,0 +1,19 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9bc7aea1dee188b69ff181e3406aabf6fedfa4446b834ed6adf68b94b6ebebd5'] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', '1.7.1'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2021-foss-2020b.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2021-foss-2020b.eb new file mode 100644 index 0000000000..491b8b4a24 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2021-foss-2020b.eb @@ -0,0 +1,81 @@ +# 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], +} + +exts_list = [ + ('gmxapi', '0.2.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb new file mode 100644 index 0000000000..86fb64c1c5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb @@ -0,0 +1,82 @@ +# 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', + 'GROMACS-2021_add-missing-sync.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', + '52ee257309ff7761c2dd5b26de7dbc63f8ba698082adb88e2843f90e3f9168bf', # GROMACS-2021_add-missing-sync.patch +] + +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], +} + +exts_list = [ + ('gmxapi', '0.2.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..b194b5deb3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb @@ -0,0 +1,82 @@ +# 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', + 'GROMACS-2021_add-missing-sync.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', + '52ee257309ff7761c2dd5b26de7dbc63f8ba698082adb88e2843f90e3f9168bf', # GROMACS-2021_add-missing-sync.patch +] + +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], +} + +exts_list = [ + ('gmxapi', '0.2.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GSL/GSL-2.6-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GSL/GSL-2.6-GCC-10.2.0.eb new file mode 100644 index 0000000000..46c108f2f4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/GSL/GSL-2.6-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/g/GSL/GSL-2.6-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..3757a22104 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..cc7e4f4623 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +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] +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'), + ('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 = '-Dlibdw=disabled ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb new file mode 100644 index 0000000000..f54f1f06fb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb @@ -0,0 +1,38 @@ +# 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', '', SYSTEM), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.56.2'), +] + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb new file mode 100644 index 0000000000..752b7e13b1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb @@ -0,0 +1,40 @@ +# 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', '', SYSTEM), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.56.2'), +] + + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb new file mode 100644 index 0000000000..7630d98dcb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb @@ -0,0 +1,38 @@ +# 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', '', SYSTEM), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.56.2'), +] + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..627eb4f9fe --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb @@ -0,0 +1,76 @@ +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'), + ('Autotools', '20200321'), + ('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 = [ + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes", + }), + ('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], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + }), +] + +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/__archive__/g/GTS/GTS-0.7.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GTS/GTS-0.7.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e38f674aa1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a931bf0671 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = "--default-library=both " +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], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-10.7.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..ac7d832cd0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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=$EBROOTEXPAT/include" +configopts += " -DCLHEP_ROOT_DIR=$EBROOTCLHEP -DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7ff097babf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GeneMark-ET/GeneMark-ET-4.65-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +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'} + +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'] + +sanity_check_paths = { + 'files': ['gmes.cfg', 'gmes_petap.pl'], + 'dirs': ['lib'], +} + +skip_mod_files_sanity_check = True + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..7b91aa07cb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +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', # 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, +# 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 + +builddependencies = [('pkg-config', '0.29.2')] +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' diff --git a/easybuild/easyconfigs/__archive__/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..ee75208982 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GenomeWorks/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -0,0 +1,87 @@ +# author: Denis Kristak (INUITS) +easyblock = 'CMakePythonPackage' + +name = 'GenomeWorks' +version = '2021.02.2' +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" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +sources = [{ + 'filename': SOURCE_TAR_XZ, + 'git_config': { + 'url': 'https://github.com/clara-parabricks', + 'repo_name': name, + 'commit': local_commit, + 'recursive': True, + }, +}] +checksums = ['ac3946d7172853efe3260339e7edc430bbbd585ed490c7f1ad9f7644446a5ae6'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Autoconf', '2.69'), + ('matplotlib', '3.3.3'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), + ('tqdm', '4.56.2'), +] + +# 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/==/>=/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 += " -Dgw_build_shared=ON " + +# no test targets +skipsteps = ['test'] + +exts_defaultclass = 'PythonPackage' + +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 && " + +exts_list = [ + ('sortedcollections', '2.1.0', { + 'source_urls': [PYPI_SOURCE], + 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], + }), + ('genomeworks', version, { + 'sources': sources, + 'checksums': checksums, + 'start_dir': 'pygenomeworks', + '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'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb new file mode 100644 index 0000000000..4212fd0def --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb @@ -0,0 +1,39 @@ +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', SYSTEM), + ('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') +] + +options = {'modulename': False} + +fix_python_shebang_for = ['bin/*.py'] + +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/__archive__/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e12d5fc6ba --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/Ghostscript/Ghostscript-9.53.3-GCCcore-10.2.0.eb @@ -0,0 +1,61 @@ +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] +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'), + ('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/__archive__/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..08b6924204 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +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'), +] + +exts_list = [ + ('smmap', '4.0.0', { + 'checksums': ['7e65386bd122d45405ddf795637b7f7d2b532e7e401d46bbe3fb49b9986d5182'], + }), + ('gitdb', '4.0.7', { + 'checksums': ['96bf5c08b157a666fec41129e6d327235284cca4c81e92109260f353ba138005'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['be27633e7509e58391f10207cd32b2a6cf5b908f92d9cd30da2e514e1137af61'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb new file mode 100644 index 0000000000..947e4cda9a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1713346d42 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.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 = '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'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb b/easybuild/easyconfigs/__archive__/g/GraphicsMagick/GraphicsMagick-1.3.36-foss-2020b.eb new file mode 100644 index 0000000000..6a9fc591e5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = {MODULE_LOAD_ENV_HEADERS: ['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/__archive__/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb new file mode 100644 index 0000000000..8fd6567150 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), + ('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': {'paths': 'lib/graphviz/tcl', 'delimiter': ' '}, +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0319076daf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cd161186df --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/Gurobi/Gurobi-9.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/Gurobi/Gurobi-9.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d0177b1ef1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a7024a6c42 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +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'] +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/g/Gurobi/Gurobi-9.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/Gurobi/Gurobi-9.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c505ea66ee --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e549e59d5b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 +maxparallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d1f966b463 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 +maxparallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/g/garnett/garnett-0.1.20-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..5c7ed9eed8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 facilitates 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' diff --git a/easybuild/easyconfigs/__archive__/g/gawk/gawk-5.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gawk/gawk-5.1.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..03d927882b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/gc/gc-8.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gc/gc-8.2.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5061399f2f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/gcccuda/gcccuda-2020b.eb b/easybuild/easyconfigs/__archive__/g/gcccuda/gcccuda-2020b.eb new file mode 100644 index 0000000000..7b990a8842 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9072dc51ea --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..19471a207a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/gdc-client/gdc-client-1.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,79 @@ +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'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('libxslt', '1.1.34'), + ('libyaml', '0.2.5'), +] + +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'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gdc-client'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e753b9bd2b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/gemmi/gemmi-0.4.5-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# 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} + +github_account = 'project-gemmi' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['af462dbb3a2a144b1437700637e78c0365a5273dc5bffadeea80f73765ab15c7'] + +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 ' + +runtest = 'cpptest ftest ftest_grid test' + +sanity_check_paths = { + 'files': ['bin/gemmi'], + 'dirs': ['bin', 'lib', 'include/gemmi'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/gengetopt/gengetopt-2.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gengetopt/gengetopt-2.23-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..27bd0e0e7a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/gensim/gensim-3.8.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/g/gensim/gensim-3.8.3-foss-2020b.eb new file mode 100644 index 0000000000..e18b6b9c19 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/gensim/gensim-3.8.3-foss-2020b.eb @@ -0,0 +1,26 @@ +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 +] + +exts_list = [ + ('smart_open', '4.1.2', { + 'checksums': ['4bbb6233364fc1173cc0af6b7a56ed76fce32509514f1978a995a5835f3177f1'], + }), + (name, version, { + 'checksums': ['786adb0571f75114e9c5f7a31dd2e6eb39a9791f22c8757621545e2ded3ea367'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/gensim/gensim-3.8.3-intel-2020b.eb b/easybuild/easyconfigs/__archive__/g/gensim/gensim-3.8.3-intel-2020b.eb new file mode 100644 index 0000000000..b66e79c460 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/gensim/gensim-3.8.3-intel-2020b.eb @@ -0,0 +1,26 @@ +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 +] + +exts_list = [ + ('smart_open', '4.1.2', { + 'checksums': ['4bbb6233364fc1173cc0af6b7a56ed76fce32509514f1978a995a5835f3177f1'], + }), + (name, version, { + 'checksums': ['786adb0571f75114e9c5f7a31dd2e6eb39a9791f22c8757621545e2ded3ea367'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e41f1355ea --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/geopy/geopy-2.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +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')] + +exts_list = [ + ('geographiclib', '1.50', { + 'checksums': ['12bd46ee7ec25b291ea139b17aa991e7ef373e21abd053949b75c0e9ca55c632'], + }), + (name, version, { + 'checksums': ['892b219413e7955587b029949af3a1949c6fbac9d5ad17b79d850718f6a9550f'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.21-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1303c6d192 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.21-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +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 = ['c77d0da3102aec9c07f43671e60611ebff89a996ef159497ce8e59d075786b12'] + +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'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c4ec8d0dba --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/giflib/giflib-5.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/giflib/giflib-5.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0a9b9da5c1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb b/easybuild/easyconfigs/__archive__/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb new file mode 100644 index 0000000000..0ca0d915f4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['02016d16dbce553699db5c9c04f6d13a3f50727c652061b7eb97a828d045e534'] + +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' diff --git a/easybuild/easyconfigs/__archive__/g/glew/glew-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/glew/glew-2.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bee02ca561 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb b/easybuild/easyconfigs/__archive__/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb new file mode 100644 index 0000000000..e6424a8a5c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/glew/glew-2.2.0-GCCcore-10.2.0-egl.eb @@ -0,0 +1,44 @@ +# 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/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.35')] +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system +dependencies = [ + ('Mesa', '20.2.1'), + ('X11', '20201008'), +] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +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/__archive__/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb b/easybuild/easyconfigs/__archive__/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb new file mode 100644 index 0000000000..2d7aeeae60 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/glew/glew-2.2.0-GCCcore-10.2.0-glx.eb @@ -0,0 +1,44 @@ +# 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/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.35')] +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system +dependencies = [ + ('Mesa', '20.2.1'), + ('X11', '20201008'), +] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +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/__archive__/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb b/easybuild/easyconfigs/__archive__/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb new file mode 100644 index 0000000000..89901c2114 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/glew/glew-2.2.0-GCCcore-10.2.0-osmesa.eb @@ -0,0 +1,44 @@ +# 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/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.35')] +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system +dependencies = [ + ('Mesa', '20.2.1'), + ('X11', '20201008'), +] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +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/__archive__/g/glog/glog-0.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/glog/glog-0.5.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d6dded4986 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb new file mode 100644 index 0000000000..4c5ca952c1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/gmpy2/gmpy2-2.1.0b5-GCC-10.2.0.eb @@ -0,0 +1,21 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8951bcfc61c0f40102b92a4777daf9eb85445b537c4d09086deb0e097190bef0'] + +dependencies = [ + ('Python', '3.8.6'), + ('GMP', '6.2.0'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..6d5a48514a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb @@ -0,0 +1,21 @@ +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'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..afa4c64d21 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb @@ -0,0 +1,59 @@ +## +# 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 = 'http://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 && ' + +# 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 = { + '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/__archive__/g/gobff/gobff-2020b.eb b/easybuild/easyconfigs/__archive__/g/gobff/gobff-2020b.eb new file mode 100644 index 0000000000..2ed4f4e1c2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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_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), + ('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/__archive__/g/goblf/goblf-2020b.eb b/easybuild/easyconfigs/__archive__/g/goblf/goblf-2020b.eb new file mode 100644 index 0000000000..3b85015988 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '3.9.1', '', local_comp), + ('ScaLAPACK', '2.1.0', '-bl', local_comp_mpi_tc), + ('FFTW', '3.3.8', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/g/gomkl/gomkl-2020b.eb b/easybuild/easyconfigs/__archive__/g/gomkl/gomkl-2020b.eb new file mode 100644 index 0000000000..d2743a6546 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/gompi/gompi-2020b.eb b/easybuild/easyconfigs/__archive__/g/gompi/gompi-2020b.eb new file mode 100644 index 0000000000..2738c8a249 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/gompic/gompic-2020b.eb b/easybuild/easyconfigs/__archive__/g/gompic/gompic-2020b.eb new file mode 100644 index 0000000000..b5d2a9fd20 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/googletest/googletest-1.10.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/googletest/googletest-1.10.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ff55b9164e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/gperf/gperf-3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gperf/gperf-3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..570faad38a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/g/gperftools/gperftools-2.9.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gperftools/gperftools-2.9.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e29ea9698a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb b/easybuild/easyconfigs/__archive__/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb new file mode 100644 index 0000000000..050847af16 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/g/gpustat/gpustat-0.6.0-gcccuda-2020b.eb @@ -0,0 +1,35 @@ +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'), +] + +exts_list = [ + ('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"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/graphite2/graphite2-1.3.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/graphite2/graphite2-1.3.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0a3fc8da20 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..76c7be899c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '-minimal'), +] + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a046e06c02 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HAL/HAL-2.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/h/HAL/HAL-2.1-foss-2020b.eb new file mode 100644 index 0000000000..923a257f23 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HAL/HAL-2.1-foss-2020b.eb @@ -0,0 +1,109 @@ +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_sonLib_datetime = '20210415' +local_sonLib_hash = '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_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 = [ + '540255be1af55abf390359fe034b82d7e61bdf6c3277df3cc01259cd450994e5', # release-V2.1.tar.gz + # sonLib-20210415-562a466e4570c93a647ffb10aa2628143b4ee9f4.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 = { + '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'], + }), +] + +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'" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..801944ccbe --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +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://git.earthdata.nasa.gov/rest/git-lfs/storage/DAS/hdfeos/'] +sources = [ + {'download_filename': 'cb0f900d2732ab01e51284d6c9e90d0e852d61bba9bce3b43af0430ab5414903', + 'filename': '%(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=$EBROOTSZIP --enable-install-include" + +sanity_check_paths = { + 'files': ['include/HdfEosDef.h', 'include/HDFEOSVersion.h', 'lib/libGctp.a', 'lib/libhdfeos.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb new file mode 100644 index 0000000000..49eb02b40f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HDF-EOS5' +version = '1.16' + +homepage = 'https://hdfeos.org/' +description = """HDF-EOS libraries are software libraries built on HDF libraries. + It supports three data structures for remote sensing data: Grid, Point and Swath.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://git.earthdata.nasa.gov/rest/git-lfs/storage/DAS/hdfeos5/'] +sources = [ + {'download_filename': '7054de24b90b6d9533329ef8dc89912c5227c83fb447792103279364e13dd452', + 'filename': '%(name)s.%(version)s.tar.Z'} +] +checksums = ['7054de24b90b6d9533329ef8dc89912c5227c83fb447792103279364e13dd452'] + +dependencies = [ + ('HDF5', '1.10.7'), + ('Szip', '2.1.1'), +] + +preconfigopts = 'export CC="$EBROOTHDF5/bin/h5pcc -Df2cFortran" && ' + +configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" + +sanity_check_paths = { + 'files': ['include/HE5_HdfEosDef.h', 'include/HE5_GctpFunc.h', 'lib/libGctp.a', 'lib/libhe5_hdfeos.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6b70706ce3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.15' + +homepage = 'https://support.hdfgroup.org/products/hdf4/' + +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['HDF-4.2.15_fix-aarch64.patch'] +checksums = [ + 'dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459', # hdf-4.2.15.tar.gz + '1b4341e309cccefc6ea4310c8f8b08cc3dfe1fa9609b7fa7aee80e4dac598473', # HDF-4.2.15_fix-aarch64.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '2.0.5'), + ('Szip', '2.1.1'), + ('zlib', '1.2.11'), + ('libtirpc', '1.3.1'), +] + +preconfigopts = "LIBS='-ltirpc' " +local_common_configopts = '--with-szlib=$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 = {MODULE_LOAD_ENV_HEADERS: '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' diff --git a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.7-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.7-gompi-2020b.eb new file mode 100644 index 0000000000..df02939510 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HDF5/HDF5-1.10.7-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.7-gompic-2020b.eb new file mode 100644 index 0000000000..351bed5f26 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HDF5/HDF5-1.10.7-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.7-iimpi-2020b.eb new file mode 100644 index 0000000000..4e1c74a08b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HDF5/HDF5-1.10.7-iimpic-2020b.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.7-iimpic-2020b.eb new file mode 100644 index 0000000000..e0191b8fb7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb new file mode 100644 index 0000000000..cf409c8474 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -0,0 +1,70 @@ +## +# 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'), +] + +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', +} + +modextravars = { + 'HHLIB': '%(installdir)s', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb new file mode 100644 index 0000000000..76feb218e0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb @@ -0,0 +1,70 @@ +## +# 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', +} + +modextravars = { + 'HHLIB': '%(installdir)s', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HISAT2/HISAT2-2.2.1-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/h/HISAT2/HISAT2-2.2.1-gompi-2020b.eb new file mode 100644 index 0000000000..71d572cce9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HMMER/HMMER-3.3.2-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-gompi-2020b.eb new file mode 100644 index 0000000000..55a9044d7f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-gompi-2020b.eb @@ -0,0 +1,78 @@ +## +# 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 = [SOURCELOWER_TAR_GZ] +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'), + ('Perl', '5.32.0', '-minimal'), +] + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +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' diff --git a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-gompic-2020b.eb new file mode 100644 index 0000000000..bb4ec04a67 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-gompic-2020b.eb @@ -0,0 +1,78 @@ +## +# 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 = [SOURCELOWER_TAR_GZ] +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'), + ('Perl', '5.32.0', '-minimal'), +] + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +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' diff --git a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb new file mode 100644 index 0000000000..3c33d7fa1e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb @@ -0,0 +1,78 @@ +## +# 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 = [SOURCELOWER_TAR_GZ] +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'), + ('Perl', '5.32.0', '-minimal'), +] + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +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' diff --git a/easybuild/easyconfigs/__archive__/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..496d7c1314 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb b/easybuild/easyconfigs/__archive__/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb new file mode 100644 index 0000000000..73180a361b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb @@ -0,0 +1,57 @@ +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'}] +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'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('Python', '3.8.6'), + ('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', +] + +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' diff --git a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-foss-2020b.eb new file mode 100644 index 0000000000..ff80fe6d13 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HPL/HPL-2.3-gobff-2020b.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-gobff-2020b.eb new file mode 100644 index 0000000000..45ff15f21a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HPL/HPL-2.3-goblf-2020b.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-goblf-2020b.eb new file mode 100644 index 0000000000..d62ec42b41 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-gomkl-2020b.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-gomkl-2020b.eb new file mode 100644 index 0000000000..5e2c0185cc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-gomkl-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': 'gomkl', '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/__archive__/h/HPL/HPL-2.3-iibff-2020b.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-iibff-2020b.eb new file mode 100644 index 0000000000..44e88d0c15 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HPL/HPL-2.3-intel-2020.12.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intel-2020.12.eb new file mode 100644 index 0000000000..8aabdc2f01 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HPL/HPL-2.3-intel-2020b.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intel-2020b.eb new file mode 100644 index 0000000000..49bf61f015 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb new file mode 100644 index 0000000000..31bc978aab --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/HTSeq/HTSeq-0.11.3-foss-2020b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +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'} + +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'), +] + +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'] + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.11-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.11-GCC-10.2.0.eb new file mode 100644 index 0000000000..341fd40e5f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.11-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.11-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..6716a07996 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/HTSlib/HTSlib-1.12-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.12-GCC-10.2.0.eb new file mode 100644 index 0000000000..9e08f3401e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb b/easybuild/easyconfigs/__archive__/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb new file mode 100644 index 0000000000..25dd11aae6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', 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'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +# https://cwiki.apache.org/confluence/display/HADOOP/Hadoop+Java+Versions +dependencies = [ + ('Java', '1.8', '', SYSTEM), + ('libtirpc', '1.3.1'), +] + +build_native_libs = True + +extra_native_libs = [ + ('snappy', 'lib*/libsnappy.%s*' % SHLIB_EXT), + ('zlib', 'lib*/libz.%s*' % SHLIB_EXT), +] + +maxparallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a44e86d5ff --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/Harminv/Harminv-1.4.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/h/Harminv/Harminv-1.4.2-foss-2020b.eb new file mode 100644 index 0000000000..7065f827a2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0f1af103e8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/Highway/Highway-0.12.2-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 = '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'), + ('googletest', '1.10.0'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb new file mode 100644 index 0000000000..cf272d473d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.1-fosscuda-2020b-TensorFlow-2.4.1.eb @@ -0,0 +1,42 @@ +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), +] + +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 ' + +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', { + 'checksums': ['820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82'], + }), + ('horovod', version, { + 'checksums': ['874dd3ac469944464bb77e1a42296500d0028177183ad5ab5af8ec61a34a1ed7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..c318277eb4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,42 @@ +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'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('PyTorch', local_pt_version), +] + +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 ' + +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', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + 'checksums': ['dee8b2387b1ec9f54fe1737a95b992a52ce20cb3f1a4388017215fae14978f95'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb new file mode 100644 index 0000000000..fc64a6544d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -0,0 +1,42 @@ +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'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('PyTorch', local_pt_version), +] + +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 ' + +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', { + '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/__archive__/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..475597d798 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,43 @@ +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), +] + +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 ' + +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', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + 'checksums': ['c45bfcb9bd96852d79c62976eda12e9320b58b64f55bee3772877b3fc6243f2a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..8d34023ef1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,43 @@ +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), +] + +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 ' + +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', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + 'checksums': ['72ab3e5f59df6a000473999937e52e6831ad1a5e4e7bd23885a04bcdd4d8691c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 0000000000..dd6af99bcc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,40 @@ +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), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..efecbc6544 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb @@ -0,0 +1,46 @@ +# 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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.20.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.20.0-foss-2020b.eb new file mode 100644 index 0000000000..666f85cc71 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/Hypre/Hypre-2.20.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.20.0-intel-2020b.eb new file mode 100644 index 0000000000..6b3ba1660e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..de1ee211cf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb new file mode 100644 index 0000000000..50fe19e455 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'h4toh5' +version = '2.2.3' + +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://support.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' diff --git a/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-foss-2020b.eb new file mode 100644 index 0000000000..88ca816ac3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-foss-2020b.eb @@ -0,0 +1,30 @@ +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} + +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'), +] + +# 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. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..d1de160e97 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-fosscuda-2020b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.1.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2'] + +builddependencies = [('pkgconfig', '1.5.1', '-python')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), +] + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-intel-2020b.eb new file mode 100644 index 0000000000..63aebd44bf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-intel-2020b.eb @@ -0,0 +1,30 @@ +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} + +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'), +] + +# 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. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-intelcuda-2020b.eb new file mode 100644 index 0000000000..cbf5fd8210 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/h5py/h5py-3.1.0-intelcuda-2020b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.1.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2'] + +builddependencies = [('pkgconfig', '1.5.1', '-python')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), +] + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/harmony/harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..48daa7126a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..98698a165f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb b/easybuild/easyconfigs/__archive__/h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb new file mode 100644 index 0000000000..91fe900751 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/__archive__/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb new file mode 100644 index 0000000000..ee5c6c8ec6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb @@ -0,0 +1,51 @@ +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'} + +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 = [ + ('Clang', '11.0.1'), + # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', SYSTEM), + # ('Python', '3.8.6'), +] + +# 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' + +# 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' diff --git a/easybuild/easyconfigs/__archive__/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f3d9db107b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +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 = "--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/__archive__/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..26c09f0d05 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-4.53.1-GCCcore-10.2.0.eb @@ -0,0 +1,20 @@ +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')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c03620d197 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-5.41.2-GCCcore-10.2.0.eb @@ -0,0 +1,21 @@ +# 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' + +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 = ['f8c281355aaba1da696e40f1488c2bb47c42660424f5750daea45a85e2d047b3'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f433d5203d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-5.41.5-GCCcore-10.2.0.eb @@ -0,0 +1,20 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a74e127a865fde12b853cc00f5f52a3a1601d2a1c311b3ffc8de92a4c06778f7'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e6d7a93bd7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-6.7.0-GCCcore-10.2.0.eb @@ -0,0 +1,20 @@ +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')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/ICU/ICU-67.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/ICU/ICU-67.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4b6277c96f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/i/IMB/IMB-2021.3-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/i/IMB/IMB-2021.3-gompi-2020b.eb new file mode 100644 index 0000000000..9b368a912c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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"' + +maxparallel = 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' diff --git a/easybuild/easyconfigs/__archive__/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/i/IMOD/IMOD-4.11.5-foss-2020b.eb new file mode 100644 index 0000000000..44f212cc01 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -0,0 +1,93 @@ +# 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] +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 +] +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'), + ('Qt5', '5.14.2'), + ('Java', '11', '', SYSTEM), + ('HDF5', '1.10.7'), + ('Python', '3.8.6'), +] + +# parallel build sometimes fails +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)' {} \\; &&" + +# 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 && ' + +# 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", + '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/__archive__/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..fedcca873c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -0,0 +1,106 @@ +# 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] +# 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 +] +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'), + ('Qt5', '5.14.2'), + ('Java', '11', '', SYSTEM), + ('HDF5', '1.10.7'), + ('Python', '3.8.6'), +] + +# parallel build sometimes fails +maxparallel = 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 \'{' +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 &&' + +# 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", + '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/__archive__/i/IOR/IOR-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/i/IOR/IOR-3.3.0-gompi-2020b.eb new file mode 100644 index 0000000000..da2da4d12f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0fb450ad45 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb @@ -0,0 +1,143 @@ +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'), +] + +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'], + }), +] + +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/IPython', + 'share/jupyter' + ], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "NOSE_EXCLUDE='system_interrupt' iptest", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/IQ-TREE/IQ-TREE-2.1.2-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/i/IQ-TREE/IQ-TREE-2.1.2-gompi-2020b.eb new file mode 100644 index 0000000000..9f3d8686a6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..22b310f46f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' % x for x 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/__archive__/i/ISL/ISL-0.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/ISL/ISL-0.23-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0aac5d8b60 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/ISL/ISL-0.23-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +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] +checksums = ['c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d'] + +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/__archive__/i/ITK/ITK-5.2.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.2.1-foss-2020b.eb new file mode 100644 index 0000000000..b689599457 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.2.1-foss-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': 'foss', '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' % (x, SHLIB_EXT) for x in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.2.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..a72a767497 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' % (x, SHLIB_EXT) for x in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f0077dead9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +# 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', '2.0.24'), + ('libjpeg-turbo', '2.0.5'), + ('LibTIFF', '4.1.0'), + ('LittleCMS', '2.11'), + ('Pango', '1.47.0'), +] + +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/__archive__/i/Infernal/Infernal-1.1.4-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1.4-gompi-2020b.eb new file mode 100644 index 0000000000..3cf3368886 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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': 'gompi', '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' diff --git a/easybuild/easyconfigs/__archive__/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb new file mode 100644 index 0000000000..52512fdf4b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -0,0 +1,63 @@ +# 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', '4.56.2'), + ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! +] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('fire', '0.4.0', { + 'modulename': 'fire', + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], + 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], + }), +] + +modextrapaths = { + 'PATH': 'lib/python%(pyshortver)s/site-packages/IsoNet/bin', +} +sanity_check_commands = [ + 'isonet.py check', + 'isonet.py --help', +] +sanity_check_paths = { + 'files': [], + 'dirs': ["lib/python%(pyshortver)s/site-packages/IsoNet"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/i/iVar/iVar-1.3.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/iVar/iVar-1.3.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..c254db7175 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/iccifort/iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/i/iccifort/iccifort-2020.4.304.eb new file mode 100644 index 0000000000..056539c7f7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/iccifortcuda/iccifortcuda-2020b.eb b/easybuild/easyconfigs/__archive__/i/iccifortcuda/iccifortcuda-2020b.eb new file mode 100644 index 0000000000..ffe511679a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c801e2d60d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +# 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'), +] + +exts_list = [ + ('pytest-runner', '5.3.0', { + 'modulename': 'ptr', + 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], + }), + ('tqdm', '4.60.0', { + 'checksums': ['ebdebdb95e3477ceea267decfc0784859aa3df3e27e22d23b83e9b272bf157ae'], + }), + (name, version, { + 'checksums': ['590980baaf810c8a02705efd50eb4ace644c360470fc3dc4491d077bbb6b26fc'], + }), +] + +sanity_check_paths = { + 'files': ['bin/idemux'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["idemux -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/i/igraph/igraph-0.8.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/i/igraph/igraph-0.8.5-foss-2020b.eb new file mode 100644 index 0000000000..0177350f16 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/igraph/igraph-0.8.5-foss-2020b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +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 +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' diff --git a/easybuild/easyconfigs/__archive__/i/igraph/igraph-0.9.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/i/igraph/igraph-0.9.1-foss-2020b.eb new file mode 100644 index 0000000000..227d6a8a2e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/i/igraph/igraph-0.9.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/i/igraph/igraph-0.9.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..8a232120a0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/iibff/iibff-2020b.eb b/easybuild/easyconfigs/__archive__/i/iibff/iibff-2020b.eb new file mode 100644 index 0000000000..9759ceacc9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/i/iimpi/iimpi-2020.12.eb b/easybuild/easyconfigs/__archive__/i/iimpi/iimpi-2020.12.eb new file mode 100644 index 0000000000..9cf9d3045b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/i/iimpi/iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/i/iimpi/iimpi-2020b.eb new file mode 100644 index 0000000000..656957fc24 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/i/iimpic/iimpic-2020b.eb b/easybuild/easyconfigs/__archive__/i/iimpic/iimpic-2020b.eb new file mode 100644 index 0000000000..bb2d747fe5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/__archive__/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb new file mode 100644 index 0000000000..9b0fed9db7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -0,0 +1,68 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'imagecodecs' +version = '2021.8.26' + +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.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +local_openjpeg_maj_min = '2.4' +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy + ('matplotlib', '3.3.3'), + ('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', '0.6.1'), + ('LibLZF', '3.4'), + ('libpng', '1.6.37'), + ('XZ', '5.2.5'), + ('LibTIFF', '4.1.0'), + ('libwebp', '1.1.0'), + ('lz4', '1.9.2'), + ('OpenJPEG', local_openjpeg_maj_min + '.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_list = [ + ('bitshuffle', '0.3.5', { + '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", + '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 = 'lib' diff --git a/easybuild/easyconfigs/__archive__/i/imageio/imageio-2.9.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/i/imageio/imageio-2.9.0-foss-2020b.eb new file mode 100644 index 0000000000..90b1d5b148 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imageio/imageio-2.9.0-foss-2020b.eb @@ -0,0 +1,21 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/i/imageio/imageio-2.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/i/imageio/imageio-2.9.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..e9a4559326 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imageio/imageio-2.9.0-fosscuda-2020b.eb @@ -0,0 +1,21 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/i/imake/imake-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/imake/imake-1.0.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..773071072b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imake/imake-1.0.8-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +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'} + +source_urls = ['https://artfiles.org/x.org/pub/individual/util/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8178a09bfef33ad5f61cb5cb62283df7d3a5682f014507d2e7cfd922485a5c00'] + +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', + 'makeg', 'mergelib', 'mkdirhier', + 'mkhtmlindex', 'revpath', 'xmkmf']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb new file mode 100644 index 0000000000..f777a7fe46 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imbalanced-learn/imbalanced-learn-0.7.0-foss-2020b.eb @@ -0,0 +1,22 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da59de0d1c0fa66f62054dd9a0a295a182563aa1abbb3bf9224a3678fcfe8fa4'] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-learn', '0.23.2'), +] + +options = {'modulename': 'imblearn'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb new file mode 100644 index 0000000000..71a9f0f37b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-NVHPC-21.2.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': '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 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-gompi-2020b.eb new file mode 100644 index 0000000000..1526523c78 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-gompi-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': '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 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-gompic-2020b.eb new file mode 100644 index 0000000000..570499af77 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-iimpi-2020b.eb new file mode 100644 index 0000000000..15ccb6b8c7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-iimpi-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': '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 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-iimpic-2020b.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-iimpic-2020b.eb new file mode 100644 index 0000000000..73aac3a85e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-iimpic-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': '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 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-iompi-2020b.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-iompi-2020b.eb new file mode 100644 index 0000000000..68e2a157d3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.4.304-iompi-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': '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 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb new file mode 100644 index 0000000000..363e95f7dc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..2bf8b19fb2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..d723d12dc1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb b/easybuild/easyconfigs/__archive__/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb new file mode 100644 index 0000000000..7082d103ec --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/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 new file mode 100644 index 0000000000..d8a92d6db7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb @@ -0,0 +1,16 @@ +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'] + +dependencies = [('UCX', '1.9.0')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/i/imutils/imutils-0.5.4-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/i/imutils/imutils-0.5.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..db3b0b207b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/imutils/imutils-0.5.4-fosscuda-2020b.eb @@ -0,0 +1,21 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/i/inferCNV/inferCNV-1.3.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/i/inferCNV/inferCNV-1.3.3-foss-2020b.eb new file mode 100644 index 0000000000..7236c47e7f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/__archive__/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..8f55b4abbf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/inline/inline-0.3.19-foss-2020b-R-4.0.4.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'inline' +version = '0.3.19' +versionsuffix = '-R-%(rver)s' + +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.""" + +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 = ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'] + +dependencies = [ + ('R', '4.0.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['inline'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/i/intel-compilers/intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/__archive__/i/intel-compilers/intel-compilers-2021.1.2.eb new file mode 100644 index 0000000000..67a5c1f570 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/intel-compilers/intel-compilers-2021.1.2.eb @@ -0,0 +1,31 @@ +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/articles/oneapi-standalone-components.html +sources = [ + { + '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 = [ + '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)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/i/intel/intel-2020.12.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2020.12.eb new file mode 100644 index 0000000000..ce1386acf6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/intel/intel-2020b.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2020b.eb new file mode 100644 index 0000000000..f1e345c4cf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/intelcuda/intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/i/intelcuda/intelcuda-2020b.eb new file mode 100644 index 0000000000..c9456eab5c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/intervaltree/intervaltree-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/intervaltree/intervaltree-0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bdf771c099 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/i/intltool/intltool-0.51.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/intltool/intltool-0.51.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8c601251e7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/i/iomkl/iomkl-2020b.eb b/easybuild/easyconfigs/__archive__/i/iomkl/iomkl-2020b.eb new file mode 100644 index 0000000000..994e712f40 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/i/iompi/iompi-2020b.eb b/easybuild/easyconfigs/__archive__/i/iompi/iompi-2020b.eb new file mode 100644 index 0000000000..7a81cae9fa --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/i/iperf/iperf-2.1.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..baf0cfe8d0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/iperf/iperf-2.1.9-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 +# $Id$ +# +# 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 = 'https://sourceforge.net/projects/iperf2/' +description = """Iperf 2: TCP and UDP bandwidth performance measurement tool""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('https://sourceforge.net/projects/iperf2/files', 'download')] +checksums = ['5c0771aab00ef14520013aef01675977816e23bb8f5d9fde016f90eb2f1be788'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/iperf'], + 'dirs': [] +} + +sanity_check_commands = ["iperf --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb new file mode 100644 index 0000000000..1c05b20306 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb @@ -0,0 +1,64 @@ +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'), + ('pyfaidx', '0.5.9.5'), +] + +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'], + }), + ('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' diff --git a/easybuild/easyconfigs/__archive__/j/JAGS/JAGS-4.3.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/j/JAGS/JAGS-4.3.0-foss-2020b.eb new file mode 100644 index 0000000000..ceb7e97810 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..78f0374a76 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/Jansson/Jansson-2.13.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..ec96079841 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/j/Jansson/Jansson-2.13.1-GCC-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 = 'ConfigureMake' + +name = 'Jansson' +version = "2.13.1" + +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 + * 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 && ' +builddependencies = [('Autotools', '20200321')] + +sanity_check_paths = { + 'files': ['lib/libjansson.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +runtest = 'check' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2398c04fb1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-2.0.24-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +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'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..d5418f668d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'] + +maxparallel = 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 = {MODULE_LOAD_ENV_HEADERS: 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/j/Jorg/Jorg-1.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/j/Jorg/Jorg-1.0.1-foss-2020b.eb new file mode 100644 index 0000000000..582026b28f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['90a63d9dcd32fe7f65946798c98f1551cea20ceab6446e9e5898cbbe6f0be52d'] +prepend_to_path = ['.'] + +dependencies = [ + ('MIRA', '5.0rc2'), + ('seqtk', '1.3'), +] + +sanity_check_paths = { + 'files': ['jorg'], + 'dirs': [], +} + +sanity_check_commands = ['jorg --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/j/JsonCpp/JsonCpp-1.9.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/JsonCpp/JsonCpp-1.9.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dccb8a613b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/j/Judy/Judy-1.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/Judy/Judy-1.0.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9988efaf33 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9879509ec7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,111 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '1.1.0' + +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.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = { + ('binutils', '2.35'), +} + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), + ('Mako', '1.1.3'), + ('configurable-http-proxy', '4.2.1'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +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'], + }), +] + +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/__archive__/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a0d9aaa592 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +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'), +] + +exts_list = [ + ('json5', '0.9.5', { + 'checksums': ['703cfee540790576b56a92e1c6aaa6c4b0d98971dc358ead83812aa4d06bdb96'], + }), + ('jupyterlab_server', '1.2.0', { + 'checksums': ['5431d9dde96659364b7cc877693d5d21e7b80cea7ae3959ecc2b87518e5f5d8c'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['c8377bee30504919c1e79949f9fe35443ab7f5c4be622c95307e8108410c8b8c'], + }), +] + +sanity_check_commands = ["jupyter lab --help"] + +modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/__archive__/j/jax/jax-0.2.19-foss-2020b.eb new file mode 100644 index 0000000000..f99474f1c5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/j/jax/jax-0.2.19-foss-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': 'foss', 'version': '2020b'} + +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 = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('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_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir + +# 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 + +default_easyblock = 'PythonPackage' +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'}, + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + }), + ('jaxlib', '0.1.70', { + '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), + ], + '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', + ], + '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/'], + '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', + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/j/jax/jax-0.2.19-fosscuda-2020b.eb new file mode 100644 index 0000000000..ba868854c6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -0,0 +1,118 @@ +# 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'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.28.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('flatbuffers-python', '1.12'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), + ('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 + +default_easyblock = 'PythonPackage' +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'}, + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + }), + ('jaxlib', '0.1.70', { + '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', + '%(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), + ], + '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', + # jaxlib-0.1.70_fix-gpu-translation-rule.patch + 'ce3cf8ee3b393f6580fb88bc39cc2660be46f2a48a315a3779403725ad49f946', + # 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/'], + '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', + ], + # deliberately not testing in parallel, as that results in (additional) failing tests; + # 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 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + "JAX_ENABLE_X64=true pytest tests", + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cc565979b7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '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_ar.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/j/jemalloc/jemalloc-5.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/jemalloc/jemalloc-5.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8e43deb719 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/j/joypy/joypy-0.2.4-intel-2020b.eb b/easybuild/easyconfigs/__archive__/j/joypy/joypy-0.2.4-intel-2020b.eb new file mode 100644 index 0000000000..f408b376c5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/j/joypy/joypy-0.2.4-intel-2020b.eb @@ -0,0 +1,23 @@ +# 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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['55d268386a1d2d974aa90cbf6dcca3ad943d17075987dfb8c4a772852fbe79c7'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11',), + ('matplotlib', '3.3.3',), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/j/jq/jq-1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/jq/jq-1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..926327a17f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/j/jq/jq-1.5-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +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': [], +} + +sanity_check_commands = ["jq --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/j/json-c/json-c-0.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/json-c/json-c-0.15-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..150611776a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/j/json-c/json-c-0.15-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +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'), +] + +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' +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/__archive__/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8ee634ca4f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/j/jxrlib/jxrlib-1.1-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 = 'CMakeMake' + +name = 'jxrlib' +version = '1.1' + +homepage = 'https://github.com/4creators/jxrlib' +description = """Open source implementation of jpegxr""" + +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 = [('jxrlib-%(version)s_cmake.patch', 1)] +checksums = [ + 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303', # jxrlib_1.1.orig.tar.gz + 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74', # jxrlib-1.1_cmake.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] + +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/jxrlib'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c065d25b93 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/k/Kaleido/Kaleido-0.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,20 @@ +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'} + +sources = ['kaleido-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'] +checksums = ['8d0403b1eb21080e09d6d728c1ea7170fd4763c415fe89dfea6edf35ec36f8e7'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [('Python', '3.8.6')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dd1f62fb09 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..aeeec32aa8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +# 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'), + ('Autotools', '20200321'), +] + +configure_cmd_prefix = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/kchaos', 'bin/kalign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb new file mode 100644 index 0000000000..49423ef592 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb @@ -0,0 +1,37 @@ +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'), +] + +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++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.4.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.4.3-foss-2020b.eb new file mode 100644 index 0000000000..756c1e7c80 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.4.3-foss-2020b.eb @@ -0,0 +1,32 @@ +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'), + ('TensorFlow', '2.4.1'), # provides h5py 2.1.0 +] + +exts_list = [ + ('Keras_Applications', '1.0.8', { + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'checksums': ['fedd729b52572fb108a98e3d97e1bac10a81d3917d2103cc20ab2a5f03beb973'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..ec8929b7b5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,34 @@ +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 +] + +exts_list = [ + ('Keras_Applications', '1.0.8', { + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'checksums': ['fedd729b52572fb108a98e3d97e1bac10a81d3917d2103cc20ab2a5f03beb973'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.4.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.4.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..4fc733084c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.4.3-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +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'), + ('TensorFlow', '2.4.1'), # provides h5py 2.1.0 +] + +exts_list = [ + ('Keras_Applications', '1.0.8', { + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'checksums': ['fedd729b52572fb108a98e3d97e1bac10a81d3917d2103cc20ab2a5f03beb973'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/k/Kraken/Kraken-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/k/Kraken/Kraken-1.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..de1ed07683 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb new file mode 100644 index 0000000000..7069cfa02d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb @@ -0,0 +1,53 @@ +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', + '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 = [ + ('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' diff --git a/easybuild/easyconfigs/__archive__/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9bd5a84885 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/k/KronaTools/KronaTools-2.8-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +# 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 = 'Tarball' + +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 = ['%(name)s-%(version)s.tar'] +checksums = ['56efc028b6226a1aea8ec4e9f049836b07d4833e7e4d5b9189118ed51a47c9c0'] + +dependencies = [('Perl', '5.32.0')] + +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', + 'bin/updateAccessions.sh', 'bin/updateTaxonomy.sh'], + 'dirs': ['data', 'img', 'scripts'], +} + +sanity_check_commands = [ + "updateAccessions.sh --help", + "ktImportText", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/k/kallisto/kallisto-0.46.1-iimpi-2020b.eb new file mode 100644 index 0000000000..fafcee6308 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 - &&" + +maxparallel = 1 + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/k/kallisto/kallisto-0.46.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/k/kallisto/kallisto-0.46.2-foss-2020b.eb new file mode 100644 index 0000000000..b8b39f95ff --- /dev/null +++ b/easybuild/easyconfigs/__archive__/k/kallisto/kallisto-0.46.2-foss-2020b.eb @@ -0,0 +1,39 @@ +# 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 - &&" +configopts = '-DUSE_HDF5=ON' + +maxparallel = 1 + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/k/kim-api/kim-api-2.2.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..12adff577b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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. +] + +maxparallel = 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' diff --git a/easybuild/easyconfigs/__archive__/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/k/kim-api/kim-api-2.2.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..e2f93a06fe --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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. +] + +maxparallel = 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' diff --git a/easybuild/easyconfigs/__archive__/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6128a9ac49 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +# 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 +maxparallel = 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 = [( + r"prover9 -h 2>&1 | grep 'Usage: prover9 \[-h\] \[-x\] \[-p\] \[-t \] \[-f \]'", '' +)] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/l/LAME/LAME-3.100-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LAME/LAME-3.100-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ecd79e6d2f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..14d4bb284c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb @@ -0,0 +1,16 @@ +name = 'LAPACK' +version = '3.9.1' + +homepage = 'https://www.netlib.org/lapack/' +description = """LAPACK is written in Fortran90 and provides routines for solving systems of + simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue + problems, and singular value problems.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Reference-LAPACK/lapack/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d0085d2caf997ff39299c05d4bacb6f3d27001d25a4cc613d48c1f352b73e7e0'] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/l/LAST/LAST-1179-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LAST/LAST-1179-GCC-10.2.0.eb new file mode 100644 index 0000000000..ed590fe3da --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LAST/LAST-1179-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'LAST' +version = '1179' + +homepage = 'http://last.cbrc.jp/' +description = "LAST finds similar regions between sequences." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['http://last.cbrc.jp/'] +sources = ['last-%(version)s.zip'] +checksums = ['f78f68884ed936408e26e38afe1b8f9023747384e555a4ec92405ed23a1cd075'] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS -pthread -DHAS_CXX_THREADS"' +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['fastq-interleave', 'lastal', 'lastal8', 'lastdb', 'lastdb8', 'last-dotplot', + 'last-map-probs', 'last-merge-batches', 'last-pair-probs', 'last-postmask', + 'last-split', 'last-split8', 'last-train', 'maf-convert', 'maf-cut', + 'maf-join', 'maf-sort', 'maf-swap', 'parallel-fasta', 'parallel-fastq']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a022ed94c4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeNinja' + +name = 'LDC' +version = '1.25.1' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s'] +sources = ['ldc-%(version)s-src.tar.gz'] +checksums = ['0e3716fe9927be91264d1fde5c41071026f6c44262735e9ebda538089b612d40'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Ninja', '1.10.1'), + # building LDC from source required LDC 0.17.x + ('LDC', '0.17.6', '-%(arch)s', SYSTEM), +] + +dependencies = [ + ('LLVM', '11.0.0'), +] + +configopts = "-DLLVM_ROOT_DIR=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/ldc2', 'bin/ldmd2'], + 'dirs': ['include/d', 'lib'], +} + +sanity_check_commands = [ + "ldc2 --help", + "ldmd2 --help", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LERC/LERC-3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a731819812 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +# 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'), +] + +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", + "mkdir %(installdir)s/LercTest", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/LercTest/main.cpp", + "cd %(installdir)s/LercTest && ${CXX} ${CXXFLAGS} main.cpp -o LercTest -I../include -L../lib -lLerc", +] + +sanity_check_commands = [ + "%(installdir)s/LercTest/LercTest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..54bac051fb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/LLVM/LLVM-10.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LLVM/LLVM-10.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fd3c955057 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..88f9f8de51 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/LMDB/LMDB-0.9.24-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LMDB/LMDB-0.9.24-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..155ad1c68c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/LMfit/LMfit-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/LMfit/LMfit-1.0.2-foss-2020b.eb new file mode 100644 index 0000000000..4d2634b42d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LMfit/LMfit-1.0.2-foss-2020b.eb @@ -0,0 +1,30 @@ +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'), +] + +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/__archive__/l/LMfit/LMfit-1.0.2-intel-2020b.eb b/easybuild/easyconfigs/__archive__/l/LMfit/LMfit-1.0.2-intel-2020b.eb new file mode 100644 index 0000000000..60cd617730 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LMfit/LMfit-1.0.2-intel-2020b.eb @@ -0,0 +1,30 @@ +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'), +] + +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/__archive__/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb new file mode 100644 index 0000000000..3291ad1ac3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LPJmL/LPJmL-4.0.003-iimpi-2020b.eb @@ -0,0 +1,47 @@ +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'), +] + +configure_cmd = './configure.sh' +prefix_opt = '-prefix ' + +buildopts = 'all LPJFLAGS="-DUSE_MPI -DUSE_NETCDF4 -DUSE_UDUNITS -DUSE_JSON" OPTFLAGS="$CFLAGS" ' + +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' diff --git a/easybuild/easyconfigs/__archive__/l/LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d0801000f6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..82407cd707 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/LTR_retriever/LTR_retriever-2.9.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/LTR_retriever/LTR_retriever-2.9.0-foss-2020b.eb new file mode 100644 index 0000000000..35d99a92ae --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.3.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.3.1-foss-2020b.eb new file mode 100644 index 0000000000..6b1e20f8df --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2898f75e50 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7b980f3eae --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LibLZF/LibLZF-3.4-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 = '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'] +checksums = ['ec62974877b4b85f6e37db97e71678c7abfe83091b57d32ec69fa37b2c3c9499'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_commands = ['lzf -h'] + +sanity_check_paths = { + 'files': ['bin/lzf', 'lib/liblzf.a'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/LibSoup/LibSoup-2.72.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LibSoup/LibSoup-2.72.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7481e75050 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9e430cbd05 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +## +# 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: +# https://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'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('zstd', '1.4.5'), +] + +configopts = "--enable-ld-version-script " +configopts += "--disable-webp " + +sanity_check_paths = { + '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': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.6-foss-2020b.eb new file mode 100644 index 0000000000..b85944e7d7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/Libint/Libint-2.6.0-GCC-10.2.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/l/Libint/Libint-2.6.0-iccifort-2020.4.304-lmax-6-cp2k.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..aa4fb28b4c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LittleCMS/LittleCMS-2.11-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.11' + +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 = ['https://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' diff --git a/easybuild/easyconfigs/__archive__/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb new file mode 100644 index 0000000000..a290fefcd6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb @@ -0,0 +1,62 @@ +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'), + ('pyBigWig', '0.3.18'), + ('networkx', '2.5'), +] + +exts_list = [ + ('amply', '0.1.4', { + 'checksums': ['cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38'], + }), + ('PuLP', '2.4', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/coin-or/pulp/archive/'], + 'checksums': ['d52d52b6078ea2c503b33814738866902d661cfe60d7a76251d50423e4af3ad0'], + }), + (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_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/__archive__/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f3c93e26ad --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +# 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'), + ('Perl', '5.32.0'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..125417a6c6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/Lua/Lua-5.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/Lua/Lua-5.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2179e5f542 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb new file mode 100644 index 0000000000..459b91dad0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/leidenalg/leidenalg-0.8.3-foss-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': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('PyYAML', '5.3.1'), + ('Bison', '3.7.1'), + ('libtool', '2.4.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('igraph', '0.9.1'), + ('python-igraph', '0.9.0'), +] + +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/__archive__/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..ae2f5af19b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), + ('Bison', '3.7.1'), + ('libtool', '2.4.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('igraph', '0.9.1'), + ('python-igraph', '0.9.0'), +] + +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/__archive__/l/libFLAME/libFLAME-5.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libFLAME/libFLAME-5.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6751c8d65b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5ebb3d807a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9f77d11e01 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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://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://archive.mesa3d.org/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/__archive__/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb new file mode 100644 index 0000000000..4cfcff47e5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb new file mode 100644 index 0000000000..e8ca5b5883 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/l/libPSML/libPSML-1.1.10-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libPSML/libPSML-1.1.10-GCC-10.2.0.eb new file mode 100644 index 0000000000..080cda40c5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libPSML/libPSML-1.1.10-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/l/libPSML/libPSML-1.1.10-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..ae80d7188d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..991bb64101 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), +] + +maxparallel = 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/__archive__/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..bbf22c8faf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb @@ -0,0 +1,79 @@ +## +# 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.%s' % SHLIB_EXT, 'lib64/perl5/vendor_perl/LibSBML.pm'], + 'dirs': ['lib64', 'include', 'share'] +} + +modextrapaths = { + 'PERL5LIB': 'lib64/perl5/vendor_perl/', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..06c1b1a902 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libStatGen/libStatGen-1.0.15-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +# 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' + +keepsymlinks = False +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' diff --git a/easybuild/easyconfigs/__archive__/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d5fc64c036 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# 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', 'include/libaec.h', 'include/szlib.h', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["aec --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9392190354 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.112' +_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')] + +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + +files_to_copy = [ + (["src/libaio.a", "src/%s" % _soname], "lib"), + (["src/libaio.h"], "include"), +] + +# 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, x) for x in _solinks] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7214c3ae94 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# 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'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/l/libavif/libavif-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/libavif/libavif-0.9.0-foss-2020b.eb new file mode 100644 index 0000000000..6e46d36eea --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libavif/libavif-0.9.0-foss-2020b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = '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'] +checksums = ['ea1603fc18e7dd20cf01f0b405156576886ecb5df84db8c0e87187cd2f8a00f4'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('NASM', '2.15.05'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('Rust', '1.52.1'), +] + +sanity_check_paths = { + 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2e95fab49e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libbaseencode/libbaseencode-1.0.11-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 = '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'), + ('binutils', '2.35'), +] + +maxparallel = 1 + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libbaseencode.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..863a2d13b9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libcerf/libcerf-1.14-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +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'), + ('Perl', '5.32.0'), # required for pod2html +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/l/libcint/libcint-4.4.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/libcint/libcint-4.4.0-foss-2020b.eb new file mode 100644 index 0000000000..f8db3f095f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libcint/libcint-4.4.0-foss-2020b.eb @@ -0,0 +1,39 @@ +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 ' + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/libcint.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libcircle/libcircle-0.3-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/l/libcircle/libcircle-0.3-gompi-2020b.eb new file mode 100644 index 0000000000..7044e9c9fe --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4e37d805f1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +# 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'), + ('pkg-config', '0.29.2'), + ('binutils', '2.35'), +] + +dependencies = [ + ('libgcrypt', '1.9.2'), + ('libbaseencode', '1.0.11'), +] + +maxparallel = 1 + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libcotp.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libcroco/libcroco-0.6.13-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libcroco/libcroco-0.6.13-GCC-10.2.0.eb new file mode 100644 index 0000000000..29daab547e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3dfc9fe295 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..88a8de8e31 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libdap/libdap-3.20.7-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +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] +checksums = ['6856813d0b29e70a36e8a53e9cf20ad680d21d615952263e9c6586704539e78c'] + +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/__archive__/l/libdeflate/libdeflate-1.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libdeflate/libdeflate-1.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c517a5b337 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a9b29e1cd1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MesonNinja' +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'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), +] +dependencies = [('X11', '20201008')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '-Dman-pages=false' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..82b24be6a2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libdwarf/libdwarf-20201201-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '20201201' + +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 = ['https://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' diff --git a/easybuild/easyconfigs/__archive__/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dabbb48b3e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libelf/libelf-0.8.13-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'libelf' +version = '0.8.13' + +homepage = 'https://sourceware.org/elfutils' +description = """libelf is a free ELF object file access library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://fossies.org/linux/misc/old/'] +sources = [SOURCE_TAR_GZ] +checksums = ['591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d'] + +builddependencies = [ + ('binutils', '2.35'), +] + +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'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a1bd6be54f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +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=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + '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'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libevent/libevent-2.1.12-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libevent/libevent-2.1.12-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..22b850f842 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5deaf391f9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +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_IBVERBS_DEV] + +# Disable deprecated "sockets" provider +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'] + + ['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/__archive__/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb b/easybuild/easyconfigs/__archive__/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb new file mode 100644 index 0000000000..4f17eb894d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb @@ -0,0 +1,21 @@ +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': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb b/easybuild/easyconfigs/__archive__/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb new file mode 100644 index 0000000000..12c8f37583 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb @@ -0,0 +1,21 @@ +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'] + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..49b562a9cb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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': [], +} + +maxparallel = 1 + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6ccf73557b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libgcrypt/libgcrypt-1.9.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..53c4550ea8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libgd/libgd-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libgd/libgd-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dc2c2c7aa9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libgeotiff/libgeotiff-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libgeotiff/libgeotiff-1.6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a739034a87 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libgeotiff/libgeotiff-1.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.6.0' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['9311017e5284cffb86f2c7b7a9df1fb5ebcdc61c30468fb2e6bca36e4272ebca'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('PROJ', '7.2.1'), + ('libjpeg-turbo', '2.0.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('LibTIFF', '4.1.0'), + ('cURL', '7.72.0'), +] + +configopts = ' --with-libtiff=$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/__archive__/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3826f08432 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libgit2/libgit2-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +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'), + # ('OpenSSL', '1.1.1h') + # OS dependency should be preferred if the os version is more recent than this version +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7495fa8b56 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +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'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), +] + +dependencies = [('X11', '20201008')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +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' diff --git a/easybuild/easyconfigs/__archive__/l/libgpg-error/libgpg-error-1.41-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libgpg-error/libgpg-error-1.41-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..652f4aa22a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb new file mode 100644 index 0000000000..f1ee0b724d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -0,0 +1,41 @@ +# 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-%(cudaver)s'), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + (name, version, { + 'modulename': 'pygpu', + 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], + 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], + }), +] + +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/__archive__/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libharu/libharu-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..02a5143fe7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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')] + +maxparallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libiconv/libiconv-1.16-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libiconv/libiconv-1.16-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6b87eb86c4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libidn/libidn-1.36-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libidn/libidn-1.36-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6a64b05a39 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..684e717287 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libidn2/libidn2-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'libidn2' +version = '2.3.0' + +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.""" + +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/__archive__/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1214eaa1d2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['16f8f6f2715b3a38ab562a84357c793dd56ae9899ce130563c72cd93d8357b5d'] + +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/__archive__/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4bd51b12d1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -0,0 +1,71 @@ +# 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 + '1948d2527c658637939327eec093301539b164714f5bf146ed2e0dcadffadf00', # libjxl-0.6.1_external_lcms2.patch + '11b7cf639049afd9acd1c362287a743cdbe1a6f55e6f9d42b6eaa75ac6a0e6da', # 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/jxl'], +} + +sanity_check_commands = [ + "cjxl --help", + "djxl --help", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/libmbd/libmbd-0.10.4-foss-2020b.eb new file mode 100644 index 0000000000..028b219dd1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -0,0 +1,49 @@ +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 = ['0f9ee2c69dfc2fd085127aae4b3b794fad20ef5c2dad6c89728ce5fbf300eb75'] + +builddependencies = [ + ('CMake', '3.18.4') +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" + +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 +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd.h', 'include/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/__archive__/l/libmbd/libmbd-0.10.4-intel-2020b.eb new file mode 100644 index 0000000000..f45c4de511 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -0,0 +1,49 @@ +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 = ['0f9ee2c69dfc2fd085127aae4b3b794fad20ef5c2dad6c89728ce5fbf300eb75'] + +builddependencies = [ + ('CMake', '3.18.4') +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" + +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 +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd.h', 'include/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libmicrohttpd/libmicrohttpd-0.9.73-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8665a8d9e2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libogg/libogg-1.3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libogg/libogg-1.3.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b215ccb49f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libpci/libpci-3.7.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libpci/libpci-3.7.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..acbdbf0ad9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.16-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.16-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7e7b8c982a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1ed15d2e2e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libpsl/libpsl-0.21.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libpsl/libpsl-0.21.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..56cfaf83bd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..87e76b10a6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'} + +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' diff --git a/easybuild/easyconfigs/__archive__/l/libpspio/libpspio-0.2.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/l/libpspio/libpspio-0.2.4-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..6b551f2ed9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cb086a8416 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb new file mode 100644 index 0000000000..e61290dd63 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb new file mode 100644 index 0000000000..fac25cf212 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/librsb/librsb-1.2.0.9-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/librsb/librsb-1.2.0.9-GCC-10.2.0.eb new file mode 100644 index 0000000000..1e66ae9aa3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..41f09407b0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -0,0 +1,37 @@ +## +# 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'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('zlib', '1.2.11') +] + +# 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' + +sanity_check_paths = { + 'files': ['bin/rsbench', 'lib/librsb.a', 'lib/librsb.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..52dbf8d89f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libsigsegv/libsigsegv-2.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libsigsegv/libsigsegv-2.13-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2f09752a34 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ffbc20beb7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libsndfile/libsndfile-1.0.28-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +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'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('FLAC', '1.3.3'), + ('libvorbis', '1.3.7'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/l/libsodium/libsodium-1.0.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libsodium/libsodium-1.0.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a9b32bf628 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libtasn1/libtasn1-4.16.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libtasn1/libtasn1-4.16.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c422aeee5a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..383ab0e181 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libtirpc/libtirpc-1.3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7b3c578596 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = {MODULE_LOAD_ENV_HEADERS: 'include/tirpc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dd1e6e9fa2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d783490e21 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), +] + +maxparallel = 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/__archive__/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1073232ea5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +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', + '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')] + +dependencies = [ + ('XZ', '5.2.5'), +] + +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], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb new file mode 100644 index 0000000000..0e414c5d72 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +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.""" + +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/__archive__/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb new file mode 100644 index 0000000000..a610d3ec77 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +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.""" + +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'], +} + +# MKL FFTW does not have all the features of fftw3 and libvdwxc is using them +dependencies = [ + ('FFTW', '3.3.8') +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libvorbis/libvorbis-1.3.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libvorbis/libvorbis-1.3.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..92bb35e68f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libwebp/libwebp-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1e22cfc835 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' % x for x in ['webp', 'webpdemux', 'webpmux']] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['webp', 'webpdemux', 'webpmux']], + 'dirs': ['lib/'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libxc/libxc-3.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-3.0.1-foss-2020b.eb new file mode 100644 index 0000000000..414380e8b4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'], +} + +maxparallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..0df5335e2e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-GCC-10.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '4.3.4' + +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.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(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', + '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 +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Perl', '5.32.0'), +] + +separate_build_dir = True + +maxparallel = 1 + +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', +] + +# 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': ['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' diff --git a/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..6253121a11 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '4.3.4' + +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.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(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', + '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 + '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', +] + +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 +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +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' diff --git a/easybuild/easyconfigs/__archive__/l/libxc/libxc-5.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-5.1.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..70940c1854 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libxc/libxc-5.1.2-GCC-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '5.1.2' + +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.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = [('180d52b5552921d1fac8a10869dd30708c0fb41dc202a3bbee0e36f43872718a', + '3fe05ccf7033622112f7d6ab28ac82301f5840b8d1bbe8b6df1022dbc732883f')] + +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', +] + +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 +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libxc/libxc-5.1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-5.1.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..5b2dc43c0a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libxc/libxc-5.1.3-GCC-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '5.1.3' + +homepage = 'https://libxc.gitlab.io' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = [('0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd', + '53cbccae4227794c4f4e042d0c20c3171894d8eacd13fd78aab376d5971a966c')] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Perl', '5.32.0'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +maxparallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +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'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..aeed9cfa94 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +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 = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2c20332345 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +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 = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('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': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libxsmm/libxsmm-1.16.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..0d233d0fee --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/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/libxsmm/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/__archive__/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/l/libxsmm/libxsmm-1.16.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..4d9093e4d2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/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/libxsmm/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/__archive__/l/libyaml/libyaml-0.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libyaml/libyaml-0.2.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ca89e6e47b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/libzip/libzip-1.7.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/libzip/libzip-1.7.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fed83245aa --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..1955082621 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb @@ -0,0 +1,42 @@ +# 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'), +] + +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 = 'bio' diff --git a/easybuild/easyconfigs/__archive__/l/likwid/likwid-5.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/likwid/likwid-5.2.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..c723d1fccb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/likwid/likwid-5.2.0-GCC-10.2.0.eb @@ -0,0 +1,60 @@ +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', # v5.2.0.tar.gz + '76ef41001efcdd107e34e2833325ffa876b8ac526740301ae9bace91150cfb8f', # likwid-5.2.0_use_EB_hwloc.patch +] + +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 ' +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' diff --git a/easybuild/easyconfigs/__archive__/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..e2774c4ac8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb @@ -0,0 +1,54 @@ +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', # v5.2.0.tar.gz + '76ef41001efcdd107e34e2833325ffa876b8ac526740301ae9bace91150cfb8f', # likwid-5.2.0_use_EB_hwloc.patch +] + +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' diff --git a/easybuild/easyconfigs/__archive__/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb new file mode 100644 index 0000000000..b6bbb0b3fd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -0,0 +1,75 @@ +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', '1.4.21'), + ('SAMtools', '1.11'), + ('seqtk', '1.3'), + ('VSEARCH', '2.18.0'), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + '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'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'], + 'start_dir': '%(name)s-%(version)s', + }), +] + +# 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 " + "-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', + # 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, +] + +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', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/l/loompy/loompy-3.0.6-intel-2020b.eb b/easybuild/easyconfigs/__archive__/l/loompy/loompy-3.0.6-intel-2020b.eb new file mode 100644 index 0000000000..75c2751715 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/loompy/loompy-3.0.6-intel-2020b.eb @@ -0,0 +1,34 @@ +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'), +] + +exts_list = [ + ('numpy_groupies', '0.9.13', { + 'checksums': ['7b17b291322353f07c51598512d077e3731da0a048cfa8f738f3460d1ef0658d'], + }), + (name, version, { + 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], + }), +] + +sanity_check_paths = { + 'files': ['bin/loompy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["loompy --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/l/lpsolve/lpsolve-5.5.2.11-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/lpsolve/lpsolve-5.5.2.11-GCC-10.2.0.eb new file mode 100644 index 0000000000..a4a64c04b9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb new file mode 100644 index 0000000000..10d0197ebd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..da0865afaa --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/lxml/lxml-4.6.2-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['cd11c7e8d21af997ee8079037fff88f16fda188a9776eb4b81c7e4c9c0a7d7fc'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e192b5b004 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a8d9bfb519 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +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', + '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 +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 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.475-GCC-10.2.0-with-extensions.eb b/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.475-GCC-10.2.0-with-extensions.eb new file mode 100644 index 0000000000..70eb55dda6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/m/MAFFT/MAFFT-7.475-gompi-2020b-with-extensions.eb b/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.475-gompi-2020b-with-extensions.eb new file mode 100644 index 0000000000..6d0bc5ea12 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c8a95327a3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['2ac1d5406e51f2bdfaa545a535d6dbf6347be89891a06323961d7a2acbf37be9'] + +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' diff --git a/easybuild/easyconfigs/__archive__/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b2753431c9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +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'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('MATLAB', _matlab_version, '', SYSTEM), + ('Python', '3.8.6'), +] + +exts_list = [ + ('matlabengine', _engine_version, { + 'modulename': 'matlab.engine', + 'checksums': ['c1610690dbe58ac00e74e8cbb20406208235ede47da7960238e0c2fd3bd496c0'], + }), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/m/MCL/MCL-14.137-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MCL/MCL-14.137-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9aaca698b9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb new file mode 100644 index 0000000000..31d808c243 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb @@ -0,0 +1,48 @@ +## +# 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', '4.56.2'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb new file mode 100644 index 0000000000..61672a415b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.5-foss-2020b.eb @@ -0,0 +1,40 @@ +# 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': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('zlib', '1.2.11'), +] + +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 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..a14e188d5d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.5-fosscuda-2020b.eb @@ -0,0 +1,40 @@ +# 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'), +] + +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 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb b/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb new file mode 100644 index 0000000000..f4d415e26b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.5-intel-2020b.eb @@ -0,0 +1,40 @@ +# 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': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('zlib', '1.2.11'), +] + +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 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6216f2aace --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'https://karypis.github.io/glaros/projects/gp.html' + +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 = [ + 'https://karypis.github.io/glaros/files/sw/metis', + 'https://karypis.github.io/glaros/files/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' diff --git a/easybuild/easyconfigs/__archive__/m/MIRA/MIRA-5.0rc2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/MIRA/MIRA-5.0rc2-foss-2020b.eb new file mode 100644 index 0000000000..062d990ae9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MIRA/MIRA-5.0rc2-foss-2020b.eb @@ -0,0 +1,34 @@ +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 CXXFLAGS="$CXXFLAGS -fpermissive" && ' + +configopts = '--with-boost=$EBROOTBOOST --with-expat=$EBROOTEXPAT --with-zlib=$EBROOTZLIB ' + +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' diff --git a/easybuild/easyconfigs/__archive__/m/MITObim/MITObim-1.9.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/MITObim/MITObim-1.9.1-foss-2020b.eb new file mode 100644 index 0000000000..283dde5a2d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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" diff --git a/easybuild/easyconfigs/__archive__/m/MMseqs2/MMseqs2-13-45111-20211006-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/m/MMseqs2/MMseqs2-13-45111-20211006-gompi-2020b.eb new file mode 100644 index 0000000000..59646fc55e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/MMseqs2/MMseqs2-13-45111-20211019-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/m/MMseqs2/MMseqs2-13-45111-20211019-gompi-2020b.eb new file mode 100644 index 0000000000..0277029f5d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb new file mode 100644 index 0000000000..0e1cf8f454 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb @@ -0,0 +1,27 @@ +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'] +checksums = ['6444bb682ebf5ced54b2eda7a301fa3e933c2a28b7661f96ef5bdab1d53695a2'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [('bzip2', '1.0.8')] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MPB/MPB-1.11.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/MPB/MPB-1.11.1-foss-2020b.eb new file mode 100644 index 0000000000..bff6686a32 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/m/MPC/MPC-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MPC/MPC-1.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..29b4a95e74 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b43fbb0dc5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +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] +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': '039fad7a79ec4a9fd9ce77c9a73d9278187b8430087bc1afec18883df40321ae'}, +] + +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' diff --git a/easybuild/easyconfigs/__archive__/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MPICH/MPICH-3.3.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..0b28d5921b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/downloads/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4bfaf8837a54771d3e4922c84071ef80ffebddbb6971a006038d91ee7ef959b9'] + +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" ' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb new file mode 100644 index 0000000000..7e85bf5569 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb @@ -0,0 +1,38 @@ +name = 'MUMPS' +version = '5.3.5' +versionsuffix = '-metis' + +homepage = 'https://mumps-solver.org' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +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 + '%(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'), + ('METIS', '5.1.0'), +] + +maxparallel = 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/__archive__/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb new file mode 100644 index 0000000000..8b3508f0a5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -0,0 +1,38 @@ +name = 'MUMPS' +version = '5.3.5' +versionsuffix = '-metis' + +homepage = 'https://mumps-solver.org' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +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 + '%(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'), + ('METIS', '5.1.0'), +] + +maxparallel = 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/__archive__/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ac9a89a287 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb new file mode 100644 index 0000000000..75cf15432a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2230dff6fc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +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 +] + +builddependencies = [ + ('binutils', '2.35'), +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MUST/MUST-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/MUST/MUST-1.7.1-foss-2020b.eb new file mode 100644 index 0000000000..b7aef9fc7f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MUST/MUST-1.7.1-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = "CMakeMake" + +name = 'MUST' +version = '1.7.1' + +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" diff --git a/easybuild/easyconfigs/__archive__/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..79f314e1fb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +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'} + +sources = [SOURCE_TAR_GZ] +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': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/MariaDB-connector-c/MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MariaDB-connector-c/MariaDB-connector-c-3.1.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..22c8a33e99 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = { + MODULE_LOAD_ENV_HEADERS: ['include/mariadb'], + 'LD_LIBRARY_PATH': ['lib/mariadb'], + 'LIBRARY_PATH': ['lib/mariadb'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb new file mode 100644 index 0000000000..0b8c7c5e09 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb @@ -0,0 +1,71 @@ +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'} + +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, +] +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 +] + +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 +] + +# 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_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' diff --git a/easybuild/easyconfigs/__archive__/m/Maude/Maude-3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/Maude/Maude-3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f9de690f36 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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': ['bin/maude'] + ['share/%s.maude' % x for x in ['file', 'linear', 'prelude', 'smt']], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb new file mode 100644 index 0000000000..535fd62d21 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb @@ -0,0 +1,40 @@ +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 = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] + +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 = ['*'] + +fix_perl_shebang_for = ['run_MaxBin.pl'] + +sanity_check_paths = { + 'files': ['run_MaxBin.pl', 'src/MaxBin'], + 'dirs': [], +} + +modextrapaths = {'PATH': ['', 'src']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MbedTLS/MbedTLS-2.26.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..aa73c698f4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = 'https://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 PYTHON=python' + +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' diff --git a/easybuild/easyconfigs/__archive__/m/MedPy/MedPy-0.4.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/MedPy/MedPy-0.4.0-foss-2020b.eb new file mode 100644 index 0000000000..94295f1343 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MedPy/MedPy-0.4.0-foss-2020b.eb @@ -0,0 +1,24 @@ +# 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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..3767368ae1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb @@ -0,0 +1,24 @@ +# 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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.26.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.26.0-foss-2020b.eb new file mode 100644 index 0000000000..28f24d9a3b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.26.0-foss-2020b.eb @@ -0,0 +1,50 @@ +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 " + +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'", +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb new file mode 100644 index 0000000000..1c51b68308 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb @@ -0,0 +1,53 @@ +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', '4.56.2'), + ('Pysam', '0.16.0.1'), + ('Seaborn', '0.11.1'), +] + +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", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..c60f26b61a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb @@ -0,0 +1,53 @@ +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'), +] + +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", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..995a851ffc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-5.7.1-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +easyblock = "PythonPackage" + +name = 'Mercurial' +version = '5.7.1' + +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. +""" + +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') +] + +sanity_check_commands = ["hg --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..352626800c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,67 @@ +# 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://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'] +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', '1.3.2'), + ('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"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..213225dfb5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6bed2a25a128bbabe97cf40f63165ebe800e4fcb46db8ab7ef5c2b5789f092a5'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Ninja', '1.10.1'), +] + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d28f9928ee --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +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'], +} + +sanity_check_commands = [ + "msqquality -h", + "msqshape -h", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..0852b759a0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -0,0 +1,51 @@ +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'] +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 = [ + ('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'), +] + +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" ' + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MetaEuk/MetaEuk-4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MetaEuk/MetaEuk-4-GCC-10.2.0.eb new file mode 100644 index 0000000000..16d2dcc3cc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb new file mode 100644 index 0000000000..5d713d8d11 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMakeCp' + +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')] + +files_to_copy = [(['metal/metal'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/metal'], + 'dirs': [''], +} + +sanity_check_commands = ['%(namelower)s'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/__archive__/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 0000000000..1b08034e2a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Mish-Cuda' +version = '20210309' +local_commit = '6f38976' +local_ptver = '1.9.0' +versionsuffix = '-PyTorch-%s' % local_ptver + +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" && ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4245f9b4d6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..fdeb49b42a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/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/monocle3/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': 'Monocle3-%(version)s.tar.gz'}], + 'checksums': ['fe95f724ff7a8f35cc4c8152865052c3a6d44332485b0626fbc3e1af09c17738'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['leidenbase', '%(namelower)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..280bf3a6dd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'} + +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 +# 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', '', SYSTEM), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5'), + ('XZ', '5.2.5'), + ('LibTIFF', '4.1.0'), + ('jbigkit', '2.1'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c4d1ce0d0d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +# 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 = ['%(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] + +# 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'), + ('CUDA', '11.3.1', '', SYSTEM), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5'), + ('LibTIFF', '4.1.0'), +] +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb new file mode 100644 index 0000000000..417331a216 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.7-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.7-gompi-2020b.eb new file mode 100644 index 0000000000..a0ef1f5ec7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb new file mode 100644 index 0000000000..9dee95e4e4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb @@ -0,0 +1,69 @@ +# 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' +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'), +] + +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"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/Myokit/Myokit-1.32.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/Myokit/Myokit-1.32.0-foss-2020b.eb new file mode 100644 index 0000000000..6a5d45cbf2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Myokit/Myokit-1.32.0-foss-2020b.eb @@ -0,0 +1,41 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['393ebc85413bd1b573909736caeadd9d7757f41cceb7bd29f3b30f5107237cba'] + +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_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/__archive__/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..3a55db7a48 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Myokit/Myokit-1.32.0-fosscuda-2020b.eb @@ -0,0 +1,41 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['393ebc85413bd1b573909736caeadd9d7757f41cceb7bd29f3b30f5107237cba'] + +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_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/__archive__/m/magma/magma-2.5.4-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/m/magma/magma-2.5.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..daaf3b0b03 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/magma/magma-2.5.4-fosscuda-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': 'fosscuda', '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' diff --git a/easybuild/easyconfigs/__archive__/m/magma/magma-2.5.4-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/m/magma/magma-2.5.4-intelcuda-2020b.eb new file mode 100644 index 0000000000..8fe0d955a9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/make/make-4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/make/make-4.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..98544f1366 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3295f02cc8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0-minimal.eb b/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0-minimal.eb new file mode 100644 index 0000000000..bd55c1413d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f24d92de95 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +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')] +dependencies = [('Perl', '5.32.0')] + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..ff224b45ba --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,72 @@ +## +# 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'), +] + +# 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 +# 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 = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] + +modextrapaths = { + 'PATH': 'libexec', + 'PYTHONPATH': 'lib/python', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/__archive__/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..acf2310cd7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb @@ -0,0 +1,33 @@ +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'] +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'), + ('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/__archive__/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..03648a4381 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,21 @@ +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'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), # has traitlets +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..171f790a64 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,61 @@ +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'), +] + +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/__archive__/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb new file mode 100644 index 0000000000..17d226d026 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-foss-2020b.eb @@ -0,0 +1,51 @@ +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'), + ('Pillow', '8.0.1'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..e8f714c5d4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-fosscuda-2020b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.3.3' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb new file mode 100644 index 0000000000..403fa88da2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-intel-2020b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.3.3' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb new file mode 100644 index 0000000000..0ae55de9ae --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.3.3-intelcuda-2020b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.3.3' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': ['b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb new file mode 100644 index 0000000000..9f7fcdae7c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.1' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), + ('Qhull', '2020.2') +] + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template > mplsetup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$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/__archive__/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb new file mode 100644 index 0000000000..2ef0b7945f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb @@ -0,0 +1,62 @@ +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'), + ('Qhull', '2020.2') +] + +# 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/__archive__/m/maze/maze-20170124-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/maze/maze-20170124-foss-2020b.eb new file mode 100644 index 0000000000..4e70c7b7c0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/maze/maze-20170124-foss-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +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'} + +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'), + ('LAST', '1179'), + ('Flask', '1.1.2'), + ('Pysam', '0.16.0.1'), +] + +preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ + +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/__archive__/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/medaka/medaka-1.4.3-foss-2020b.eb new file mode 100644 index 0000000000..5859e4cb68 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -0,0 +1,92 @@ +# 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 2.2.3 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'), + # Pysam 0.16.0.1 is strictly required, see requirements.txt + ('Pysam', '0.16.0.1'), + ('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 + ('Racon', '1.4.21'), + ('spoa', '4.0.7'), + ('networkx', '2.5'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.8'), + ('pyfaidx', '0.5.9.5'), + ('python-isal', '0.11.1'), + ('BCFtools', '1.11'), +] + +exts_list = [ + # required for ont-fast5-api + ('progressbar33', '2.4', { + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + # 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'], + }), + ('mappy', '2.22', { + 'checksums': ['219c93ab7f8d5d7c26face512a9e738a7306f3376ebfa3017eac70676ba97840'], + }), + ('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'], + 'checksums': [ + '59997b5fdaff6f2040f2df2d3d3eb2d6d1805916a720e8275309caf4d2d4b8a5', # medaka-1.4.3.tar.gz + '06b1d8344035ebcfaf1893e62f37db9b4cab0053ad7a073113630872d44be33e', # medaka-1.4.3_use-SAMtools-dep.patch + ], + # loosen up TensorFlow version requirements, see also https://github.com/nanoporetech/medaka/issues/323 + 'preinstallopts': "sed -i 's/tensorflow==/tensorflow~=/g' requirements.txt && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/meshalyzer/meshalyzer-2.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/meshalyzer/meshalyzer-2.2-foss-2020b.eb new file mode 100644 index 0000000000..04d794caa9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/m/meshtool/meshtool-16-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/meshtool/meshtool-16-GCC-10.2.0.eb new file mode 100644 index 0000000000..4225f3c60e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/meshtool/meshtool-16-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'meshtool' +version = '16' + +homepage = 'https://bitbucket.org/aneic/meshtool' +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'} + +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 = { + 'files': ['bin/meshtool'], + 'dirs': [], +} + +sanity_check_commands = ["meshtool help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..382b15693e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,57 @@ +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'] +checksums = ['ffdbccf340dc0b1ebd0ad6f222e3bdef1e22bbd6e4e5156bf93500a3a834dd52'] + +builddependencies = [ + ('Java', '11', '', SYSTEM), +] + +# 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', SYSTEM), + ('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/__archive__/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb new file mode 100644 index 0000000000..31c671af27 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'mhcnuggets' +version = '2.3' + +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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..413db008b1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'mhcnuggets' +version = '2.3' + +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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/__archive__/m/microctools/microctools-0.1.0-20201209-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..205c6e8881 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d159c3b396 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# 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')] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + +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' diff --git a/easybuild/easyconfigs/__archive__/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..abd40a4d87 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb @@ -0,0 +1,52 @@ +# 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')] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + +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'), + (['test/MT-human.fa', 'test/MT-orang.fa'], 'test'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include', 'test'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(installdir)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb new file mode 100644 index 0000000000..66be6f2401 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/mkl-service/mkl-service-2.3.0-intel-2020b.eb @@ -0,0 +1,26 @@ +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 +] + +options = {'modulename': 'mkl'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/mmtf-cpp/mmtf-cpp-1.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..06408c9c90 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = '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 +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/__archive__/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb b/easybuild/easyconfigs/__archive__/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb new file mode 100644 index 0000000000..ce073ff093 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb @@ -0,0 +1,60 @@ +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')] + +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'] + +sanity_check_paths = { + 'files': ['bin/gsm.%s.exe' % x for x in _bins], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.8-foss-2020b.eb new file mode 100644 index 0000000000..cce1209d0b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many components 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] +patches = ['molmod-1.4.8_fix-git-version-check.patch'] +checksums = [ + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'}, +] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i && pytest -ra" + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/mongolite/mongolite-2.3.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/m/mongolite/mongolite-2.3.0-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/motif/motif-2.3.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/motif/motif-2.3.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a1e88b5290 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/motif/motif-2.3.8-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +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'), + ('binutils', '2.35'), + ('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 +maxparallel = 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' diff --git a/easybuild/easyconfigs/__archive__/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f1dfa5cec5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +# 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'), +] + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb new file mode 100644 index 0000000000..c60ba7e918 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/mrcfile/mrcfile-1.3.0-foss-2020b.eb @@ -0,0 +1,27 @@ +# 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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..ede48f5e30 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/mrcfile/mrcfile-1.3.0-fosscuda-2020b.eb @@ -0,0 +1,27 @@ +# 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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c85cf60f99 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/msgpack-c/msgpack-c-3.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# 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 = ['https://github.com/msgpack/msgpack-c/releases/download/cpp-%(version)s'] +sources = ['msgpack-%(version)s.tar.gz'] +checksums = ['6e114d12a5ddb8cb11f669f83f32246e484a8addd0ce93f274996f1941c1f07b'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + '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' diff --git a/easybuild/easyconfigs/__archive__/m/muParser/muParser-2.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/muParser/muParser-2.3.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d7822f8a35 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..423504cb40 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb b/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb new file mode 100644 index 0000000000..69bd6e602f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb @@ -0,0 +1,29 @@ +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 = [ + ('tcsh', '6.22.03'), + ('Tcl', '8.6.10'), +] + +# 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/__archive__/n/NAMD/NAMD-2.14-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.14-fosscuda-2020b.eb new file mode 100644 index 0000000000..bb7d42b87f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.14-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +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 = [ + ('tcsh', '6.22.03'), + ('Tcl', '8.6.10'), +] + +charm_arch = "multicore-linux-%(arch)s" +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..27a05a06c8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['3c4b8339e5ab54b1bcb2316101f8985a5da50a3f9e504d43fa6f35668bee2fd0'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/n/NBO/NBO-7.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/NBO/NBO-7.0.10-GCC-10.2.0.eb new file mode 100644 index 0000000000..e642d4a9c2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/NBO/NBO-7.0.10-GCC-10.2.0.eb @@ -0,0 +1,55 @@ +# 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 + +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', +] +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 += 'INT=%s ' % local_intlength + +maxparallel = 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' diff --git a/easybuild/easyconfigs/__archive__/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/__archive__/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb new file mode 100644 index 0000000000..3c825519ba --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -0,0 +1,29 @@ +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, '', SYSTEM)] +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', + 'NCCL-2.16.2_fix-cpuid.patch', +] +checksums = [ + {'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' diff --git a/easybuild/easyconfigs/__archive__/n/NCL/NCL-6.6.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/NCL/NCL-6.6.2-foss-2020b.eb new file mode 100644 index 0000000000..898a5271a1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/NCO/NCO-4.9.7-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/NCO/NCO-4.9.7-foss-2020b.eb new file mode 100644 index 0000000000..cc1f44d3a1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = ['934e247d9592f3e6087ea8985507077873559b52679b9c9a1ecae40668a352dc'] + +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' diff --git a/easybuild/easyconfigs/__archive__/n/NFFT/NFFT-3.1.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/NFFT/NFFT-3.1.3-foss-2020b.eb new file mode 100644 index 0000000000..011d4f4624 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/n/NFFT/NFFT-3.1.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..4550457df6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3ef383ecc8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM)] + +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/__archive__/n/NLopt/NLopt-2.6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/NLopt/NLopt-2.6.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9d4bf341cd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a796b4e421 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/NSS/NSS-3.57-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7ff8ade27f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -0,0 +1,58 @@ +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', + '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')] +dependencies = [ + ('NSPR', '4.29'), + ('zlib', '1.2.11'), +] + +# building in parallel fails +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 ' +# 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 -" +# 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')] +# symlinks in bin/ would point to outside of installation directory, so can't keep them +keepsymlinks = False + +sanity_check_paths = { + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], +} + +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + +modextrapaths = {MODULE_LOAD_ENV_HEADERS: 'include/nss'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb new file mode 100644 index 0000000000..f2706a745d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb new file mode 100644 index 0000000000..e6a73c74e3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb new file mode 100644 index 0000000000..1aca5fd3cf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-21.2.eb b/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-21.2.eb new file mode 100644 index 0000000000..628b83138b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 +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' diff --git a/easybuild/easyconfigs/__archive__/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb new file mode 100644 index 0000000000..e540bfa733 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/NanoComp/NanoComp-1.13.1-intel-2020b.eb @@ -0,0 +1,39 @@ +# 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'} + +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'), + ('plotly-orca', '1.3.1'), + ('joypy', '0.2.4'), +] + +# 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"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb new file mode 100644 index 0000000000..6a853d802c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/NanoPlot/NanoPlot-1.33.0-intel-2020b.eb @@ -0,0 +1,42 @@ +# 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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['caf69a5789625e746814238cb4f0d510ed6768a094566e8f1dcaa77933c4d6fd'] + +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', '0.10.1'), + ('plotly.py', '4.14.3'), + ('pauvre', '0.1924'), + ('statsmodels', '0.12.1'), + ('Arrow', '0.17.1'), # for pyarrow + ('Kaleido', '0.1.0'), +] + +# 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"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb new file mode 100644 index 0000000000..daf63dd2f9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/Nektar++/Nektar++-5.0.1-foss-2020b.eb @@ -0,0 +1,57 @@ +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 = ['https://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 ' + +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 ['Collections', 'FieldUtils', 'GlobalMapping', 'LibUtilities', 'LocalRegions', + 'MultiRegions', 'NekMeshUtils', 'SolverUtils', 'SpatialDomains', 'StdRegions']], + 'dirs': ['include/nektar++', 'lib/nektar++/cmake'], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/n/NetPIPE/NetPIPE-5.1.4-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/n/NetPIPE/NetPIPE-5.1.4-gompi-2020b.eb new file mode 100644 index 0000000000..fa9aaae018 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/n/NetPIPE/NetPIPE-5.1.4-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/n/NetPIPE/NetPIPE-5.1.4-iimpi-2020b.eb new file mode 100644 index 0000000000..73fab7b548 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb new file mode 100644 index 0000000000..ed75c66e78 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/NewHybrids/NewHybrids-1.1_Beta3-GCC-10.2.0.eb @@ -0,0 +1,51 @@ +# Author: Denis Krišťák (INUITS) +# License: GPLv2 + +easyblock = 'Binary' + +name = 'NewHybrids' +version = '1.1_Beta3' + +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.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [{ + 'filename': SOURCE_TAR_XZ, + 'git_config': { + 'url': 'https://github.com/eriqande', + 'repo_name': 'newhybrids', + 'commit': '6fc8fd9ca6e64ee0be08af12ec8bfe73a7de00cc', + 'recursive': True, + } +}] +checksums = ['cdb3f922bfb63a740ac0e56af77b15cf83a111e40dec3a12bb9d4bc0464c8520'] + +extract_sources = True + +# 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'], + 'dirs': ['test_data'], +} + +sanity_check_commands = [ + # 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' diff --git a/easybuild/easyconfigs/__archive__/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb new file mode 100644 index 0000000000..c17c0e3c95 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/NiBabel/NiBabel-3.2.1-foss-2020b.eb @@ -0,0 +1,42 @@ +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'), +] + +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", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..77723e4527 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/NiBabel/NiBabel-3.2.1-fosscuda-2020b.eb @@ -0,0 +1,42 @@ +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'), +] + +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", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb new file mode 100644 index 0000000000..7b1e5a4bac --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/Nilearn/Nilearn-0.7.1-foss-2020b.eb @@ -0,0 +1,25 @@ +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] +checksums = ['8b1409a5e1f0f6d1a1f02555c2f11115a2364f45f1e57bcb5fb3c9ea11f346fa'] + +dependencies = [ + ('Python', '3.8.6'), + ('NiBabel', '3.2.1'), + ('scikit-learn', '0.23.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/n/Nim/Nim-1.4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/Nim/Nim-1.4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..58f3d9cdb0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..afa160c101 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +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': [], +} + +sanity_check_commands = ["ninja --version"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/Nipype/Nipype-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/Nipype/Nipype-1.6.0-foss-2020b.eb new file mode 100644 index 0000000000..d9654ab450 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/Nipype/Nipype-1.6.0-foss-2020b.eb @@ -0,0 +1,81 @@ +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'), +] + +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'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/n/nanoget/nanoget-1.15.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/n/nanoget/nanoget-1.15.0-intel-2020b.eb new file mode 100644 index 0000000000..44e8e2cf53 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/nanoget/nanoget-1.15.0-intel-2020b.eb @@ -0,0 +1,25 @@ +# 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'} + +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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/n/nanomath/nanomath-1.2.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/n/nanomath/nanomath-1.2.0-intel-2020b.eb new file mode 100644 index 0000000000..b516e1b8e3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/nanomath/nanomath-1.2.0-intel-2020b.eb @@ -0,0 +1,29 @@ +# 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'), +] + +exts_list = [ + ('Python-Deprecated', '1.1.0', { + 'modulename': 'deprecated', + 'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'], + }), + (name, version, { + 'checksums': ['b12bf23762fc30be4550d7a8582233bd6f128a1c97477ffb27730bbb8a77f606'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb new file mode 100644 index 0000000000..c4a0d9b383 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb @@ -0,0 +1,23 @@ +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'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..ebd8ab21d6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb @@ -0,0 +1,23 @@ +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'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb new file mode 100644 index 0000000000..9d020bb9a5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -0,0 +1,53 @@ +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', '3.3.9')] + +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'), + ('VBZ-Compression', '1.0.1'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2020b.eb new file mode 100644 index 0000000000..2c3c97317d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' % (x, e), 'lib64/libncbi-%s.%s' % (x, e)) + for x in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/n/ncdf4/ncdf4-1.17-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/n/ncdf4/ncdf4-1.17-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..01ddd2ceed --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3e4cbc865c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +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 --with-versioned-syms " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# 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 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]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +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' % (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'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb new file mode 100644 index 0000000000..b872b8da2f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb @@ -0,0 +1,64 @@ +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'), +] + +exts_list = [ + ('monotonic', '1.6', { + 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], + }), + ('swagger-spec-validator', '2.7.3', { + 'checksums': ['f4f23ee4dbd52bfcde90b1144dde22304add6260e9f29252e9fd7814c9b8fd16'], + }), + ('jsonref', '0.2', { + 'checksums': ['f3c45b121cf6257eafabdc3a8008763aed1cd7da06dbabc59a9e4d2a5e4e6697'], + }), + ('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'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2020b.eb new file mode 100644 index 0000000000..423dff0c34 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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) +maxparallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompic-2020b.eb new file mode 100644 index 0000000000..c9ca60d0c3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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) +maxparallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2020b.eb new file mode 100644 index 0000000000..542fca7fe9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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) +maxparallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-gompi-2020b.eb new file mode 100644 index 0000000000..a4b54ce60d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-gompi-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': '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', + '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/__archive__/n/netCDF/netCDF-4.7.4-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-gompic-2020b.eb new file mode 100644 index 0000000000..9558e24aa1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/n/netCDF/netCDF-4.7.4-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-iimpi-2020b.eb new file mode 100644 index 0000000000..10064fa9b0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-iimpic-2020b.eb b/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-iimpic-2020b.eb new file mode 100644 index 0000000000..e21bf6a3c6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb new file mode 100644 index 0000000000..7721fd2c2e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb @@ -0,0 +1,48 @@ +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..1ecd816cd0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.5.1-fosscuda-2020b.eb @@ -0,0 +1,50 @@ +# Author: Denis Krišťák (INUITS) + +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} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('netCDF', '4.7.4'), + ('cURL', '7.72.0'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb new file mode 100644 index 0000000000..325f42d0fd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.5.1-intel-2020b.eb @@ -0,0 +1,37 @@ +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} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('netCDF', '4.7.4'), + ('cURL', '7.72.0'), +] + +exts_list = [ + ('cftime', '1.2.0', { + 'checksums': ['ff0a175edda260357ff7d24a32bbe0a8c72eafd5f6a404ce487127f9d01836db'], + }), + (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/*'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/nettle/nettle-3.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/nettle/nettle-3.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..76ecdf835b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/n/networkx/networkx-2.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-foss-2020b.eb new file mode 100644 index 0000000000..e2e3222eb0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-foss-2020b.eb @@ -0,0 +1,20 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..4d40433ae0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-fosscuda-2020b.eb @@ -0,0 +1,20 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-intel-2020b.eb b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-intel-2020b.eb new file mode 100644 index 0000000000..6f756c62f7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-intel-2020b.eb @@ -0,0 +1,20 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-intelcuda-2020b.eb new file mode 100644 index 0000000000..5e991b35af --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.5-intelcuda-2020b.eb @@ -0,0 +1,20 @@ +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, ... +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.6.2-foss-2020b.eb new file mode 100644 index 0000000000..00fb9d1646 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.6.2-foss-2020b.eb @@ -0,0 +1,20 @@ +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, ... +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb new file mode 100644 index 0000000000..a00ea50fc2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb @@ -0,0 +1,79 @@ +# 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': 'foss', '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'), +] + +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/__archive__/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..dee8909b57 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb @@ -0,0 +1,79 @@ +# 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'), +] + +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/__archive__/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..56583356f9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +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', '2.7.18'), +] + +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'] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/n/nsync/nsync-1.24.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/nsync/nsync-1.24.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0f9cc830a4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/n/numactl/numactl-2.0.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/numactl/numactl-2.0.13-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9de001385a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/n/numba/numba-0.52.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/numba/numba-0.52.0-foss-2020b.eb new file mode 100644 index 0000000000..7e8cf418ac --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/numba/numba-0.52.0-foss-2020b.eb @@ -0,0 +1,46 @@ +# 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'), +] + +exts_list = [ + ('llvmlite', '0.35.0', { + 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", + 'checksums': [ + '80e51d5aa02ad72da9870e89d21f9b152b0220ca551b4596a6c0614bcde336fc', # llvmlite-0.35.0.tar.gz + # llvmlite-0.31.0_fix-ffi-Makefile.patch + '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', + ], + }), + (name, version, { + 'checksums': ['44661c5bd85e3d3619be0a40eedee34e397e9ccb3d4c458b70e10bf95d1ce933'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/n/numba/numba-0.52.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/n/numba/numba-0.52.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..979731abbd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/numba/numba-0.52.0-fosscuda-2020b.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.52.0' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('LLVM', '10.0.1'), +] + +exts_list = [ + ('llvmlite', '0.35.0', { + 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], + 'preinstallopts': "export LLVM_CONFIG=${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/__archive__/n/numba/numba-0.52.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/n/numba/numba-0.52.0-intel-2020b.eb new file mode 100644 index 0000000000..a97a815853 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/numba/numba-0.52.0-intel-2020b.eb @@ -0,0 +1,46 @@ +# 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'), +] + +exts_list = [ + ('llvmlite', '0.35.0', { + 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", + 'checksums': [ + '80e51d5aa02ad72da9870e89d21f9b152b0220ca551b4596a6c0614bcde336fc', # llvmlite-0.35.0.tar.gz + # llvmlite-0.31.0_fix-ffi-Makefile.patch + '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', + ], + }), + (name, version, { + 'checksums': ['44661c5bd85e3d3619be0a40eedee34e397e9ccb3d4c458b70e10bf95d1ce933'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/n/numba/numba-0.53.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/n/numba/numba-0.53.1-foss-2020b.eb new file mode 100644 index 0000000000..ceb0717012 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/numba/numba-0.53.1-foss-2020b.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.53.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('LLVM', '11.0.0'), +] + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${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/__archive__/n/numba/numba-0.53.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/n/numba/numba-0.53.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..1f5d36b949 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/numba/numba-0.53.1-fosscuda-2020b.eb @@ -0,0 +1,48 @@ +# 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'), +] + +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/__archive__/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b8f9bfcd13 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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://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 + (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' diff --git a/easybuild/easyconfigs/__archive__/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5d464d98c1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +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'] +checksums = ['9b9d8159b95be5cbd9bf6904b44c212e820f17c9009e36e5cfeac43bbb059340'] + +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' diff --git a/easybuild/easyconfigs/__archive__/n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c047696132 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5425817e36 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OBITools3/OBITools3-3.0.1b8-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'OBITools3' +version = '3.0.1b8' + +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['33e10ffced0ef34829d6929180d5012afd6857ae87de420f65d789ebe2bb7741'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-2.0.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0849295e0d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = [ + ('binutils', '2.35'), +] + + +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/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb new file mode 100644 index 0000000000..d97ead0d86 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb @@ -0,0 +1,26 @@ +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'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +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 = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb new file mode 100644 index 0000000000..270c18b7eb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb @@ -0,0 +1,26 @@ +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'} +toolchainopts = {'usempi': True} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +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 = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb new file mode 100644 index 0000000000..8d4a54aa05 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-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': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] + +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 = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb new file mode 100644 index 0000000000..90d4b73806 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb @@ -0,0 +1,31 @@ +## +# 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'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] + +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA' + +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 = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb new file mode 100644 index 0000000000..fed8129584 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-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': 'iimpi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] + +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 = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-2.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a59b3c5ca9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = [ + ('binutils', '2.35'), +] +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/__archive__/o/Octave/Octave-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/Octave/Octave-6.2.0-foss-2020b.eb new file mode 100644 index 0000000000..03e6837966 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), + ('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/__archive__/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb new file mode 100644 index 0000000000..191282689e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/Octopus-vcf/Octopus-vcf-0.7.1-foss-2020b.eb @@ -0,0 +1,49 @@ +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'] + +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=$EBROOTHTSLIB ' + +separate_build_dir = True + +files_to_copy = [ + (['%(builddir)s/easybuild_obj/src/octopus'], 'bin'), + 'doc', 'lib', 'LICENSE', 'logo.png', 'README.md', + 'resources', 'scripts', 'test' +] + +sanity_check_commands = ['octopus -h'] + +sanity_check_paths = { + 'files': ['bin/octopus'], + 'dirs': ['doc', 'lib', 'resources'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/Octopus-vcf/Octopus-vcf-0.7.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/Octopus-vcf/Octopus-vcf-0.7.2-foss-2020b.eb new file mode 100644 index 0000000000..4ee59d1df1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/Octopus-vcf/Octopus-vcf-0.7.2-foss-2020b.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMakeCp' + +# To avoid a naming clash +name = 'Octopus-vcf' +version = '0.7.2' + +homepage = 'https://github.com/luntergroup/octopus' +description = """Octopus is a mapping-based variant caller that implements several calling models within + a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a + tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities + in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in + reasonable time.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/luntergroup/octopus/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['887096c7357b1ba7f0653f9ad34fa32f56f80ba618fe4daaf6837d4737e7838d'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('git', '2.28.0', '-nodocs'), +] + +dependencies = [ + ('Boost', '1.74.0'), + ('HTSlib', '1.11'), + ('GMP', '6.2.0'), + ('Python', '3.8.6'), +] + +configopts = '-DHTSlib_NO_SYSTEM_PATHS=TRUE -DHTSLIB_ROOT=$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' diff --git a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb new file mode 100644 index 0000000000..48333ab642 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -0,0 +1,41 @@ +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', '.'), + '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-%(version)s_add-missing-params-for-power.patch', + '%(name)s-0.3.12_icelake-detection.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', + # OpenBLAS-0.3.12_add-missing-params-for-power.patch + '4454af07290d1fe33e414023a41bb8999d6ee31887e194daa72bd23d46a0072a', + # OpenBLAS-0.3.12_icelake-detection.patch + '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', +] + +builddependencies = [ + ('make', '4.3'), +] + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb new file mode 100644 index 0000000000..526c20bde1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb @@ -0,0 +1,84 @@ +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'), + ('freetype', '2.10.3'), + ('HarfBuzz', '2.6.7'), + ('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', '', 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 +] + +# 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 + +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' % (x, SHLIB_EXT) for x in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb new file mode 100644 index 0000000000..45c90226c4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb @@ -0,0 +1,84 @@ +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'), + ('freetype', '2.10.3'), + ('HarfBuzz', '2.6.7'), + ('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', '', 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 +] + +# 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 + +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' % (x, SHLIB_EXT) for x in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/o/OpenEXR/OpenEXR-2.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OpenEXR/OpenEXR-2.5.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..179dd3fa79 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-8-foss-2020b-20210316.eb b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-8-foss-2020b-20210316.eb new file mode 100644 index 0000000000..4d4dd88545 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb new file mode 100644 index 0000000000..5129ca3258 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-8-foss-2020b.eb @@ -0,0 +1,40 @@ +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'), + ('gnuplot', '5.4.1'), +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb new file mode 100644 index 0000000000..c39a721d0c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb @@ -0,0 +1,50 @@ +## +# Author: Robert Mijakovic +## +# Modified by: Ben Langenberg +## +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'} +# 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/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2112-cleanup.patch', 1), + 'OpenFOAM-v2112-wmake-ompi.patch', +] +checksums = [ + '3e838731e79db1c288acc27aad8cc8a43d9dac1f24e5773e3b9fa91419a8c3f7', # OpenFOAM-v2112.tgz + 'e883f628cb393b3ab60317304d7085d0a6ba7b8992feb12c2fab20389af34f1c', # OpenFOAM-v2112-cleanup.patch + '8cc2d9feac07b564abb4a16614f142a7c1aceedc4ad6ee02836e7d4f654410cd', # OpenFOAM-v2112-wmake-ompi.patch +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), +] + +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'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f82a18a53a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = '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 + (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' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb new file mode 100644 index 0000000000..8a8eafaed2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-foss-2020b.eb @@ -0,0 +1,55 @@ +# 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 = '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 = ['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 = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..b9e09be200 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-fosscuda-2020b.eb @@ -0,0 +1,63 @@ +# 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 = '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 = [ + '516748b4f1ae936c4d70cc6401174fc9384244c65cd3aef27bc2c53eac6d6de5', # 7.5.0.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 = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb new file mode 100644 index 0000000000..c771c0aa1d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-intel-2020b.eb @@ -0,0 +1,59 @@ +# 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 = 'https://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 = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb new file mode 100644 index 0000000000..177ce80391 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb @@ -0,0 +1,57 @@ +# 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 = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..a0469cd4a4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.1-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 +# 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-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 +] + +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 = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb new file mode 100644 index 0000000000..184de98e33 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -0,0 +1,46 @@ +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] +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 + # 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', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, +] + +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/__archive__/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb new file mode 100644 index 0000000000..bb1fb2730a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -0,0 +1,50 @@ +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] +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 + # 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', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, +] + +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'), +] + +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' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb new file mode 100644 index 0000000000..838b2563b3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -0,0 +1,46 @@ +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] +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 + # 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', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, +] + +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/__archive__/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..08a4dbccb2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -0,0 +1,46 @@ +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] +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 + # 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', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, +] + +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/__archive__/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..ec897b5c4c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -0,0 +1,54 @@ +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] +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', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', +] +checksums = [ + {'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 = [ + ('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' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..153e0299b7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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] +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'), +] + +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 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/__archive__/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c5c3f86e07 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +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'] +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', '3.8.6'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ea54770e27 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5927a9835b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -0,0 +1,129 @@ +# 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_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'], + }), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb new file mode 100644 index 0000000000..145640746b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb @@ -0,0 +1,39 @@ +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', '2.0.7'), + ('FastME', '2.1.6.1'), + ('MCL', '14.137'), + ('MMseqs2', '13-45111'), +] + +# 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"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb new file mode 100644 index 0000000000..d1fdb60855 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb @@ -0,0 +1,36 @@ +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f41e73a22d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = {MODULE_LOAD_ENV_HEADERS: 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/__archive__/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/onedrive/onedrive-2.4.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dab738f167 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb new file mode 100644 index 0000000000..fdc7fcadf1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/ont-fast5-api/ont-fast5-api-3.3.0-foss-2020b.eb @@ -0,0 +1,39 @@ +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'), +] + +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", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..6d009fdf1b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/ont-fast5-api/ont-fast5-api-3.3.0-fosscuda-2020b.eb @@ -0,0 +1,39 @@ +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'), +] + +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", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/openCARP/openCARP-6.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/o/openCARP/openCARP-6.0-foss-2020b.eb new file mode 100644 index 0000000000..12b4155a3d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/o/openkim-models/openkim-models-20190725-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/openkim-models/openkim-models-20190725-GCC-10.2.0.eb new file mode 100644 index 0000000000..90c5ae682e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/o/openkim-models/openkim-models-20210128-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/openkim-models/openkim-models-20210128-GCC-10.2.0.eb new file mode 100644 index 0000000000..2e2b058ef6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1401c9209b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +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'), +] + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['6456a3b472e1ef0facb1129f3c6ef00713cebf62e736cd7a75bcc3247432f251'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1a78c40f46 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8055bdba34 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +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'] + +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'], ''), + (['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': ['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' diff --git a/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-6.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3c3d70d453 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' + +# 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 = { + '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' diff --git a/easybuild/easyconfigs/__archive__/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b.eb new file mode 100644 index 0000000000..2ee4d8e8eb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1dec4bf1fa --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b44919660c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] +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/__archive__/p/PDT/PDT-3.25-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PDT/PDT-3.25-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4e8554240a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = [ + ('binutils', '2.35'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.14.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.14.4-foss-2020b.eb new file mode 100644 index 0000000000..ec7ec7d65c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.14.4-foss-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': 'foss', '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="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.14.4-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.14.4-intel-2020b.eb new file mode 100644 index 0000000000..5e792a3e97 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.14.4-intel-2020b.eb @@ -0,0 +1,47 @@ +name = 'PETSc' +version = '3.14.4' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + '2fb431434b91e054cc3a176f7cb008951088243b5dcb3efc8eec8ce589a2658e', # petsc-3.14.4.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('MUMPS', '5.3.5', '-metis'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('Hypre', '2.20.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$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' diff --git a/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb new file mode 100644 index 0000000000..73cd893be2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -0,0 +1,64 @@ +# 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'] + +builddependencies = [ + ('xxd', '8.2.4220'), +] + +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 ' +if ARCH == 'x86_64': + # the flag is not supported on aarch64 + 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/__archive__/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb new file mode 100644 index 0000000000..86b9edfe39 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb @@ -0,0 +1,62 @@ +# 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'] + +builddependencies = [ + ('xxd', '8.2.4220'), +] + +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/__archive__/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb new file mode 100644 index 0000000000..dc86085993 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -0,0 +1,62 @@ +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'] + +builddependencies = [ + ('xxd', '8.2.4220'), +] + +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 ' +if ARCH == 'x86_64': + # the flag is not supported on aarch64 + 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/__archive__/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fa9cd00470 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +# 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'] +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')] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb new file mode 100644 index 0000000000..d62876e7b1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/POV-Ray/POV-Ray-3.7.0.8-GCC-10.2.0.eb @@ -0,0 +1,63 @@ +## +# 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 = '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 + 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 +] + +builddependencies = [ + ('Autotools', '20200321'), +] + +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'), +] + +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/__archive__/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..6891669c1a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/POV-Ray/POV-Ray-3.7.0.8-iccifort-2020.4.304.eb @@ -0,0 +1,63 @@ +## +# 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 = '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 + 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 +] + +builddependencies = [ + ('Autotools', '20200321'), +] + +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'), +] + +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/__archive__/p/PRANK/PRANK-170427-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PRANK/PRANK-170427-GCC-10.2.0.eb new file mode 100644 index 0000000000..87a94a348d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PRANK/PRANK-170427-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 + +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': [], +} + +sanity_check_commands = ['prank -help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb new file mode 100644 index 0000000000..d0822cc92c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb @@ -0,0 +1,100 @@ +# 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 ", "") + +# 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', + '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'], + }), +] + +fix_perl_shebang_for = ["*.pl"] + +postinstallcmds = ["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' diff --git a/easybuild/easyconfigs/__archive__/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4d8bb71381 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +## +# 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'), + ('XZ', '5.2.5'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/PSolver/PSolver-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PSolver/PSolver-1.8.3-foss-2020b.eb new file mode 100644 index 0000000000..f0a3a90c1f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PSolver/PSolver-1.8.3-foss-2020b.eb @@ -0,0 +1,44 @@ +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 = {'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'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libyaml', '0.2.5'), + ('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="$LIBSCALAPACK" ' + +prebuildopts = local_cddir +preinstallopts = local_cddir + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + ['lib/libPSolver-1.a', 'lib/libPSolver-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/p/PSolver/PSolver-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PSolver/PSolver-1.8.3-intel-2020b.eb new file mode 100644 index 0000000000..beb8698e91 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PSolver/PSolver-1.8.3-intel-2020b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3'), +] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-futile-incs=-I$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', 'lib/libPSolver-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb new file mode 100644 index 0000000000..721821f7ae --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb @@ -0,0 +1,20 @@ +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'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..41c1257895 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = "--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/__archive__/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb new file mode 100644 index 0000000000..b7216ae5a6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-gompi-2020b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +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 + 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 = [ + 'https://karypis.github.io/glaros/files/sw/parmetis', + 'https://karypis.github.io/glaros/files/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.18.4')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb new file mode 100644 index 0000000000..5e75abae96 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb @@ -0,0 +1,25 @@ +name = 'ParMETIS' +version = '4.0.3' + +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 + 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 = [ + 'https://karypis.github.io/glaros/files/sw/parmetis', + 'https://karypis.github.io/glaros/files/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.18.4')] + +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb b/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb new file mode 100644 index 0000000000..bed1948538 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-5.8.1-foss-2020b-mpi.eb @@ -0,0 +1,55 @@ +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 ' + +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"'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PartitionFinder/PartitionFinder-2.1.1-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb new file mode 100644 index 0000000000..d3674a9d64 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb @@ -0,0 +1,31 @@ +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] +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'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7340496b8a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -0,0 +1,1811 @@ +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] +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'), + ('groff', '1.22.4'), +] + +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 + ('DB', '18.1.40'), # for DB_File +] + +# OpenSSL is required for Net::SSLeay +osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# !! order of extensions is important !! +# extensions updated on Aug 21st 2020 +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/G/GR/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/handy_tied_functions'], + 'checksums': ['0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117'], + }), + ('Template::Plugin::Number::Format', '1.06', 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['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'], + }), + ('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', '2.093', { + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], + 'checksums': ['5f8f5d06913f16c16759cc4e06749692208b8947910ffedd2c00a74ed0d60ba2'], + }), + ('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'], + }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + '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' diff --git a/easybuild/easyconfigs/__archive__/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb new file mode 100644 index 0000000000..65e6aa83ba --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = 'sh autogen.sh && ' + +configopts = ['--enable-phyml', '--enable-phytime', '--enable-phyrex', '--enable-mpi '] + +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/phyml', 'bin/phyml-mpi', 'bin/phyrex', 'bin/phytime'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0e831be23b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +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'] +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')] + +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') +] + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..ff4e25b298 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,28 @@ +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') +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d3fb87a4e4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +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'} + +sources = [SOURCE_TAR_GZ] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + '11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e', # Pillow-8.0.1.tar.gz + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch +] + +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') +] + +# 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' " + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c7507ca063 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +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') +] + +# 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' " + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.2-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.2-gompi-2020b.eb new file mode 100644 index 0000000000..2132d9c00f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/p/PnetCDF/PnetCDF-1.12.2-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.2-gompic-2020b.eb new file mode 100644 index 0000000000..fc395be789 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-13.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4aee97b7c9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb new file mode 100644 index 0000000000..af50932ddf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyAMG/PyAMG-4.0.0-foss-2020b.eb @@ -0,0 +1,21 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ceb38ffd86e29774e759486f2961599c8ed847459c68727493cadeaf115a38a'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +options = {'modulename': 'pyamg'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb new file mode 100644 index 0000000000..cc7ab66ab7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyAMG/PyAMG-4.0.0-intel-2020b.eb @@ -0,0 +1,21 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ceb38ffd86e29774e759486f2961599c8ed847459c68727493cadeaf115a38a'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +options = {'modulename': 'pyamg'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..cbf8defe8d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyCUDA/PyCUDA-2020.1-fosscuda-2020b.eb @@ -0,0 +1,36 @@ +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 && ' + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.2', { + 'checksums': ['50f2d5b2196a18950fa1397d5ad7ea52daa5985e6196bfd06ba608a7caf93d07'], + }), + (name, version, { + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'preinstallopts': local_preinstallopts, + 'checksums': ['effa3b99b55af67f3afba9b0d1b64b4a0add4dd6a33bdd6786df1aa4cc8761a5'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9658c9544e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyCairo/PyCairo-1.20.0-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'PyCairo' +version = '1.20.0' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5695a10cb7f9ae0d01f665b56602a845b0a8cb17e2123bfece10c2e58552468c'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('cairo', '1.16.0'), +] + +# PyGTK needs PyCairo installed by pip + +# 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/py3cairo.%s' % (p, e) for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')]], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +options = {'modulename': 'cairo'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..df5b2f160e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +# +easyblock = 'PythonBundle' + +name = 'PyClone' +version = '2020.9b2' + +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'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), +] + +exts_list = [ + ('Logbook', '1.5.3', { + 'checksums': ['66f454ada0f56eae43066f604a222b09893f98c1adc18df169710761b8f32fe8'], + }), + ('arrow', '0.17.0', { + 'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'], + }), + (name, version, { + 'checksums': ['e294e875fdd9131526ba9974ad478f213c6d982d273b4b385346e3147e672bc0'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/PyFoam/PyFoam-2020.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyFoam/PyFoam-2020.5-foss-2020b.eb new file mode 100644 index 0000000000..b70b3f82df --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyFoam/PyFoam-2020.5-foss-2020b.eb @@ -0,0 +1,30 @@ +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 +] + +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')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb b/easybuild/easyconfigs/__archive__/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb new file mode 100644 index 0000000000..a9df7f318e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', + 'bb47a31f14329f5ccb7b58e03ce4bde133739acccc76e65ca0e1d69a8ac3694e', # 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' diff --git a/easybuild/easyconfigs/__archive__/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb new file mode 100644 index 0000000000..75e88368c3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb @@ -0,0 +1,22 @@ +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'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..a62733510b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyMC3/PyMC3-3.11.1-fosscuda-2020b.eb @@ -0,0 +1,48 @@ +# 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'), +] + +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/__archive__/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb new file mode 100644 index 0000000000..9da8425123 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyMC3/PyMC3-3.11.1-intel-2020b.eb @@ -0,0 +1,49 @@ +# 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'), +] + +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/__archive__/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb new file mode 100644 index 0000000000..da23337767 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +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! +""" + +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'), +] + +toolchain = {'name': 'foss', 'version': '2020b'} + +use_pip = False + +exts_list = [ + ('Pmw', '2.0.1', { + 'modulename': 'Pmw', + 'source_tmpl': '8bedfc8747e7757c1048bc5e11899d1163717a43.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_check_paths = { + 'files': ['bin/pymol'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PyOD/PyOD-0.8.7-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyOD/PyOD-0.8.7-foss-2020b.eb new file mode 100644 index 0000000000..154b8a0dcd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyOD/PyOD-0.8.7-foss-2020b.eb @@ -0,0 +1,25 @@ +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'] + +sanity_check_commands = ["python -c 'from pyod.models.knn import KNN'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/PyOD/PyOD-0.8.7-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyOD/PyOD-0.8.7-intel-2020b.eb new file mode 100644 index 0000000000..90de91c1f8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyOD/PyOD-0.8.7-intel-2020b.eb @@ -0,0 +1,25 @@ +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'] + +sanity_check_commands = ["python -c 'from pyod.models.knn import KNN'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb new file mode 100644 index 0000000000..2ea0722046 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyOpenCL/PyOpenCL-2021.1.2-foss-2020b.eb @@ -0,0 +1,30 @@ +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'), +] + +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/__archive__/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..94d57e6466 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb @@ -0,0 +1,29 @@ +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'), +] + +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/__archive__/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb new file mode 100644 index 0000000000..11e0d3d783 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyOpenCL/PyOpenCL-2021.1.2-intel-2020b.eb @@ -0,0 +1,30 @@ +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'), +] + +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/__archive__/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..73977bc211 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +## +# 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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4107ba0d0390da5766a08c242cf0cf3404c377ed293c5f6d701e457c57ba3424'] + +builddependencies = [ + ('binutils', '2.35'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('Mesa', '20.2.1'), + ('Python', '3.8.6'), +] + +options = {'modulename': 'OpenGL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb new file mode 100644 index 0000000000..931260b56a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb @@ -0,0 +1,46 @@ +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'], + }), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fd2d0b018d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -0,0 +1,88 @@ +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', '5.14.2'), +] + +default_easyblock = 'PythonPackage' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +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, + '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', + }), + ('PyQt5_sip', '12.8.1', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], + 'start_dir': 'PyQt5_sip-%(version)s', + }), + (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 = { + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5f11b9d4cf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb @@ -0,0 +1,108 @@ +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_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 " + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +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], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], + 'start_dir': 'sip-%s' % local_sipver, + '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', + }), + + ('PyQt5_sip', '12.9.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], + 'start_dir': 'PyQt5_sip-%(version)s', + }), + + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts + }), + + ('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/%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 = { + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb new file mode 100644 index 0000000000..4e34ea0b66 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyQtGraph/PyQtGraph-0.11.1-foss-2020b.eb @@ -0,0 +1,24 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..5c40d2fe13 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyQtGraph/PyQtGraph-0.11.1-fosscuda-2020b.eb @@ -0,0 +1,24 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb new file mode 100644 index 0000000000..db8b6d538b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb @@ -0,0 +1,42 @@ +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'), +] + +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/__archive__/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb new file mode 100644 index 0000000000..2b41d869f4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb @@ -0,0 +1,42 @@ +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'), +] + +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/__archive__/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb new file mode 100644 index 0000000000..ad589671f9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PySAT/PySAT-0.1.7.dev1-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +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'), +] + +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/__archive__/p/PySCF/PySCF-1.7.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PySCF/PySCF-1.7.6-foss-2020b.eb new file mode 100644 index 0000000000..d83b01a813 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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:$EBROOTLIBXC/lib && " + +files_to_copy = ['pyscf'] + +sanity_check_paths = { + 'files': ['pyscf/__init__.py'], + 'dirs': ['pyscf/data', 'pyscf/lib'], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1505bcb68e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'PySide2' +version = '5.14.2.3' + +homepage = 'https://pypi.python.org/pypi/PySide2' +description = """PySide2 is the official Python module from the Qt for Python project, + which provides access to the complete Qt 5.12+ framework.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://download.qt.io/official_releases/QtForPython/%(namelower)s/%(name)s-%(version)s-src/'] +sources = ['pyside-setup-opensource-src-%(version)s.tar.xz'] +checksums = ['032de309505c78ba52c225aaf5fd717b8d87ae863aa7cee8ba58ba6141c59022'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Clang', '11.0.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Qt5', '5.14.2'), +] + +use_pip = False + +preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' + +prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' +buildopts = '--parallel=%(parallel)s' + +preinstallopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' +install_target = 'install --parallel=%(parallel)s' + +options = {'modulename': 'PySide2'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb new file mode 100644 index 0000000000..cb5f68f439 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonBundle' + +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'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +exts_list = [ + (name, version, { + 'modulename': '%(namelower)s', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038'] + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb new file mode 100644 index 0000000000..77d2e587e0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyStan/PyStan-2.19.1.1-intel-2020b.eb @@ -0,0 +1,20 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..6c632eb5c9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,46 @@ +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/refs/tags/'] +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-foss-2020b.eb new file mode 100644 index 0000000000..2b26340937 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-foss-2020b.eb @@ -0,0 +1,44 @@ +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'), +] + +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/__archive__/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..590ad898b3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-fosscuda-2020b.eb @@ -0,0 +1,46 @@ +# Author: Denis Krišťák (INUITS) + +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'), +] + +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/__archive__/p/PyTables/PyTables-3.6.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-intel-2020b.eb new file mode 100644 index 0000000000..408f28c82c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-intel-2020b.eb @@ -0,0 +1,44 @@ +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'), +] + +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/__archive__/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb new file mode 100644 index 0000000000..26e003457d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-foss-2020b.eb @@ -0,0 +1,52 @@ +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', '3.20.1'), +] + +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'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..647000e5bb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2020b.eb @@ -0,0 +1,52 @@ +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', '3.20.1'), +] + +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'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/__archive__/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 0000000000..2bbb7cf4f1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,55 @@ +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', '0.53.1'), + ('h5py', '3.1.0'), + ('tqdm', '4.56.2'), + ('RDFlib', '5.0.0'), + ('ASE', '3.20.1'), + ('YACS', '0.1.8'), +] + +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'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..ffbf98f586 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -0,0 +1,147 @@ +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'} + +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', + '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_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-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', + '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-nnapi-test-without-qnnpack.patch', +] +checksums = [ + '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 + '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_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.patch + '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 + '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-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', +] + +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', SYSTEM), + ('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' + +# 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' diff --git a/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..1e64c9e1b9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb @@ -0,0 +1,316 @@ +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-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', + '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', + '%(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 = [ + '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 + # 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 + '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 + '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', +] + +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', SYSTEM), + ('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 = { + '': [ + # 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 + '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/__archive__/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb new file mode 100644 index 0000000000..785a48ff87 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.7.1-foss-2020b.eb @@ -0,0 +1,322 @@ +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'), +] + +# 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_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 = [ + '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 + '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', + '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', +] + +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 + '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 --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/__archive__/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..63ff087989 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -0,0 +1,352 @@ +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-%(cudaver)s', SYSTEM), + ('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'] + +# 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_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', + '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-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', + '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 + '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 + '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 + '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', + '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 + '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 + '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 + '2a9df4face04798f51eee0db83d28a905ea7ac53569cf25ed9f049b0a547702e', +] + +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 --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/__archive__/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb new file mode 100644 index 0000000000..20131a617e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -0,0 +1,98 @@ +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': SOURCE_TAR_XZ, + '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-1.8.0_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_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', +] +checksums = [ + '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 + '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', + # 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', + 'a8fcb63cf963dc743e8b0a96b966f18d8edde6a4e76365d6de56aa2c71ce6d3f', # PyTorch-1.8.1_fix-vsx-vector-functions.patch + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', + # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch + 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', +] + +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 = { + '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', + # 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 --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/__archive__/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..dc9f7ac60e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -0,0 +1,129 @@ +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': SOURCE_TAR_XZ, + '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_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', + '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', + 'PyTorch-1.8.1_fix_test_collect_shards.patch', +] +checksums = [ + '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 + '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_disable-tf32-in-distributed-tests.patch + '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 + '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', + '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 + '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 + 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', + # 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] + +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', SYSTEM), + ('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 = { + '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', + # 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 --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/__archive__/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb new file mode 100644 index 0000000000..4576b15fb6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -0,0 +1,107 @@ +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': SOURCE_TAR_XZ, + '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-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 = [ + '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 + '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 + '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-autograd-thread_shutdown-test.patch + '94957de0fd5bcbea37482cb6d0d12b4608dccf50a10da0836e151b414954ccc3', + # PyTorch-1.9.0_skip-lstm-serialization-test.patch + '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', +] + +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', + # 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', + ], + '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' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb new file mode 100644 index 0000000000..9911b4ab5f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -0,0 +1,141 @@ +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': SOURCE_TAR_XZ, + '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-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', + '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', +] +checksums = [ + '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 + '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 + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', + # 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', + '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', + # 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-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 +] + +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', SYSTEM), + ('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/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', + ], + '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' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..3f3661e997 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -0,0 +1,139 @@ +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': SOURCE_TAR_XZ, + '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-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', + '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', +] +checksums = [ + '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 + '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 + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', + # 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', + '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', + # 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-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 +] + +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', SYSTEM), + ('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', + # 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', + ], + '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' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/__archive__/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..59975bdece --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,48 @@ +# 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), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb new file mode 100644 index 0000000000..e503721fc1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb @@ -0,0 +1,21 @@ +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 +] + +options = {'modulename': 'pywt'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1430010d3f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/PyYAML/PyYAML-5.3.1-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d'] + +builddependencies = [('binutils', '2.35')] + +multi_deps = {'Python': ['3.8.6', '2.7.18']} + +dependencies = [('libyaml', '0.2.5')] + +options = {'modulename': 'yaml'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..14ede1b9c4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Pylint/Pylint-2.7.4-GCCcore-10.2.0.eb @@ -0,0 +1,56 @@ +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'), +] + +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_check_paths = { + 'files': ['bin/pylint'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb new file mode 100644 index 0000000000..37d49a3312 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb @@ -0,0 +1,35 @@ +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'], + }), +] + +sanity_check_commands = ['pyomo -h'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..7a71f6aeeb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,34 @@ +# 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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..3729fe4b2d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-GCC-10.2.0.eb @@ -0,0 +1,33 @@ +# 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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..ce7a2d484c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-iccifort-2020.4.304.eb @@ -0,0 +1,35 @@ +# 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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..41a5b4d0ad --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -0,0 +1,419 @@ +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 = { + 'source_urls': [PYPI_SOURCE], +} + +# order is important! +# 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', + 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], + }), + ('wheel', '0.35.1', { + 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], + }), + ('pip', '20.3.4', { + 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], + }), + ('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'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('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': 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['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), + ('futures', '3.3.0', { + 'modulename': False, + 'checksums': ['7e033af76a5e35f58e56da7a91e687706faf4e7bdfb2cbc3f2cca6b9bcda9794'], + }), + ('glob2', '0.6', { + 'checksums': ['f5b0a686ff21f820c4d3f0c4edd216704cea59d79d00fa337e244a2f2ff83ed6'], + }), + ('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', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], + }), + ('clikit', '0.6.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + }), + ('entrypoints', '0.3', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['589f874b313739ad35be6e0cd7efde2a4e9b6fea91edcc34e58ecbb8dbe56d19'], + }), + ('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', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6babbd33b17d5c9691896b0e68159215a9387ebfa938aa3ac42f4a4beeb2b831'], + }), + ('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', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.0', { + 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], + }), + ('CacheControl', '0.12.6', { + 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], + }), + ('ptyprocess', '0.6.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['d7cc528d76e76342423ca640335bd3633420dc1366f258cb31d05e865ef5ca1f'], + }), + ('lockfile', '0.12.2', { + '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'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-3.8.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9540cbf9f3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -0,0 +1,423 @@ +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.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21'] + +builddependencies = [ + ('UnZip', '6.0'), + ('git', '2.28.0', '-nodocs'), # required for pbr +] + +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'), + # 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] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} + +# order is important! +# package versions updated 13 October 2020 +exts_list = [ + ('setuptools', '50.3.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['39060a59d91cf5cf403fa3bacbb52df4205a8c3585e0b9ba4b30e0e19d4c4b18'], + }), + ('wheel', '0.35.1', { + 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], + }), + ('pip', '20.2.3', { + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), + ('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'], + }), + ('importlib_metadata', '2.0.0', { + 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], + }), + ('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'], + }), + ('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'], + 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('sphinx-bootstrap-theme', '0.7.1', { + 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('psutil', '5.7.2', { + 'checksums': ['90990af1c3c67195c44c9a889184f84f5b2320dce3ee3acbd054e3ba0b4a7beb'], + }), + ('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'], + }), + ('pylev', '1.3.0', { + 'checksums': ['063910098161199b81e453025653ec53556c1be7165a9b7c50be2f4d57eae1c3'], + }), + ('pastel', '0.2.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], + }), + ('clikit', '0.6.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + }), + ('SecretStorage', '3.1.2', { + 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], + }), + ('keyring', '21.4.0', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], + }), + ('keyrings.alt', '4.0.0', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], + }), + ('tomlkit', '0.7.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6babbd33b17d5c9691896b0e68159215a9387ebfa938aa3ac42f4a4beeb2b831'], + }), + ('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', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.0', { + 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], + }), + ('CacheControl', '0.12.6', { + 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], + }), + ('ptyprocess', '0.6.0', { + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.0.0', { + 'modulename': 'poetry.core', + 'checksums': ['6a664ff389b9f45382536f8fa1611a0cb4d2de7c5a5c885db1f0c600cd11fbd5'], + }), + ('poetry', '1.1.3', { + 'checksums': ['49eae89e2c44b0323214d0bbcefc21ebe3a19baa44db98eefabd4db9e82c7253'], + }), + ('crashtest', '0.3.1', { + 'checksums': ['42ca7b6ce88b6c7433e2ce47ea884e91ec93104a4b754998be498a8e6c3d37dd'], + }), + ('jeepney', '0.4.3', { + 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], + }), + ('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/__archive__/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9ceffd4c10 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '17.03' + +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 = 'p7zip-project' +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"' + +files_to_copy = [ + (['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', 'libexec/7z.%s' % SHLIB_EXT], + 'dirs': ['libexec/Codecs'], +} + +sanity_check_commands = [ + '7z --help', + '7z x || test $? -gt 0', + "! 7z i | grep -q \"Can't load\" ", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb new file mode 100644 index 0000000000..39abe70edb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pFUnit/pFUnit-4.2.0-gompi-2020b.eb @@ -0,0 +1,60 @@ +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'} + +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')] + +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, + ], +} + +sanity_check_commands = ["funitproc --help"] + +modextrapaths = { + 'PATH': ['PFUNIT-%(version_major_minor)s/bin'], + 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, + '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', + ], +} + +modextravars = {'PFUNIT': '%(installdir)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/packmol/packmol-20.2.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/packmol/packmol-20.2.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..3f8f47c180 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/pagmo/pagmo-2.17.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pagmo/pagmo-2.17.0-foss-2020b.eb new file mode 100644 index 0000000000..7458df08fd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/p/panaroo/panaroo-1.2.8-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/panaroo/panaroo-1.2.8-foss-2020b.eb new file mode 100644 index 0000000000..4d357e0549 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/panaroo/panaroo-1.2.8-foss-2020b.eb @@ -0,0 +1,57 @@ +# 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', '4.56.2'), + ('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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/pandapower/pandapower-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pandapower/pandapower-2.7.0-foss-2020b.eb new file mode 100644 index 0000000000..2e56be59de --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pandapower/pandapower-2.7.0-foss-2020b.eb @@ -0,0 +1,25 @@ +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' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/pangolin/pangolin-3.1.11-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pangolin/pangolin-3.1.11-foss-2020b.eb new file mode 100644 index 0000000000..d691f5d633 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pangolin/pangolin-3.1.11-foss-2020b.eb @@ -0,0 +1,78 @@ +# 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', '', SYSTEM), + ('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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb new file mode 100644 index 0000000000..062e88a43a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb @@ -0,0 +1,38 @@ +# 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'), +] + +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"] + +moduleclass = "bio" diff --git a/easybuild/easyconfigs/__archive__/p/parallel/parallel-20210322-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/parallel/parallel-20210322-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a5bb031caf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/parallel/parallel-20210322-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +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] +checksums = ['98f71b445a23a18bb4e9bce4f374b93e6a6d9decdf892be8d22459f224b85694'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Perl', '5.32.0')] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = ["parallel --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/parasail/parasail-2.4.3-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/parasail/parasail-2.4.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..9ad845641f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/p/patchelf/patchelf-0.12-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/patchelf/patchelf-0.12-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..af356f8b6c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/pauvre/pauvre-0.1924-intel-2020b.eb b/easybuild/easyconfigs/__archive__/p/pauvre/pauvre-0.1924-intel-2020b.eb new file mode 100644 index 0000000000..5cafc5395f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pauvre/pauvre-0.1924-intel-2020b.eb @@ -0,0 +1,35 @@ +# 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'} + +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'), +] + +# 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"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/phonopy/phonopy-2.12.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/phonopy/phonopy-2.12.0-foss-2020b.eb new file mode 100644 index 0000000000..74174de396 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/phonopy/phonopy-2.12.0-foss-2020b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '2.12.0' + +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'} + +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'), +] + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["phonopy --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/photontorch/photontorch-0.4.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/photontorch/photontorch-0.4.1-foss-2020b.eb new file mode 100644 index 0000000000..c0947588f3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/photontorch/photontorch-0.4.1-foss-2020b.eb @@ -0,0 +1,35 @@ +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'), +] + +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/__archive__/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..07a2db3b05 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb @@ -0,0 +1,35 @@ +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'), +] + +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/__archive__/p/pigz/pigz-2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pigz/pigz-2.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a660349126 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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$EBROOTZLIB/lib"' + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/pigz/pigz-2.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pigz/pigz-2.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c97ee4199c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pigz/pigz-2.6-GCCcore-10.2.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# +# 2.4.0: +# Jonas Demeulemeester +# The Francis Crick Institute +## +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.6' + +homepage = 'https://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://zlib.net/pigz/', + 'https://zlib.net/pigz/fossils/', +] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + '2eed7b0d7449d1d70903f2a62cd6005d262eb3a8c9e98687bc8cbb5809db2a7d', # pigz-2.6.tar.gz + '7e37175714d43c946373d07c522ec98a77c0f8572a9d448f759c41f6f060275d', # pigz-2.6_makefile.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = 'CC="$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/__archive__/p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..21519920c8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/pkg-config/pkg-config-0.29.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb b/easybuild/easyconfigs/__archive__/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb new file mode 100644 index 0000000000..fa0adac445 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb @@ -0,0 +1,22 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('pkg-config', '0.29.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/plotly-orca/plotly-orca-1.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/plotly-orca/plotly-orca-1.3.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5131a11ee7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bf91c7f773 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/plotly.py/plotly.py-4.14.3-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +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')] + +exts_list = [ + ('retrying', '1.3.3', { + 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], + }), + ('plotly', version, { + 'checksums': ['7d8aaeed392e82fb8e0e48899f2d3d957b12327f9d38cdd5802bc574a8a39d91'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..8b082eb66d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,28 @@ +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', versionsuffix), + ('matplotlib', '2.2.5', versionsuffix), +] + +sanity_check_commands = ['pmx --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.6-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.6-GCC-10.2.0.eb new file mode 100644 index 0000000000..949bd6168a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.6-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +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=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.6-gcccuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.6-gcccuda-2020b.eb new file mode 100644 index 0000000000..b6ff23250e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.6-gcccuda-2020b.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '1.6' + +homepage = 'https://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'gcccuda', 'version': '2020b'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b0a4c0c056371b6f0db726b88fbb76bbee94948fb2abd4dbc8d958f7c42f766c'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Clang', '11.0.1'), + ('hwloc', '2.2.0'), + ('libtool', '2.4.6'), + ('libxml2', '2.9.10'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# 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], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.6-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.6-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..257dcb0f4d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.6-iccifort-2020.4.304.eb @@ -0,0 +1,42 @@ +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 " +# 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], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/poppler/poppler-21.06.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/poppler/poppler-21.06.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..50d2925719 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/popt/popt-1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/popt/popt-1.16-GCC-10.2.0.eb new file mode 100644 index 0000000000..b455329798 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/popt/popt-1.16-GCC-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'popt' +version = '1.16' + +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://ftp.osuosl.org/pub/rpm/popt/releases/historical/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e728ed296fe9f069a0e005003c3d6b2dde3d9cad453422a10d6558616d304cc8'] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/prodigal/prodigal-2.6.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/prodigal/prodigal-2.6.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2f72278b36 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/p/prokka/prokka-1.14.5-gompi-2020b.eb new file mode 100644 index 0000000000..d5adf00b38 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -0,0 +1,50 @@ +# 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', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20210322'), + ('tbl2asn', '20220427', '-linux64', SYSTEM), +] + +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/__archive__/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8d86d99895 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/protobuf-python/protobuf-python-3.14.0-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +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'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('protobuf', version) +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/p/protobuf/protobuf-2.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/protobuf/protobuf-2.5.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..2bfabbaa61 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/protobuf/protobuf-3.14.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/protobuf/protobuf-3.14.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..83617c750d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..615cf62352 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +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')] + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['7ccfcdfea4fc4b0a02ca2c31de7fcd186beb9cff8207800e14ab66f79c773af6'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..748a3d36bd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/py-aiger/py-aiger-6.1.14-GCCcore-10.2.0.eb @@ -0,0 +1,74 @@ +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 +] + +# 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/__archive__/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cee4a5c5d5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyBigWig/pyBigWig-0.3.18-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +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'), +] + +options = {'modulename': name} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb new file mode 100644 index 0000000000..59e60d255a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pyFAI' +version = '0.20.0' + +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'} + +modextravars = { + 'PYFAI_OPENCL': '0', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..20969e97fe --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pyFAI' +version = '0.20.0' + +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'} + +modextravars = { + 'PYFAI_OPENCL': '0', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb new file mode 100644 index 0000000000..6b9656132e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb @@ -0,0 +1,21 @@ +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'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..df834c210e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb @@ -0,0 +1,21 @@ +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'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..b905ef059a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0-Python-2.7.18.eb @@ -0,0 +1,21 @@ +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), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..e5cfa19ed6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pybedtools/pybedtools-0.8.2-GCC-10.2.0.eb @@ -0,0 +1,20 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a184a36099458627e7ef52ea88218f7c00dc9c505b4256ece9ede58b1efa8771'] + +dependencies = [ + ('Python', '3.8.6'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.16.0.1'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..e4a7c9273c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pybedtools/pybedtools-0.8.2-iccifort-2020.4.304.eb @@ -0,0 +1,20 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a184a36099458627e7ef52ea88218f7c00dc9c505b4256ece9ede58b1efa8771'] + +dependencies = [ + ('Python', '3.8.6'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.16.0.1'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c3601acf52 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# 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' + +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'] +patches = ['pybind11-2.6.0_fix-test-extra-whitespace.patch'] +checksums = [ + '90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571', + # pybind11-2.6.0_fix-test-extra-whitespace.patch: + 'f0ff7416d14f9589b5d100ad021e18690cb08cb662df9d0ac21327d04bdb96fc', +] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f1415c207f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pydicom/pydicom-2.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..84abe7301d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pydot/pydot-1.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,21 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f8220244a9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyfaidx/pyfaidx-0.5.9.5-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +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')] + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb new file mode 100644 index 0000000000..493eae6062 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyfasta/pyfasta-0.5.2-foss-2020b.eb @@ -0,0 +1,25 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11') +] + +sanity_check_paths = { + 'files': ['bin/pyfasta'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = ['pyfasta extract --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/pygmo/pygmo-2.16.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pygmo/pygmo-2.16.1-foss-2020b.eb new file mode 100644 index 0000000000..57877c1793 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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], +} + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('dill', '0.3.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pygmo'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb new file mode 100644 index 0000000000..1be2410d55 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb @@ -0,0 +1,21 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb new file mode 100644 index 0000000000..7db5b198f8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pymatgen/pymatgen-2022.0.4-foss-2020b.eb @@ -0,0 +1,60 @@ +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'), +] + +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"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/p/pymca/pymca-5.6.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pymca/pymca-5.6.3-foss-2020b.eb new file mode 100644 index 0000000000..6a075fe950 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pymca/pymca-5.6.3-foss-2020b.eb @@ -0,0 +1,36 @@ +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'), +] + +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/__archive__/p/pymca/pymca-5.6.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/pymca/pymca-5.6.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..1a48c1777a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pymca/pymca-5.6.3-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +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'), +] + +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/__archive__/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f55e87bc23 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyproj/pyproj-3.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +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'), +] + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/__archive__/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..0c067c3cef --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb @@ -0,0 +1,40 @@ +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), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/__archive__/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb new file mode 100644 index 0000000000..e1ea6ae4f9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb @@ -0,0 +1,40 @@ +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), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..b2908699a7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyro-api/pyro-api-0.1.2-fosscuda-2020b.eb @@ -0,0 +1,27 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'pyro-api' +version = '0.1.2' + +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'] + +dependencies = [ + ('Python', '3.8.6'), +] + +options = {'modulename': 'pyroapi'} + +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/__archive__/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..5330fd6991 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyro-ppl/pyro-ppl-1.5.2-fosscuda-2020b.eb @@ -0,0 +1,31 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'pyro-ppl' +version = '1.5.2' + +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'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('pyro-api', '0.1.2'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'checksums': ['8a93af3a007ac507a8b50fd1165dbb355182d17df29d3b5bc498b02b479fdb27'], + 'modulename': 'pyro', + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb new file mode 100644 index 0000000000..159ddd871a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb @@ -0,0 +1,29 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['6d8b41934fdc700552d689f473860c64525a88600460344d0cac2095424750c6'] + +# acceptance of pysam>0.16 +preinstallopts = "sed -i -e 's/ (<0.16)//g' setup.py && " + +dependencies = [ + ('Python', '3.8.6'), + ('Pysam', '0.16.0.1'), + ('SciPy-bundle', '2020.11'), + ('PyTables', '3.6.1'), +] + +sanity_check_commands = [ + "pysamstats --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb new file mode 100644 index 0000000000..46b4726651 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pysheds/pysheds-0.2.7.1-foss-2020b.eb @@ -0,0 +1,31 @@ +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'), +] + +# 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'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e6e16e8ebf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('cURL', '7.72.0'), +] + +options = {'modulename': 'shapefile'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb new file mode 100644 index 0000000000..4193c40386 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pyspoa/pyspoa-0.0.8-GCC-10.2.0.eb @@ -0,0 +1,46 @@ +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'), +] + +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 && " + +options = {'modulename': 'spoa'} + +sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8d24623363 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +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'), +] + +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", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..e965d4a4ed --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pytest-xdist/pytest-xdist-2.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,59 @@ +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'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1bb218d676 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,59 @@ +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb new file mode 100644 index 0000000000..29ac9cd57f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb @@ -0,0 +1,20 @@ +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'), +] + +options = {'modulename': 'Levenshtein'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6c705174cf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +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'), +] + +options = {'modulename': 'docx'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb new file mode 100644 index 0000000000..8c9840297c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/python-igraph/python-igraph-0.9.0-foss-2020b.eb @@ -0,0 +1,49 @@ +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'), +] + +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'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..732eedd4b3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/python-igraph/python-igraph-0.9.0-fosscuda-2020b.eb @@ -0,0 +1,49 @@ +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'} + +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'), +] + +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'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6cd7de18a2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# 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 = ['43d885814f1ee19f5c3a7e9ada3d696fe75f19c0853728fe0ade564bc021a78f'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('ISA-L', '2.30.0'), +] + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' +installopts = '--no-binary isal' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb new file mode 100644 index 0000000000..d9e831998b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb @@ -0,0 +1,28 @@ +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'), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..9357b64bd7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.4-fosscuda-2020b.eb @@ -0,0 +1,28 @@ +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'), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a38c9f0d7e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -0,0 +1,82 @@ +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'), +] + +builddependencies = [('binutils', '2.35')] + +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'], + }), + ('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'], + }), + # to overwrite Python's requests requirement which requires older version of idna + ('requests', '2.28.1', { + 'checksums': ['7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('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' diff --git a/easybuild/easyconfigs/__archive__/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3f7b7fc300 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/p/python-xxhash/python-xxhash-2.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +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'), +] + +exts_list = [ + ('xxhash', version, { + 'preinstallopts': 'XXHASH_LINK_SO=1', + 'checksums': ['b7bead8cf6210eadf9cecf356e17af794f57c0939a3d420a00d87ea652f87b49'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb b/easybuild/easyconfigs/__archive__/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb new file mode 100644 index 0000000000..5d803a7d74 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb @@ -0,0 +1,22 @@ +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}] +checksums = ['1e5949b7d20434193d496c28070d8f2fb6406a7688a86080dfdac57fbe730624'] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['qdmod', 'qd']], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fdf7452a36 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb new file mode 100644 index 0000000000..58dc2a8e8b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '1.11'), + ('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' diff --git a/easybuild/easyconfigs/__archive__/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..a7093ce817 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +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} + +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'), + ('matplotlib', '2.2.5', versionsuffix), + ('Java', '11', '', SYSTEM), + ('Boost', '1.74.0'), +] + +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'], +} + +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", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/q/QUAST/QUAST-5.0.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/q/QUAST/QUAST-5.0.2-foss-2020b.eb new file mode 100644 index 0000000000..8122dd21f3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/q/QUAST/QUAST-5.0.2-foss-2020b.eb @@ -0,0 +1,54 @@ +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', '', SYSTEM), + ('Boost', '1.74.0'), +] + +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 -rf ./test_data.tar.gz ./test_data", + "%(namelower)s -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..363c6c51c8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/q/Qhull/Qhull-2020.2-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +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'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +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 = { + MODULE_LOAD_ENV_HEADERS: ['qhull/include'], +} + +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d9eed72478 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb @@ -0,0 +1,81 @@ +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/', + 'https://download.qt.io/new_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', + '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 + '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 + '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 = [ + ('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', '2.7.18'), + ('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', '2.0.24'), + ('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 + # ('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' diff --git a/easybuild/easyconfigs/__archive__/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d3095e4a6c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = "-DPORT=Qt -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' diff --git a/easybuild/easyconfigs/__archive__/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ebc1a1481a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/q/QtPy/QtPy-1.9.0-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2db72c44b55d0fe1407be8fba35c838ad0d6d3bb81f23007886dc1fc0f459c8d'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('PyQt5', '5.15.1') +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c9cbce1585 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/q/Qtconsole/Qtconsole-5.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['404994edfe33c201d6bd0c4bd501b00c16125071573c938533224992bea0b30f'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), + ('QtPy', '1.9.0'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..007548886b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 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'} + +source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads/'] +sources = ['qualimap_v%(version)s.zip'] +checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('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' diff --git a/easybuild/easyconfigs/__archive__/q/Quandl/Quandl-3.6.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/q/Quandl/Quandl-3.6.1-foss-2020b.eb new file mode 100644 index 0000000000..839b89e90d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/q/Quandl/Quandl-3.6.1-foss-2020b.eb @@ -0,0 +1,37 @@ +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'), +] + +exts_list = [ + ('inflection', '0.5.1', { + 'checksums': ['1a29730d366e996aaacffb2f1f1cb9593dc38e2ddd30c91250c6dde09ea9b417'], + }), + ('more-itertools', '8.8.0', { + 'checksums': ['83f0308e05477c68f56ea3a888172c78ed5d5b3c282addb67508e7ba6c8f813a'], + }), + ('pyOpenSSL', '19.1.0', { + 'modulename': 'OpenSSL', + 'checksums': ['9a24494b2602aaf402be5c9e30a0b82d4a5c67528fe8fb475e3f3bc00dd69507'], + }), + ('ndg-httpsclient', '0.5.1', { + 'modulename': 'ndg', + 'source_tmpl': 'ndg_httpsclient-%(version)s.tar.gz', + 'checksums': ['d72faed0376ab039736c2ba12e30695e2788c4aa569c9c3e3d72131de2592210'], + }), + (name, version, { + 'checksums': ['84414e5f8e870a9c8a9392e9dc639d50e839c5f5e07737a09bb57dd8b14b264b'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb new file mode 100644 index 0000000000..77c0d57fbf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 +maxparallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb b/easybuild/easyconfigs/__archive__/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb new file mode 100644 index 0000000000..6679d48bea --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 +maxparallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9ffe3f5f9d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/q/QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/q/QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0d2549e811 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/q/qrupdate/qrupdate-1.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3a7251eef1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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': [], +} + +maxparallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/__archive__/r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..79229f933d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), + ('rgdal', '1.5-23', versionsuffix), +] + +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="$LIBLAPACK"', + 'files_to_copy': [(['r-inla-*/extlibs/taucs-2.2--my-fix/lib/linux/libtaucs.a'], 'lib')], + }), + ('fmesher', version, { + 'checksums': default_component_specs['checksums'] + [ + '9ec131a8a470ea2614be77f917c0d66eacecbba4b511c90d6427059fe2c36b51', + ], + 'patches': ['R-INLA-%(version)s-skip-binaries.patch'], + 'buildopts': '-C r-inla-*/fmesher PREFIX=%(installdir)s CC="$CC" CXX="$CXX" FLAGS="$CXXFLAGS -std=c++11"', + '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'] + [ + '368bef641bbb55fe198529ee350e603936efebfca7b16f54a6c60573ecef2e9d', + ], + 'patches': ['R-INLA-%(version)s-foss-2020b-remove-hardcoding.patch'], + 'easyblock': 'RPackage', + 'start_dir': 'r-inla-Version_%s/rinla' % version, + }), + (name, version, { + 'prebuildopts': 'export CPATH=$EBROOTR/lib64/R/include/:$CPATH && ', + 'buildopts': local_inla_buildopts, + 'installopts': '-C r-inla-*/inlaprog PREFIX=%(installdir)s', + }), +] + +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] + +sanity_check_paths = { + '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 = ["Rscript -e 'library(INLA)'"] + ["%s -h" % x for x in local_bins] + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..7f84ef8fa4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb @@ -0,0 +1,1037 @@ +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 + ('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', '1.2.0', { + 'checksums': ['6c7fa4223149656077cd4ce5298f22e5dcc5feb43e533e1acda61514d2e17aa8'], + }), + ('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', { + 'checksums': ['af7c111d12acdbc2eadf49d65d6a17b07d0410bc6b9212d6281d3b478ae9a0a4'], + }), + ('AnnotationFilter', '1.14.0', { + 'checksums': ['490f083090c7f024dd011214a046a14eb86f1092337a03751e8965a11405f35a'], + }), + ('ProtGenerics', '1.22.0', { + 'checksums': ['3fbad9dc747e9bbad41f711e2934fff48bbc3f61fc18abc3761beaf9e0ed307a'], + }), + ('ensembldb', '2.14.0', { + 'checksums': ['fef2f18fc9c7931f8155315e9aae0e76c2f7d26d90f505d89eeae3cc5e4a3412'], + }), + ('biovizBase', '1.38.0', { + 'checksums': ['183a92dde383176cb1cee953fa075c11b57e02b1777667a5c0fd31d7d4a64e82'], + }), + ('OrganismDbi', '1.32.0', { + 'checksums': ['1c4b40f11464546458e28a6100d4e5c65294712fd33abe6263cf8306f4b774d6'], + }), + ('ggbio', '1.38.0', { + 'checksums': ['9c92f25dc9584703a49cb9457de7146e899df76c50e21555009be62f098d4b6d'], + }), + ('geneplotter', '1.68.0', { + 'checksums': ['1d67b3dd6e5520e46f47b53f0f19c9e9eefe2f6c9817e4db0b2fda6081c916b9'], + }), + ('DESeq2', '1.30.0', { + 'checksums': ['f762340677695ffbba86d80f4c9db41a92d9c82bc4a118cf0db7b2cc3d4b4e60'], + }), + ('ReportingTools', '2.30.0', { + 'checksums': ['6148a4621c7e26cd955593251beed790c222cf8cbbf6e0b073d213d261837a3e'], + }), + ('Glimma', '2.0.0', { + 'checksums': ['dbb9d8a0ca94bae8c77ae6ea5c24df62e78f99fa370d5e617647700ac606c33f'], + }), + ('affycoretools', '1.62.0', { + 'checksums': ['606740ad6cb3d4bf1fae0b56455fa974b6c9c3d242bd31fbe0929f473d7f4c49'], + }), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', { + 'checksums': ['063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9'], + }), + ('Homo.sapiens', '1.3.1', { + 'checksums': ['014809fc6ef6410be8dc1094c9cb083719f20d999065ae4bf388855be0913b94'], + }), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.3', { + 'checksums': ['5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a'], + }), + ('AgiMicroRna', '2.40.0', { + 'checksums': ['211f4d00f5bb537a7684a2b9a4a6f5e5d9fdd0e7b94b008d757f4af972538d67'], + }), + ('geneLenDataBase', '1.26.0', { + 'checksums': ['7fd2a9d9cbccf400278cfe19cbf9b9884a11314b4b020dae40885ed370cd940a'], + }), + ('goseq', '1.42.0', { + 'checksums': ['099415f596aa12b54f8bbb818e1fd3390ee4fb961908298885ea0f3a491ddaa1'], + }), + ('KEGGREST', '1.30.1', { + 'checksums': ['1adc48958746501ffa39742edf9c802e4556d192b555dc51f242d1e47a413f4d'], + }), + ('KEGGgraph', '1.50.0', { + 'checksums': ['5bf4f9b21f2c297abbba9b61c870ecc398dd0f9afd25b88648557b012c1c49c0'], + }), + ('KEGGprofile', '1.32.0', { + 'checksums': ['a647b5954516caab9ea3638d18ed5f645561252f0b126a8dfeaf53a341dc0091'], + }), + ('GEOquery', '2.58.0', { + 'checksums': ['245e062872a42b4fbf0b38e9c3509afee41edfe21faf8d4efa9313409a7df0cb'], + }), + ('RSpectra', '0.16-0', { + 'checksums': ['aaf1cfc9ffe3a4c6684247899924e1c18306971dfef4bae1dc596a2fb42a64a9'], + }), + ('rARPACK', '0.11-0', { + 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], + }), + ('mixOmics', '6.14.0', { + 'checksums': ['18ec071ca64cae2a38a9b4f819778dace06ba62302672be5075d63908b578360'], + }), + ('Rhdf5lib', '1.12.1', { + 'checksums': ['48c81620346c1c652d15098d1c90df749a28ca747ade82d2a1e276191fc1d691'], + }), + ('rhdf5filters', '1.2.0', { + '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'], + }), + ('HDF5Array', '1.18.1', { + 'checksums': ['ef4896a6d40f848944fb2be60a29531990d3a2db7388470662ca83c861536293'], + }), + ('sparseMatrixStats', '1.2.1', { + 'checksums': ['31269b01faa73656abf62da04a2457ad62c763c575e20d487d1e34fc93aff605'], + }), + ('DelayedMatrixStats', '1.12.3', { + 'checksums': ['f0d81f57406bee202beca5e344772d15375ed5a93e1babfa715b0fdfca9668c1'], + }), + ('minfi', '1.36.0', { + 'checksums': ['d161863b9a83491187951188092184f657227dbaa43e7e7483a450afcdd573f4'], + }), + ('FDb.InfiniumMethylation.hg19', '2.2.0', { + 'checksums': ['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'], + }), + ('BH', '1.75.0-0', { + 'checksums': ['ae4c10992607dd697663f60675a46a5770851da159330bb63c4a68890bdd6f5a'], + }), + ('cytolib', '2.2.1', { + 'checksums': ['f9c0295001cfcb1e52a4d9bace6ce8a19ea1a47f74e5e434542b41395eee1579'], + }), + ('flowCore', '2.2.0', { + 'checksums': ['28f771b8246928ff60ec55f9bcfab76784c3039d58b6cb3fa04d2b41f3643100'], + }), + ('mutoss', '0.1-12', { + 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], + }), + ('mathjaxr', '1.2-0', { + 'checksums': 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['d75132a60397a7f1202e90417a43109398dba125e47feaf395778a57032d081a'], + }), + ('flowViz', '1.54.0', { + 'checksums': ['f37c30c6864884f2937c33f1dc2246aa5a3826b2fe99ba3b4169c3a384cdd2e8'], + }), + ('ncdfFlow', '2.36.0', { + 'checksums': ['4cf1c8d49b038b9ceea3fb959690cae03035beec4d9d7aec99ec6ec1e260d8ce'], + }), + ('aws.signature', '0.6.0', { + 'checksums': ['f7fe4f686979be21e5a8ba7ae11f0fade4f5aaf4e98063b5349ee0962dbb9496'], + }), + ('aws.s3', '0.3.21', { + 'checksums': ['bd21054ab63555d294e7465dcb6c86f107db52ba841aeac5bdf4d00af0674c8c'], + }), + ('flowWorkspace', '4.2.0', { + 'checksums': ['4f15199e09ee8afe8660fbee3653435d45c017caa55de8d5c0b7052cc5805ba7'], + }), + ('ash', '1.0-15', { + 'checksums': ['8b0a7bc39dd0ce2172f09edc5b5e029347d041a4d508bbff3f3fd6f69450c2ab'], + }), + ('hdrcde', '3.4', { + 'checksums': ['4341c6a021da46dcae3b1ef6d580e84dcf625c2b2139f537d0c26ec90899149b'], + }), + ('rainbow', '3.6', { + 'checksums': ['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', { + 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'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': 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/dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/r/R-keras/R-keras-2.4.0-fosscuda-2020b-R-4.0.4.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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': 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'09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d'}, + {'R-4.x_fix-CVE-2024-27322.patch': 'd8560e15c3c5716f99e852541901014d406f2a73136b0b74f11ba529f7a7b00d'}, +] + +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', '', SYSTEM), + ('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', '1.1.1h'), +] + +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 +configopts += " --with-recommended-packages=no" + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # 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['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'], + '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', '0.6.0', { + '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'], + }), + ('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'], + }), + ('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', + ], + }), + ('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'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/r/R/R-4.0.3-fosscuda-2020b.eb new file mode 100644 index 0000000000..9448b4aad8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/R/R-4.0.3-fosscuda-2020b.eb @@ -0,0 +1,2932 @@ +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] +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'), + ('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', '', SYSTEM), + ('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" + +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 = [ + # 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', { + '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': 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'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', '1.1', { + 'checksums': ['f0af03634a05a8be3f7b5af94d40bbe59bb32f9a1a1cbe77ee74576e1edc1097'], + }), + ('extRemes', '2.0-12', { + 'checksums': ['0206ef85d5f6db33f17995e3945de538f390edfb89b730b09e722418e4fe8d72'], + }), + ('tkrplot', '0.0-24', { + 'checksums': ['2873630a37d7ae1e09a5803d9a89ca0494edd83526c7b1860d9246543722f311'], + }), + ('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', '1.11.7', { + 'checksums': ['6a6d9c2366e85a4c6af39b798f3798d20a42615ddfcebcedf6cf56087cdfd2b8'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-18.1', { + 'checksums': ['2fa5f78a7603cbae94a5e38e791938596a053d48c609a7c120a19cbb7d93c66f'], + }), + ('penalized', '0.9-51', { + 'checksums': ['eaa80dca99981fb9eb576261f30046cfe492d014cc2bf286c447b03a92e299fd'], + }), + ('clusterRepro', '0.9', { + 'checksums': ['940d84529ff429b315cf4ad25700f93e1156ccacee7b6c38e4bdfbe2d4c6f868'], + }), + ('randomForestSRC', '2.9.3', { + 'checksums': ['bc47bef9e5afade8fdf56e08ae0ad320e424dfa5b11a32cd2d166c9988dc2e16'], + }), + ('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'], + }), + ('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': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], + }), + ('dynamicTreeCut', '1.63-1', { + 'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'], + }), + ('beeswarm', '0.2.3', { + 'checksums': ['0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843'], + }), + ('vipor', '0.4.5', { + 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], + }), + ('ggbeeswarm', '0.6.0', { + 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], + }), + ('shinydashboard', '0.7.1', { + 'checksums': ['51a49945c6b8a684111a2ba4b2a5964e3a50610286ce0378e37ae02316620a4e'], + }), + ('rrcov', '1.5-5', { + 'checksums': ['1f7f07558e347e7d1f1adff68631764670bc672777a7d990901c4fa94cc0e629'], + }), + ('WriteXLS', '6.0.0', { + 'checksums': ['19dd430ed735095d7e08a15dfe1df269918b0a102737f15b4e3b03aaec4ab3d0'], + }), + ('bst', '0.3-22', { + 'checksums': ['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': ['3789461bc474e146b077ad26566b1fa05be32fc7e57ab1fb5e78bdabcc797858'], + }), + ('RInside', '0.2.16', { + 'checksums': ['7ae4ade128ea05f37068d59e610822ff0b277f9d39d8900f7eb31759ad5a2a0e'], + }), + ('limSolve', '1.5.6', { + 'checksums': ['b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0'], + }), + ('dbplyr', '2.0.0', { + 'checksums': ['ecd71936ecfefbdda0fad24e52653ac9c0913e01126e467c92c8ba9de37b4069'], + }), + ('modelr', '0.1.8', { + 'checksums': ['825ba77d95d60cfb94920bec910872ca2ffe7790a44148b2992be2759cb361c4'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('reprex', '0.3.0', { + 'checksums': ['203c2ae6343f6ff887e7a5a3f5d20bae465f6e8d9745c982479f5385f4effb6c'], + }), + ('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', '0.13.1', { + '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': ['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'], + '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', '0.6.0', { + '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'], + }), + ('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'], + }), + ('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', + ], + }), + ('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'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), + # Specific packages for GPUs + ('OpenCL', '0.2-1', { + 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], + }), + ('RViennaCL', '1.7.1.8', { + 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/R/R-4.0.4-foss-2020b.eb new file mode 100644 index 0000000000..1edbe3efd3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/R/R-4.0.4-foss-2020b.eb @@ -0,0 +1,2963 @@ +# +# 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] +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'), + ('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', '', SYSTEM), + ('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" + +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 = [ + # 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', { + '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', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '5.4.7', { + 'checksums': ['45f5a666caee5bebd3160922b8655295a25e37f624741f6574365e4ac5a14c23'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('segmented', '1.3-3', { + 'checksums': ['1e1cc37ca6ac1bfa10daa1f057a1f97a7e54f6d398308efcc7f8e0062e350398'], + }), + ('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', '7.3-53.1', { + 'checksums': ['e45b1eb97ee32db9a3a211ce42b972094827d93ef2f48bda653c121f08314465'], + }), + ('pixmap', '0.4-12', { + 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], + }), + ('lattice', '0.20-41', { + 'checksums': ['54ca557f0cb33df60eb10b883c2ed2847e061ddd57ed9b5dd7695149609d57b5'], + }), + ('sp', '1.4-5', { + 'checksums': ['6beeb216d540475cdead5f2c72d6c7ee400fe2423c1882d72cf57f6df58f09da'], + }), + ('pkgconfig', '2.0.3', { + 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], + }), + ('rlang', '0.4.10', { + 'checksums': ['07530270c4c199f2b7efc5d57a476d99babd9d0c3388a02bb7d57fe312da3576'], + }), + ('ellipsis', '0.3.1', { + 'checksums': ['4f8a15158dfc27cdc0f7554c7a61e92b02e4d70bfc3d968f01a99da2189b75db'], + }), + ('digest', '0.6.27', { + 'checksums': ['f485f75122907da24c41d4a62c91a232f0c371befd2f77e973342a1bef00253f'], + }), + ('glue', '1.4.2', { + 'checksums': ['9f7354132a26e9a876428fa87629b9aaddcd558f9932328e6ac065b95b8ef7ad'], + }), + ('vctrs', '0.3.6', { + 'checksums': ['df7d368c9f2d2ad14872ba2a09821ec4f5a8ad77c81a0b05e1f440e5ffebad25'], + }), + ('lifecycle', '1.0.0', { + 'checksums': ['03334ab213f2ad49a49e184e73f2051e04d35d43f562db903e68243cd2ec0f8e'], + }), + ('hms', '1.0.0', { + 'checksums': ['9704e903d724f0911d46e5ad18b469a7ed419c5b1f388bd064fd663cefa6c962'], + }), + ('prettyunits', '1.1.1', { + 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], + }), 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['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'], + }), + ('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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+ ('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', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], + }), + ('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': 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('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': 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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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['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'], + }), + ('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'], + }), + ('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', + ], + }), + ('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'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': 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('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/__archive__/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/r/R/R-4.0.4-fosscuda-2020b.eb new file mode 100644 index 0000000000..4d16e73c85 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/R/R-4.0.4-fosscuda-2020b.eb @@ -0,0 +1,2975 @@ +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] +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'), + ('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', '', SYSTEM), + ('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" + +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 = [ + # 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', { + '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': 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('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', '0.2-1', { + 'checksums': 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['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'], + }), + ('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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+ ('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', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], + }), + ('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'], + }), + ('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', { + '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': 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('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': 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['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'], + }), + ('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'], + }), + ('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', + ], + }), + ('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'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), + ('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'], + }), + ('RViennaCL', '1.7.1.8', { + 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/R/R-4.0.5-foss-2020b.eb new file mode 100644 index 0000000000..53fc19391a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/R/R-4.0.5-foss-2020b.eb @@ -0,0 +1,2972 @@ +## +# 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] +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'), + ('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', '', SYSTEM), + ('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" + +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 = [ + # 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', { + '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', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '5.4.7', { + 'checksums': ['45f5a666caee5bebd3160922b8655295a25e37f624741f6574365e4ac5a14c23'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('segmented', '1.3-3', { + 'checksums': ['1e1cc37ca6ac1bfa10daa1f057a1f97a7e54f6d398308efcc7f8e0062e350398'], + }), + ('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', '7.3-53.1', { + 'checksums': ['e45b1eb97ee32db9a3a211ce42b972094827d93ef2f48bda653c121f08314465'], + }), + ('pixmap', '0.4-12', { + 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], + }), + ('lattice', '0.20-41', { + 'checksums': ['54ca557f0cb33df60eb10b883c2ed2847e061ddd57ed9b5dd7695149609d57b5'], + }), + ('sp', '1.4-5', { + 'checksums': ['6beeb216d540475cdead5f2c72d6c7ee400fe2423c1882d72cf57f6df58f09da'], + }), + ('pkgconfig', '2.0.3', { + 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], + }), + ('rlang', '0.4.10', { + 'checksums': ['07530270c4c199f2b7efc5d57a476d99babd9d0c3388a02bb7d57fe312da3576'], + }), + ('ellipsis', '0.3.1', { + 'checksums': ['4f8a15158dfc27cdc0f7554c7a61e92b02e4d70bfc3d968f01a99da2189b75db'], + }), + ('digest', '0.6.27', { + 'checksums': ['f485f75122907da24c41d4a62c91a232f0c371befd2f77e973342a1bef00253f'], + }), + ('glue', '1.4.2', { + 'checksums': ['9f7354132a26e9a876428fa87629b9aaddcd558f9932328e6ac065b95b8ef7ad'], + }), + ('vctrs', '0.3.7', { + 'checksums': ['5ad9b3bcc77ca5153f21d406ea1503b38bd59e7f079c2e6c73bd0cd3c7ec1e0e'], + }), + ('lifecycle', '1.0.0', { + 'checksums': ['03334ab213f2ad49a49e184e73f2051e04d35d43f562db903e68243cd2ec0f8e'], + }), + ('hms', '1.0.0', { + 'checksums': ['9704e903d724f0911d46e5ad18b469a7ed419c5b1f388bd064fd663cefa6c962'], + }), + ('prettyunits', '1.1.1', { + 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], + }), + ('R6', '2.5.0', { + 'checksums': ['aec1af9626ec532cb883b544bf9eff4cb2d89c343c7ce0fa31761ec5a7882e02'], + }), + ('crayon', '1.4.1', { + 'checksums': ['08b6e42e748d096960b2f32b7ffe690c25742e29fe14c19d1834cd6ff43029c7'], + }), + ('progress', '1.2.2', { + 'checksums': 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['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'], + }), + ('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': ['525e61e71206feab28885d90a0311a09a2ebc66a730016d984e770eeaf7f4fcb'], + }), + ('vipor', '0.4.5', { + 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], + }), + ('ggbeeswarm', '0.6.0', { + 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], + }), + ('shinydashboard', '0.7.1', { + 'checksums': ['51a49945c6b8a684111a2ba4b2a5964e3a50610286ce0378e37ae02316620a4e'], + }), + ('rrcov', '1.5-5', { + 'checksums': ['1f7f07558e347e7d1f1adff68631764670bc672777a7d990901c4fa94cc0e629'], + }), + ('WriteXLS', '6.3.0', { + 'checksums': ['0b1d987abe4b08f6a32003b77d1cfc2eefdc5a478382e77ca0da98bccf6e526b'], + }), + ('bst', '0.3-23', { + 'checksums': ['70957f1db8800bf0d628a9e6f72b7273329786dd119427790b326844591aa0f3'], + }), + ('pamr', '1.56.1', { + 'checksums': ['d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779'], + }), + ('WeightSVM', '1.7-5', { + 'checksums': ['dd895fe3a400897cea18d9de3e406e040efca9f84495739757b52570c98f820a'], + }), + ('mpath', '0.4-2.19', { + 'checksums': ['fa0d92984910b8f556677850e3d899bc675724f0e2a3a73629d2700040335afe'], + }), + ('timereg', '1.9.8', { + 'checksums': ['00b200764743e7074d1697ddbe8534ca7599e26ef20c34020fa1f6a29fa6bb18'], + }), + ('peperr', '1.3', { + 'checksums': ['64d30b0ec09bf9b8f7b6edce67dd0f9e0e3dbe665fec8f5411f74142e53e9f5d'], + }), + ('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', '2.1.1', { + 'checksums': ['aba4cf47b85ab240fd3ec4cd8d512f6e1958201e151577c1a2ebc3d6ebc5bc08'], + }), + ('modelr', '0.1.8', { + 'checksums': ['825ba77d95d60cfb94920bec910872ca2ffe7790a44148b2992be2759cb361c4'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('reprex', '2.0.0', { + 'checksums': ['905377fcc644a485e97caffda3b077f6b3ad8fda09c0bbf378c422e13feb96d1'], + }), + ('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', '1.24.0', { + 'checksums': ['e6e69f4bf8c717b78fbf7c5507887fbd7efa7aada7b19a680eaf7eef59bf04f4'], + }), + ('future', '1.21.0', { + 'checksums': ['909e6602068eba543a6d2e464b911123cc29efdb600a7000eff0e5624ff0d12d'], + }), + ('gdistance', '1.3-6', { + 'checksums': ['2ccabeb2f8cf44630c0bd2da79815fe357b812737ebece1bed8f90b27c126a24'], + }), + ('vioplot', '0.3.6', { + 'checksums': ['d758c24da9b305dd4855266d360a4ceccf54ea793a236c2b7a0e36fe52cd7597'], + }), + ('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', '3.7.34', { + 'checksums': ['109b1b12590c30020c0b3fe2ef9f2adf11509e7a81be728d70ce76075d18ef62'], + }), + ('qgam', '1.3.2', { + 'checksums': ['273a40d0bfdc340c049bcb85aea83acd887868d8a69c0062b8399e0b24137a52'], + }), + ('DHARMa', '0.4.0', { + 'checksums': ['d38fe3673410abf8ebc0b68309b9098b519d0f93513a95cdd310bb8a6ee683b9'], + }), + ('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', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], + }), + ('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', + ], + # 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', { + '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', + ], + }), + ('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'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), + ('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/__archive__/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/r/R/R-4.0.5-fosscuda-2020b.eb new file mode 100644 index 0000000000..242f1a7d4b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/R/R-4.0.5-fosscuda-2020b.eb @@ -0,0 +1,2990 @@ +## +# 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] +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'), + ('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', '', SYSTEM), + ('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" + +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 = [ + # 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', { + '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'], + }), + 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['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'], + }), + ('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': ['525e61e71206feab28885d90a0311a09a2ebc66a730016d984e770eeaf7f4fcb'], + }), + ('vipor', '0.4.5', { + 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], + }), + ('ggbeeswarm', '0.6.0', { + 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], + }), + ('shinydashboard', '0.7.1', { + 'checksums': ['51a49945c6b8a684111a2ba4b2a5964e3a50610286ce0378e37ae02316620a4e'], + }), + ('rrcov', '1.5-5', { + 'checksums': ['1f7f07558e347e7d1f1adff68631764670bc672777a7d990901c4fa94cc0e629'], + }), + ('WriteXLS', '6.3.0', { + 'checksums': ['0b1d987abe4b08f6a32003b77d1cfc2eefdc5a478382e77ca0da98bccf6e526b'], + }), + ('bst', '0.3-23', { + 'checksums': ['70957f1db8800bf0d628a9e6f72b7273329786dd119427790b326844591aa0f3'], + }), + ('pamr', '1.56.1', { + 'checksums': ['d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779'], + }), + ('WeightSVM', '1.7-5', { + 'checksums': ['dd895fe3a400897cea18d9de3e406e040efca9f84495739757b52570c98f820a'], + }), + ('mpath', '0.4-2.19', { + 'checksums': ['fa0d92984910b8f556677850e3d899bc675724f0e2a3a73629d2700040335afe'], + }), + ('timereg', '1.9.8', { + 'checksums': ['00b200764743e7074d1697ddbe8534ca7599e26ef20c34020fa1f6a29fa6bb18'], + }), + ('peperr', '1.3', { + 'checksums': ['64d30b0ec09bf9b8f7b6edce67dd0f9e0e3dbe665fec8f5411f74142e53e9f5d'], + }), + ('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', '2.1.1', { + 'checksums': ['aba4cf47b85ab240fd3ec4cd8d512f6e1958201e151577c1a2ebc3d6ebc5bc08'], + }), + ('modelr', '0.1.8', { + 'checksums': ['825ba77d95d60cfb94920bec910872ca2ffe7790a44148b2992be2759cb361c4'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('reprex', '2.0.0', { + 'checksums': ['905377fcc644a485e97caffda3b077f6b3ad8fda09c0bbf378c422e13feb96d1'], + }), + ('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', '1.24.0', { + 'checksums': ['e6e69f4bf8c717b78fbf7c5507887fbd7efa7aada7b19a680eaf7eef59bf04f4'], + }), + ('future', '1.21.0', { + 'checksums': ['909e6602068eba543a6d2e464b911123cc29efdb600a7000eff0e5624ff0d12d'], + }), + ('gdistance', '1.3-6', { + 'checksums': ['2ccabeb2f8cf44630c0bd2da79815fe357b812737ebece1bed8f90b27c126a24'], + }), + ('vioplot', '0.3.6', { + 'checksums': ['d758c24da9b305dd4855266d360a4ceccf54ea793a236c2b7a0e36fe52cd7597'], + }), + ('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', '3.7.34', { + 'checksums': ['109b1b12590c30020c0b3fe2ef9f2adf11509e7a81be728d70ce76075d18ef62'], + }), + ('qgam', '1.3.2', { + 'checksums': ['273a40d0bfdc340c049bcb85aea83acd887868d8a69c0062b8399e0b24137a52'], + }), + ('DHARMa', '0.4.0', { + 'checksums': ['d38fe3673410abf8ebc0b68309b9098b519d0f93513a95cdd310bb8a6ee683b9'], + }), + ('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', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], + }), + ('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'], + 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}), + ('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', { + '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', + ], + }), + ('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'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.0', { + 'checksums': ['7b76de33010649bf1def4ccbd4f037148e3281408c328a2a74e1d49bc8d620ae'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.3', { + 'checksums': ['e222b3f87cf17ec9ac171063bd7789fb237d5abacd4bb7ae5315bc12cdc59737'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), + ('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'], + }), + ('RViennaCL', '1.7.1.8', { + 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb new file mode 100644 index 0000000000..8cdf1ce224 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RASPA2/RASPA2-2.0.41-foss-2020b.eb @@ -0,0 +1,34 @@ +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'] + +builddependencies = [ + ('Autotools', '20200321') +] + +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': [] +} + +sanity_check_commands = ['simulate -h'] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb new file mode 100644 index 0000000000..9510c0e8ee --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb @@ -0,0 +1,83 @@ +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 + '64f58ed77d074818505cf032c3509482c2e00ba0636990131e05f8a148e1a3a9', # pll-modules-1.0.2.tar.gz + '0d9d93fb5057048ed966a30bf8e1de84def2fd25decc45e01094722c4dd92d48', # 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 ' + +# 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' diff --git a/easybuild/easyconfigs/__archive__/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..2f0f3a144e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb @@ -0,0 +1,43 @@ +# 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 = [None] + +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' diff --git a/easybuild/easyconfigs/__archive__/r/RAxML/RAxML-8.2.12-GCC-10.2.0-pthreads-avx2.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/r/RAxML/RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb b/easybuild/easyconfigs/__archive__/r/RAxML/RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb new file mode 100644 index 0000000000..a853e77a97 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..83fa2b808e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RDFlib/RDFlib-5.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +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_list = [ + ('isodate', '0.6.0', { + 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], + }), + ('rdflib', version, { + 'checksums': ['78149dd49d385efec3b3adfbd61c87afaf1281c30d3fcaf1b323b34f603fb155'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/r/RE2/RE2-2021-06-01-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/RE2/RE2-2021-06-01-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c1e9c7de09 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/r/RECON/RECON-1.08-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/RECON/RECON-1.08-GCC-10.2.0.eb new file mode 100644 index 0000000000..cc485eefd2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/r/RMBlast/RMBlast-2.11.0-gompi-2020b.eb new file mode 100644 index 0000000000..857bf922ee --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = '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.""" + +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 = [('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 +] + +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/__archive__/r/ROOT/ROOT-6.22.08-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/ROOT/ROOT-6.22.08-foss-2020b.eb new file mode 100644 index 0000000000..ab70796cf4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/ROOT/ROOT-6.22.08-foss-2020b.eb @@ -0,0 +1,53 @@ +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' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dfa9bddcee --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/r/RagTag/RagTag-2.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/RagTag/RagTag-2.0.1-foss-2020b.eb new file mode 100644 index 0000000000..a73312d431 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RagTag/RagTag-2.0.1-foss-2020b.eb @@ -0,0 +1,48 @@ +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', '2.18'), + ('unimap', '0.1'), +] + +sanity_check_paths = { + 'files': ['bin/ragtag.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ragtag.py updategff --help', + # Ragtag exec()s these commands + 'nucmer --help', + 'minimap2 --help', + 'unimap --help', +] + +options = {'modulename': 'ragtag_utilities'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/Ragout/Ragout-2.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/Ragout/Ragout-2.3-foss-2020b.eb new file mode 100644 index 0000000000..bc288c57d2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/Ragout/Ragout-2.3-foss-2020b.eb @@ -0,0 +1,29 @@ +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'), +] + +sanity_check_commands = ['ragout --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c59421ba5d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +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'), +] + +# 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'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/r/Ratatosk/Ratatosk-0.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/Ratatosk/Ratatosk-0.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..bb1a332b58 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/r/Raysect/Raysect-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/Raysect/Raysect-0.7.1-foss-2020b.eb new file mode 100644 index 0000000000..310bcb4f96 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/Raysect/Raysect-0.7.1-foss-2020b.eb @@ -0,0 +1,21 @@ +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'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/r/Raysect/Raysect-0.7.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/r/Raysect/Raysect-0.7.1-intel-2020b.eb new file mode 100644 index 0000000000..92c63adbd4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/Raysect/Raysect-0.7.1-intel-2020b.eb @@ -0,0 +1,21 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c91f7dc406fd64dfaa4096b259c31250ac50881a301a46b2a1d607a2746f968'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/__archive__/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..0dda15cefb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'RcppGSL' +version = '0.3.8' +versionsuffix = '-R-%(rver)s' + +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++.""" + +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 = ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'] + +dependencies = [ + ('R', '4.0.4'), + ('GSL', '2.6'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['RcppGSL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/r/RegTools/RegTools-0.4.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/RegTools/RegTools-0.4.2-foss-2020b.eb new file mode 100644 index 0000000000..3e59121909 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/r/RegTools/RegTools-0.5.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/RegTools/RegTools-0.5.2-foss-2020b.eb new file mode 100644 index 0000000000..9c668e77d1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RegTools/RegTools-0.5.2-foss-2020b.eb @@ -0,0 +1,38 @@ +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'), + ('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' diff --git a/easybuild/easyconfigs/__archive__/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..22e5374dd0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb @@ -0,0 +1,81 @@ +# 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'), + # 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_script_dirs = ['DetectSelection', 'EstimatePopulationSize', 'PrepareInputFiles', 'RelateParallel', + 'SampleBranchLengths', 'TreeView'] +# un/comment as appropriate: +# 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']] +local_libs = ['lib/libtskitStatic.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 = { + 'files': local_bins + local_libs, + 'dirs': ['bin', 'lib', 'example'] + ['scripts/%s' % x for x in local_script_dirs], +} + +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_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' diff --git a/easybuild/easyconfigs/__archive__/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb new file mode 100644 index 0000000000..f342fbdcfe --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.2-p1' + +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 = ['https://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' + +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'] + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb new file mode 100644 index 0000000000..97c902e910 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), + ('TWL-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' diff --git a/easybuild/easyconfigs/__archive__/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb new file mode 100644 index 0000000000..1b471ca34d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RepeatScout/RepeatScout-1.0.6-GCC-10.2.0.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'RepeatScout' +version = '1.0.6' + +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 = ['https://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' diff --git a/easybuild/easyconfigs/__archive__/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..cbcc94ca3e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/RevBayes/RevBayes-1.1.1-GCC-10.2.0.eb @@ -0,0 +1,39 @@ +# 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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/r/Rmath/Rmath-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/Rmath/Rmath-4.0.4-foss-2020b.eb new file mode 100644 index 0000000000..5f67afb26f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/Rmath/Rmath-4.0.4-foss-2020b.eb @@ -0,0 +1,48 @@ +# 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'] +checksums = ['523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e'] + +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-pcre2" + +# 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' diff --git a/easybuild/easyconfigs/__archive__/r/Ruby/Ruby-2.7.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/Ruby/Ruby-2.7.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c82b949e90 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..7eab5f3ec8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -0,0 +1,58 @@ +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'] +patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] +checksums = [ + '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz + 'e3db7005585eb807ecb69929818740f00417cac247b1065a9d43a7f16cf05e0b', # Rust-1.52.1_sysroot-fix-interpreter.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Python', '3.8.6'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +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 " + +# 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 && " +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' diff --git a/easybuild/easyconfigs/__archive__/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb new file mode 100644 index 0000000000..b482c0cbb4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb @@ -0,0 +1,62 @@ +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'), + ('SciPy-bundle', '2020.11'), + ('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', '../rMATS_C', '../rMATS_R', '../rMATS_P'], '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', + 'options': {'modulename': 'rmatspipeline'}, + }), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/r/rampart/rampart-1.2.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/rampart/rampart-1.2.0-foss-2020b.eb new file mode 100644 index 0000000000..7f9b0f03b6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/rampart/rampart-1.2.0-foss-2020b.eb @@ -0,0 +1,64 @@ +# 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', '2.18'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/r/rasterio/rasterio-1.2.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/r/rasterio/rasterio-1.2.3-foss-2020b.eb new file mode 100644 index 0000000000..b2b28b73b4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/rasterio/rasterio-1.2.3-foss-2020b.eb @@ -0,0 +1,60 @@ +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'), +] + +exts_list = [ + ('affine', '2.3.0', { + 'checksums': ['2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102'], + }), + ('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-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", +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..dba73c221f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb b/easybuild/easyconfigs/__archive__/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb new file mode 100644 index 0000000000..a19833b9b3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/r/request/request-2.88.1-fosscuda-2020b-nodejs-12.19.0.eb @@ -0,0 +1,31 @@ +# Author: Denis Krišťák (INUITS) + +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/__archive__/r/rgdal/rgdal-1.5-23-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..415dee78ed --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/__archive__/r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..7694a11ea4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb b/easybuild/easyconfigs/__archive__/r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb new file mode 100644 index 0000000000..9de5eae895 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..42d5cdf10f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.4.eb b/easybuild/easyconfigs/__archive__/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.4.eb new file mode 100644 index 0000000000..eafcc9b44f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.5.eb b/easybuild/easyconfigs/__archive__/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.5.eb new file mode 100644 index 0000000000..bb7c0dda50 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.11-GCC-10.2.0.eb new file mode 100644 index 0000000000..735d3fa7c1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.11-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..39a2d0ca01 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.12-GCC-10.2.0.eb new file mode 100644 index 0000000000..5d5ff21de9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb new file mode 100644 index 0000000000..ce355224a7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb @@ -0,0 +1,25 @@ +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://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'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb b/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb new file mode 100644 index 0000000000..01d6e5e9fa --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb @@ -0,0 +1,24 @@ +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://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'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..220e5de607 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +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] +checksums = [ + '722ed104b5c624ecdc89bd4e02b094d2b14d99d47b5d0501961e47f579a2007c', # scons-4.0.1.tar.gz +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/sconsign'], + 'dirs': [], +} + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5ae762f6bf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SCons/SCons-4.1.0.post1-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +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')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/sconsign'], + 'dirs': [], +} + +sanity_check_commands = ["scons --help"] + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/s/SDL2/SDL2-2.0.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SDL2/SDL2-2.0.14-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bd457ee7f5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SEPP/SEPP-4.4.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SEPP/SEPP-4.4.0-foss-2020b.eb new file mode 100644 index 0000000000..8566bc73f6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SEPP/SEPP-4.4.0-foss-2020b.eb @@ -0,0 +1,38 @@ +# 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'] + +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' diff --git a/easybuild/easyconfigs/__archive__/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb new file mode 100644 index 0000000000..738044390d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020b.eb @@ -0,0 +1,45 @@ +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': '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 + 'c4a5a5d280463a7e39435239284702e0d13feb2eb10f902434874176c884516e', # 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 ' +buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS" ' + +files_to_copy = [(['bin/shapeit4.2'], 'bin'), 'maps'] + +sanity_check_paths = { + 'files': ["bin/shapeit4.2"], + 'dirs': ['maps'] +} + +sanity_check_commands = ['shapeit4.2 --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb new file mode 100644 index 0000000000..c3694317b3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = "MakeCp" + +name = 'SHAPEIT4' +version = '4.2.2' + +homepage = 'https://odelaneau.github.io/shapeit4/' +description = """ +SHAPEIT4 is a fast and accurate method for estimation of haplotypes +(aka phasing) for SNP array and high coverage sequencing data. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True, 'cstd': 'c++11'} + +github_account = 'odelaneau' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] +checksums = [ + '9f109e307b5cc22ab68e7bf77de2429a9bbb2212d66303386e6a3dd81a5bc556', # v4.2.2.tar.gz + '92ed45545bfcde7b1fbe079e6321ccae00865c8f0f66a924e872967d762df885', # SHAPEIT4_4.2.2_use_EB_settings.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('Boost', '1.74.0'), + ('HTSlib', '1.11'), +] + +buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts ' +buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options ' +buildopts += 'CXX="$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' diff --git a/easybuild/easyconfigs/__archive__/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb new file mode 100644 index 0000000000..e1bb43fce3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SIMPLE/SIMPLE-3.0.0-foss-2020b.eb @@ -0,0 +1,79 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/03 +easyblock = 'CMakeMake' + +name = 'SIMPLE' +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) +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'), ] + +# 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 &&' + +local_configopts = " -DFFTW_DIR=$EBROOTFFTW " +local_configopts += "-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include " +local_configopts += "-DJBIG_LIBRARY=$EBROOTJBIGKIT/lib/libjbig.%s " % SHLIB_EXT +local_configopts += "-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib64/libjpeg.%s " % SHLIB_EXT +local_configopts += "-DLZMA_LIBRARY=$EBROOTXZ/lib/liblzma.%s " % SHLIB_EXT +local_configopts += "-DUSE_OPENMP=ON " +local_configopts += "-DUSE_MPI=OFF " +local_configopts += "-DSIMPLE_BUILD_TESTS=ON " +local_configopts += "-DOpenMP_Fortran_FLAGS=$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 + +modextravars = { + 'SIMPLE_QSYS': 'local', + 'SIMPLE_PATH': '%(installdir)s', + 'SIMPLE_EMAIL': "my.name@uni.edu" +} + +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/SIMPLE*/{doc,LICENSE,src/inc} %(installdir)s -rpP' + '&& cd %(installdir)s/lib ' + '&& ln -s libSIMPLE%s.%s libSIMPLE.%s' % (version, SHLIB_EXT, SHLIB_EXT) + + '&& 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', 'gui_data', 'tutorials', # req. at runtime + 'doc', 'inc', ] +} + +docpaths = ['doc'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb b/easybuild/easyconfigs/__archive__/s/SIONlib/SIONlib-1.7.6-GCCcore-10.2.0-tools.eb new file mode 100644 index 0000000000..92977478d5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = [ + ('binutils', '2.35'), +] + +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/__archive__/s/SLEPc/SLEPc-3.14.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SLEPc/SLEPc-3.14.2-foss-2020b.eb new file mode 100644 index 0000000000..87ff7d8c44 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..484357754e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb @@ -0,0 +1,73 @@ +## +# 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_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=$EBROOTICCIFORT/lib64/intel64/ && " + +buildopts = ' intel_linux_64 ' + local_buildopts + +files_to_copy = [ + (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*"], 'bin'), +] + +postinstallcmds = [ + 'ln -s %(installdir)s/bin/smokeview_linux_64 %(installdir)s/bin/smokeview' +] + +sanity_check_commands = [ + "cd %(builddir)s/smv-SMV%(version)s && timeout 10 xvfb-run smokeview example 2>&1 | grep 'Terminated' ", +] + +sanity_check_paths = { + 'files': ['bin/smokeview'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb new file mode 100644 index 0000000000..d865aa10a2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb @@ -0,0 +1,50 @@ +easyblock = 'Bundle' + +name = 'SNAP-ESA-python' +version = '8.0' +local_javasuffix = '-Java-%(javaver)s' +versionsuffix = local_javasuffix + '-Python-%(pyver)s' + +homepage = 'https://step.esa.int/main/toolboxes/snap/' +description = "Python interface to the Sentinel Application Platform (SNAP) API" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Java', '1.8', '', SYSTEM), + ('SNAP-ESA', version, local_javasuffix, SYSTEM), + ('Python', '2.7.18'), +] + +local_pysite = 'lib/python%(pyshortver)s/site-packages' +local_pyinstalldir = '%%(installdir)s/%s' % local_pysite + +postinstallcmds = [ + # Install snappy from SNAP-ESA + # snappy-conf is buggy and it hangs after doing the installation of snappy, + # start snappy-conf in a new SID and kill all processes of its PGID + # whenever it prints the final line starting with "or copy" + "mkdir -p %s" % local_pyinstalldir, + ('LOG="$(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'"] + +local_javaopts = " -Dsnap.pythonExecutable=python" +local_javaopts += " -Dsnap.pythonModuleDir=%s" % local_pyinstalldir + +# 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)] ? $::env(JAVA_TOOL_OPTIONS) : ""}]' +modtclfooter = 'setenv JAVA_TOOL_OPTIONS [concat %s "%s"]' % (local_tcl_JAVA_TOOL_OPTIONS, local_javaopts) + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb new file mode 100644 index 0000000000..09eb61a850 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SNAP-HMM/SNAP-HMM-20190603-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'SNAP-HMM' +version = '20190603' +_commit = 'daf76ba' + +homepage = 'https://korflab.github.io/' +description = """SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. +SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/KorfLab/SNAP/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = ['%(name)s-%(version)s_makefile_correction.patch'] +checksums = [ + '8222e49160c9c1199664c29f9c2490f57243c896f23676dea846d34129a1638f', # 20190603.tar.gz + 'd518750d4cf01278ba5403ab5717cfcd65b75b5a7c6573ae140f1cdb56b9e655', # SNAP-HMM-20190603_makefile_correction.patch +] + +prebuildopts = 'export CFLAGS="$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' diff --git a/easybuild/easyconfigs/__archive__/s/SOCI/SOCI-4.0.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SOCI/SOCI-4.0.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..834cef5f74 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..a2f6af4df2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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://github.com/ablab/spades' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/ablab/spades/releases/download/v%(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' diff --git a/easybuild/easyconfigs/__archive__/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..4a3432922a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = 'https://github.com/ablab/spades' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/ablab/spades/releases/download/v%(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' diff --git a/easybuild/easyconfigs/__archive__/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..272f12272d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.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/ +# # + +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" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/2020/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +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'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/SRA-Toolkit-2.10.9-gompi-2020b.eb new file mode 100644 index 0000000000..4c6e55fba4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 + 'd59fe4a4fa302485f72a6313a6348c3eda3570f9c9309737ddfb77abf28701b5', + ], + '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' % (x, e), 'lib64/libncbi-%s.%s' % (x, e)) + for x in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [] +} + +sanity_check_commands = [ + "abi-dump --help", + "kar --help", + "sra-sort --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3aac6838fb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +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'] +checksums = ['93e6864b7ab18be96584950227426102b545db7d6d02762490a43e1610b7eb9b'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('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' diff --git a/easybuild/easyconfigs/__archive__/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..618bac0055 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,47 @@ +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'), +] + +# 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", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SSW/SSW-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SSW/SSW-1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..915ce0d1e9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb new file mode 100644 index 0000000000..f6bec5c108 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb @@ -0,0 +1,32 @@ +# 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'] + +dependencies = [ + ('Beast', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['stacey.src.jar'], + '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' diff --git a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.6a-GCC-10.2.0.eb new file mode 100644 index 0000000000..fd92cc12e8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' + +maxparallel = 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/__archive__/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.7a-GCC-10.2.0.eb new file mode 100644 index 0000000000..ad199055e9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' + +maxparallel = 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/__archive__/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.8a-GCC-10.2.0.eb new file mode 100644 index 0000000000..eecacf41e6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' + +maxparallel = 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/__archive__/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb new file mode 100644 index 0000000000..7dd06980ec --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -0,0 +1,46 @@ +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, 'usempi': 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'), +] + +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + + ['lib'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb new file mode 100644 index 0000000000..4f358cbc2f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '6.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['219ec7360594172464aafa6ecac1fd161097db6fb9ee35af5c1ca61531f4f5c4'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.1.0'), +] + +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DTPL_SCALAPACK_LIBRARIES="${LIBSCALAPACK_MT}" ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${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'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb new file mode 100644 index 0000000000..29b35cb830 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '5.7.0' + +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] +# 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')] + +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/__archive__/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..52675e145f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '5.7.0' + +homepage = 'https://computing.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://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +# 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')] + +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' diff --git a/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb new file mode 100644 index 0000000000..76e6c5a3a9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '5.7.0' + +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] +# 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')] + +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/__archive__/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb new file mode 100644 index 0000000000..2d5442b132 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb @@ -0,0 +1,35 @@ +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'] + +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/__archive__/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb new file mode 100644 index 0000000000..1637aac0c6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb @@ -0,0 +1,35 @@ +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'] + +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/__archive__/s/SWAT+/SWAT+-60.5.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/s/SWAT+/SWAT+-60.5.1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..a58153e87b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SWIG/SWIG-4.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..90a44c127b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-1.4.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-1.4.0-gompi-2020b.eb new file mode 100644 index 0000000000..51ca3848e2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/Sambamba/Sambamba-0.8.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..5c67c33ba0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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_XZ, + 'git_config': { + 'url': 'https://github.com/biod', + 'repo_name': 'sambamba', + 'commit': 'cdc5f84', + 'recursive': True, + } +}] +checksums = ['4a00d072ffc1d077fd8cd54294eea5ae0e890eedbaaa5b16b54fffa758caafce'] + +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' diff --git a/easybuild/easyconfigs/__archive__/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb new file mode 100644 index 0000000000..c7c6f359df --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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=$EBROOTFFTW/lib ' +# only include the solvers supported for LAMMPS +# (for p2nfft we need an additonal dependency) +configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' + +sanity_check_paths = { + 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb new file mode 100644 index 0000000000..6b0e672b3b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.1.0' +versionsuffix = '-bf' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6', # scalapack-2.1.0.tgz + 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('BLIS', '0.8.0'), + ('libFLAME', '5.2.0'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' +configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb new file mode 100644 index 0000000000..e21675f74c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.1.0' +versionsuffix = '-bl' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6', # scalapack-2.1.0.tgz + 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('BLIS', '0.8.0'), + ('LAPACK', '3.9.1'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' +configopts += '-DLAPACK_LIBRARIES="$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], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb new file mode 100644 index 0000000000..3943b1ff81 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b.eb @@ -0,0 +1,23 @@ +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 +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [('OpenBLAS', '0.3.12')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb new file mode 100644 index 0000000000..802ecd11e9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020b.eb @@ -0,0 +1,23 @@ +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] +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')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb new file mode 100644 index 0000000000..33b69ea09a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-2.6-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-2.6-gompic-2020b.eb new file mode 100644 index 0000000000..6896e705ca --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..8875e06bdc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,57 @@ +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'), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb new file mode 100644 index 0000000000..853bb1acf3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-foss-2020b.eb @@ -0,0 +1,53 @@ +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} + +builddependencies = [('hypothesis', '5.41.2')] + +dependencies = [ + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), # required by scipy +] + +# order is important! +exts_list = [ + ('numpy', '1.19.4', { + '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-1.19.4_skip-ppc-long-complex-test.patch + '31f4e64c9335edc1ae5a99cf22adf43147f3526847cca79d0e16a863a8c4da32', + ], + }), + ('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'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb new file mode 100644 index 0000000000..e62424957d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-fosscuda-2020b.eb @@ -0,0 +1,53 @@ +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 +] + +# order is important! +exts_list = [ + ('numpy', '1.19.4', { + '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-1.19.4_skip-ppc-long-complex-test.patch + '31f4e64c9335edc1ae5a99cf22adf43147f3526847cca79d0e16a863a8c4da32', + ], + }), + ('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'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb new file mode 100644 index 0000000000..1d52db5cfc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb @@ -0,0 +1,59 @@ +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} + +builddependencies = [('hypothesis', '5.41.2')] + +dependencies = [ + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), # required by scipy +] + +# 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'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb new file mode 100644 index 0000000000..ff90550cef --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.11-intelcuda-2020b.eb @@ -0,0 +1,59 @@ +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 +] + +# 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'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-7.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-7.0-gompi-2020b.eb new file mode 100644 index 0000000000..f24cb4ef9f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-7.0-gompic-2020b.eb b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-7.0-gompic-2020b.eb new file mode 100644 index 0000000000..e3bc0ac529 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb new file mode 100644 index 0000000000..459c6f9824 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.10.1-intel-2020b.eb @@ -0,0 +1,24 @@ +# 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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2d1a0c9d6bd1bc3cadb0364b8f06540f51322a670cf8438d0fde1c1c7317adc0'] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb new file mode 100644 index 0000000000..67c930bb20 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.11.1-foss-2020b.eb @@ -0,0 +1,24 @@ +# 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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..3b4ccb971c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.11.1-fosscuda-2020b.eb @@ -0,0 +1,24 @@ +# 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'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb new file mode 100644 index 0000000000..36cf7b4171 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.11.1-intel-2020b.eb @@ -0,0 +1,24 @@ +# 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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..5911f2c7c8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.9.1-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,25 @@ +# 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), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb new file mode 100644 index 0000000000..7b54e4be6f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SentencePiece/SentencePiece-0.1.96-GCC-10.2.0.eb @@ -0,0 +1,58 @@ +## +# 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': ['5198f31c3bb25e685e9e68355a3bf67a1db23c9e8bdccc33dc015f496a44df7a'], +} + +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 && ', + }), +] + +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'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/SeqAn/SeqAn-2.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SeqAn/SeqAn-2.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..cb9f064fb0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..83b25b6648 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', + '413f0ad8e0963d8922205d31e0c361cfa98a10f93e7d3e0506e0bed539ec70eb', # 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' diff --git a/easybuild/easyconfigs/__archive__/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..80f595ab28 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +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] +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', '3.8.6'), + ('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/__archive__/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..0489f0e3fc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb @@ -0,0 +1,55 @@ +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'} + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +exts_defaultclass = 'RPackage' +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', { + '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' diff --git a/easybuild/easyconfigs/__archive__/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..b8a228157b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb @@ -0,0 +1,61 @@ +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'} + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +exts_defaultclass = 'RPackage' +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', { + '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' diff --git a/easybuild/easyconfigs/__archive__/s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/s/SeuratData/SeuratData-20210514-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..1301b837a6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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_XZ, + 'git_config': { + 'url': 'https://github.com/satijalab', + 'repo_name': 'seurat-data', + 'commit': local_commit, + }, +}] +checksums = ['7bec7540f634b39089ba457b32784bb5236dfad0935937f8155240201ab862bd'] + +dependencies = [('R', '4.0.3')] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SeuratWrappers/SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/s/SeuratWrappers/SeuratWrappers-20210528-foss-2020b-R-4.0.3.eb new file mode 100644 index 0000000000..b7a771c9cb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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_XZ, + 'git_config': { + 'url': 'https://github.com/satijalab', + 'repo_name': 'seurat-wrappers', + 'commit': local_commit, + }, +}] +checksums = ['01d1bfef64cd4f5b3c209a431ecc475349d4dec513318263ddb0354cd37ca47e'] + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), + ('Seurat', '4.0.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb new file mode 100644 index 0000000000..43ae68f448 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb @@ -0,0 +1,20 @@ +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'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb new file mode 100644 index 0000000000..e6517c9c29 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb @@ -0,0 +1,22 @@ +# 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'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/Shasta/Shasta-0.8.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/Shasta/Shasta-0.8.0-foss-2020b.eb new file mode 100644 index 0000000000..b6965d55e6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 + 'd9696b8a667f6a0db724f779083accb8004398bdfdf5cf15ef5cdaed89f339d0', # Shasta-0.8.0-foss-2020b-fix_links.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Cereal', '1.3.0', '', SYSTEM), +] + +dependencies = [ + ('cURL', '7.72.0'), + ('Boost', '1.74.0'), + ('libpng', '1.6.37'), + ('SeqAn', '2.4.0'), + ('BLAST+', '2.11.0'), + ('gnuplot', '5.4.1'), + ('Graphviz', '2.47.0', '-Java-11'), + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), + ('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', 'shasta-install/bin/*.%s' % SHLIB_EXT], 'lib') +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + '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' diff --git a/easybuild/easyconfigs/__archive__/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/Sibelia/Sibelia-3.0.7-foss-2020b.eb new file mode 100644 index 0000000000..fbc2e24bc0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb new file mode 100644 index 0000000000..d85497c992 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb @@ -0,0 +1,37 @@ +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'), +] + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/simnibs/simnibs/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['ad4482b4cdd306d4356757b4d065d844ea698dab2530aa09fb59219d2a982219'], + }), +] + +sanity_check_paths = { + 'files': ['bin/headreco', 'bin/simnibs'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "headreco --help", + "simnibs --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb new file mode 100644 index 0000000000..0f3d1bad69 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb @@ -0,0 +1,47 @@ +# 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': '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 " +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 . ", +] + +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/__archive__/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..6fcd01d902 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb @@ -0,0 +1,47 @@ +# 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 . ", +] + +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/__archive__/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/Spark/Spark-3.1.1-foss-2020b.eb new file mode 100644 index 0000000000..5ef5383cb5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -0,0 +1,52 @@ +# 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://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'] +checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] + +dependencies = [ + ('Python', '3.8.6'), + ('Java', '11', '', SYSTEM), + # ('Hadoop', '2.10.0', '-native'), + ('Arrow', '0.17.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} + +exts_list = [ + ('py4j', '0.10.9.2', { + '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'} + +modextravars = {'SPARK_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/Spark/Spark-3.1.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..5c43460341 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -0,0 +1,52 @@ +# 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': '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'] +checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] + +dependencies = [ + ('Python', '3.8.6'), + ('Java', '11', '', SYSTEM), + # ('Hadoop', '2.10.0', '-native'), + ('Arrow', '0.17.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} + +exts_list = [ + ('py4j', '0.10.9.2', { + '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'} + +modextravars = {'SPARK_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..8cb83e6444 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb @@ -0,0 +1,31 @@ +# 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')] + +sanity_check_paths = { + 'files': ['include/Spectra/SymEigsSolver.h'], + 'dirs': ['include/Spectra/LinAlg', 'share/spectra/cmake'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f6273b752b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx-RTD-Theme' +version = '1.1.1' + +homepage = 'https://sphinx-rtd-theme.readthedocs.io' +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'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +exts_list = [ + ('sphinx_rtd_theme', version, { + 'checksums': ['6146c845f1e1947b3c3dd4432c28998a1693ccc742b4f9ad7c63129f0757c103'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/s/Subread/Subread-2.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/Subread/Subread-2.0.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..cb9042bbb7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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://subread.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' diff --git a/easybuild/easyconfigs/__archive__/s/Subversion/Subversion-1.14.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/Subversion/Subversion-1.14.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..fac1a9e08c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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=$EBROOTSERF" + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-5.8.1-foss-2020b-METIS-5.1.0.eb b/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-5.8.1-foss-2020b-METIS-5.1.0.eb new file mode 100644 index 0000000000..cf6bd920e1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-5.8.1-foss-2020b-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '5.8.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['06726e471fbaa55f792578f9b4ab282ea9d008cf39ddcc3b42b73400acddef40'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb new file mode 100644 index 0000000000..cc945eb512 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb new file mode 100644 index 0000000000..8504a4cba5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..576e48c80b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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://support.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://support.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/__archive__/s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/samblaster/samblaster-0.1.26-GCC-10.2.0.eb new file mode 100644 index 0000000000..d70754c056 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..372ab575da --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/sansa/sansa-0.0.7-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/s/sansa/sansa-0.0.7-gompi-2020b.eb new file mode 100644 index 0000000000..bb50f6ae9c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), + ('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/__archive__/s/scanpy/scanpy-1.7.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/scanpy/scanpy-1.7.2-foss-2020b.eb new file mode 100644 index 0000000000..250a1d0118 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scanpy/scanpy-1.7.2-foss-2020b.eb @@ -0,0 +1,74 @@ +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} + +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'), +] + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('anndata', '0.7.6', { + 'checksums': ['a3cc67bba9a4cd4b5984aec64c4f577c2d5a4695f4064027f8e6a9dac1f508b2'], + }), + ('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'], + }), + (name, version, { + 'checksums': ['ad5e7afdf1948753cd27f6f27ee904df1ce455855eec8520985effe86c53c630'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/scanpy/scanpy-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/scanpy/scanpy-1.8.1-foss-2020b.eb new file mode 100644 index 0000000000..9755e8b8fc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scanpy/scanpy-1.8.1-foss-2020b.eb @@ -0,0 +1,65 @@ +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', '0.53.1'), + ('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'), +] + +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_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' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb new file mode 100644 index 0000000000..ade17a2ca7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-allel/scikit-allel-1.3.2-foss-2020b.eb @@ -0,0 +1,28 @@ +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'), +] + +options = {'modulename': 'allel'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb new file mode 100644 index 0000000000..d4cfc0b74f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb @@ -0,0 +1,43 @@ +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb new file mode 100644 index 0000000000..3b406a03e3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-foss-2020b.eb @@ -0,0 +1,26 @@ +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'), +] + +exts_list = [ + ('distro', '1.5.0', { + 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], + }), + (name, version, { + 'modulename': 'skbuild', + 'checksums': ['da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..7c7bb3d6a9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-fosscuda-2020b.eb @@ -0,0 +1,26 @@ +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'), +] + +exts_list = [ + ('distro', '1.5.0', { + 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], + }), + (name, version, { + 'modulename': 'skbuild', + 'checksums': ['da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb new file mode 100644 index 0000000000..347af49b27 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-intel-2020b.eb @@ -0,0 +1,26 @@ +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'), +] + +exts_list = [ + ('distro', '1.5.0', { + 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], + }), + (name, version, { + 'modulename': 'skbuild', + 'checksums': ['da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb new file mode 100644 index 0000000000..c8e047ef95 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.11.1-intelcuda-2020b.eb @@ -0,0 +1,26 @@ +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'), +] + +exts_list = [ + ('distro', '1.5.0', { + 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], + }), + (name, version, { + 'modulename': 'skbuild', + 'checksums': ['da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..374a7bdf7d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +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'), +] + +exts_list = [ + ('distro', '1.7.0', { + 'checksums': ['151aeccf60c216402932b52e40ee477a939f8d58898927378a02abbe852c1c39'], + }), + (name, version, { + 'checksums': ['e723cd0f3489a042370b9ea988bbb9cfd7725e8b25b20ca1c7981821fcf65fb9'], + 'modulename': 'skbuild', + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-foss-2020b.eb new file mode 100644 index 0000000000..cf9b309d92 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..9e0cc9610a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-fosscuda-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': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('Pillow', '8.0.1'), + ('networkx', '2.5'), + ('dask', '2021.2.0'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb new file mode 100644 index 0000000000..bcfbbed25d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-intel-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': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('Pillow', '8.0.1'), + ('networkx', '2.5'), + ('dask', '2021.2.0'), +] + +exts_list = [ + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imageio', '2.9.0', { + 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], + }), + ('imread', '0.7.4', { + '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'], + }), + ('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' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb new file mode 100644 index 0000000000..506331c06b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.18.1-intelcuda-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': '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'), +] + +exts_list = [ + ('imageio', '2.9.0', { + 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], + }), + ('imread', '0.7.4', { + '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'], + }), + ('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' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb new file mode 100644 index 0000000000..3a663de17d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.20.4-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,25 @@ +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) +] + +options = {'modulename': 'sklearn'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb new file mode 100644 index 0000000000..2a26f91b08 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-foss-2020b.eb @@ -0,0 +1,24 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11') +] + +options = {'modulename': 'sklearn'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..a85846ece6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-fosscuda-2020b.eb @@ -0,0 +1,24 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11') +] + +options = {'modulename': 'sklearn'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb new file mode 100644 index 0000000000..182bc21820 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-intel-2020b.eb @@ -0,0 +1,24 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11') +] + +options = {'modulename': 'sklearn'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb new file mode 100644 index 0000000000..1f8fcbce02 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.2-intelcuda-2020b.eb @@ -0,0 +1,24 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11') +] + +options = {'modulename': 'sklearn'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..4cbca7d3c1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb @@ -0,0 +1,38 @@ +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 = ['http://legacy.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'), + ('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' diff --git a/easybuild/easyconfigs/__archive__/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 new file mode 100644 index 0000000000..8e58b77ae0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 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'} + +source_urls = ['http://legacy.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' diff --git a/easybuild/easyconfigs/__archive__/s/seqtk/seqtk-1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/seqtk/seqtk-1.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..de96dba8af --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a9387c69f6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/silx/silx-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/silx/silx-0.14.0-foss-2020b.eb new file mode 100644 index 0000000000..b7fdd41233 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/silx/silx-0.14.0-foss-2020b.eb @@ -0,0 +1,38 @@ +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/s/silx/silx-0.14.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/silx/silx-0.14.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..9dc87add1b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/silx/silx-0.14.0-fosscuda-2020b.eb @@ -0,0 +1,38 @@ +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb new file mode 100644 index 0000000000..8d2df8c73c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb @@ -0,0 +1,26 @@ +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..65ec48867c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/s/snakemake/snakemake-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/snakemake/snakemake-6.1.0-foss-2020b.eb new file mode 100644 index 0000000000..89aac47183 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/snakemake/snakemake-6.1.0-foss-2020b.eb @@ -0,0 +1,66 @@ +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'), + ('IPython', '7.18.1'), +] + +# 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'], + }), + ('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' diff --git a/easybuild/easyconfigs/__archive__/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3627cd3967 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +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'), +] + +# 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'], + 'dirs': [''] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/snippy/snippy-4.6.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/snippy/snippy-4.6.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..ac4d831cb4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/snippy/snippy-4.6.0-GCC-10.2.0.eb @@ -0,0 +1,46 @@ +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'), + ('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') +] + +sanity_check_paths = { + 'files': ['bin/snippy', 'perl5/Snippy/Version.pm'], + 'dirs': ['etc', 'test'], +} + +sanity_check_commands = [ + "snippy --version", + "snippy --check", + "snippy --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/snp-sites/snp-sites-2.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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/__archive__/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb b/easybuild/easyconfigs/__archive__/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb new file mode 100644 index 0000000000..2e5679be3c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), + ('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' diff --git a/easybuild/easyconfigs/__archive__/s/spaln/spaln-2.4.12-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/spaln/spaln-2.4.12-GCC-10.2.0.eb new file mode 100644 index 0000000000..1d2162cf61 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/spaln/spaln-2.4.12-GCC-10.2.0.eb @@ -0,0 +1,46 @@ +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'), + ('Perl', '5.32.0'), +] + +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" + +fix_perl_shebang_for = ['seqdb/*.pl'] + +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'"] + +modextrapaths = { + 'PATH': 'seqdb', + 'PERL5LIB': 'seqdb', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/sparsehash/sparsehash-2.0.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/sparsehash/sparsehash-2.0.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ce7e1010b2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/__archive__/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 0000000000..91006d1a37 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,29 @@ +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), +] + +exts_list = [ + (name, version, { + 'checksums': ['215f148e5d5067081bc28abe282bfd0942ed8be6d68f128fd7786006a884abf7'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb new file mode 100644 index 0000000000..c3fbf16ad8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-foss-2020b.eb @@ -0,0 +1,22 @@ +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'), +] + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..dd188b91fe --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-fosscuda-2020b.eb @@ -0,0 +1,22 @@ +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'), +] + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb new file mode 100644 index 0000000000..93d1d182bd --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-intel-2020b.eb @@ -0,0 +1,25 @@ +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 + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/spglib/spglib-1.16.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..6e6442b602 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/spoa/spoa-3.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/spoa/spoa-3.4.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..3d6b004f1f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = {MODULE_LOAD_ENV_HEADERS: 'include/%(namelower)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/spoa/spoa-4.0.7-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/s/spoa/spoa-4.0.7-GCC-10.2.0.eb new file mode 100644 index 0000000000..61912e520f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb new file mode 100644 index 0000000000..c416d4588c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.12.1-foss-2020b.eb @@ -0,0 +1,26 @@ +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'), +] + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + (name, version, { + 'checksums': ['a271b4ccec190148dccda25f0cbdcbf871f408fc1394a10a7dc1af4a62b91c8e'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..5d61ef7b22 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.12.1-fosscuda-2020b.eb @@ -0,0 +1,28 @@ +# Author: Denis Krišťák (INUITS) + +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'), +] + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + (name, version, { + 'checksums': ['a271b4ccec190148dccda25f0cbdcbf871f408fc1394a10a7dc1af4a62b91c8e'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb new file mode 100644 index 0000000000..e596e62187 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.12.1-intel-2020b.eb @@ -0,0 +1,26 @@ +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'), +] + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + (name, version, { + 'checksums': ['a271b4ccec190148dccda25f0cbdcbf871f408fc1394a10a7dc1af4a62b91c8e'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/suave/suave-20160529-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/suave/suave-20160529-foss-2020b.eb new file mode 100644 index 0000000000..8579f9457b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/suave/suave-20160529-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +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'} + +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'), + ('h5py', '3.1.0'), + ('Pysam', '0.16.0.1'), +] + +preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ + +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'] + +options = {'modulename': 'suave_server'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/svist4get/svist4get-1.3.1-foss-2020b.eb new file mode 100644 index 0000000000..3656ed6804 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -0,0 +1,58 @@ +# 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'), + ('ImageMagick', '7.0.10-35'), +] + +exts_list = [ + ('reportlab', '3.6.9', { + 'patches': ['reportlab-3.6.12-fontconfig.patch'], + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84', + # reportlab-3.6.12-fontconfig.patch: + '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], + }), + ('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' diff --git a/easybuild/easyconfigs/__archive__/s/swifter/swifter-1.0.9-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/swifter/swifter-1.0.9-foss-2020b.eb new file mode 100644 index 0000000000..4ac4712853 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/swifter/swifter-1.0.9-foss-2020b.eb @@ -0,0 +1,30 @@ +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'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/swifter/swifter-1.0.9-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/s/swifter/swifter-1.0.9-fosscuda-2020b.eb new file mode 100644 index 0000000000..df935fe0c8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/swifter/swifter-1.0.9-fosscuda-2020b.eb @@ -0,0 +1,30 @@ +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'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.7.1-foss-2020b.eb new file mode 100644 index 0000000000..208b51d417 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.7.1-foss-2020b.eb @@ -0,0 +1,30 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a3de9261e97535b83bb8607b0da2c7d03126650fafea2b2789657b229c246b2e'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('gmpy2', '2.1.0b5'), +] + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.7.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.7.1-intel-2020b.eb new file mode 100644 index 0000000000..5267623a56 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.7.1-intel-2020b.eb @@ -0,0 +1,30 @@ +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'), +] + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/t/TALON/TALON-5.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/TALON/TALON-5.0-foss-2020b.eb new file mode 100644 index 0000000000..60cc0f859a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TALON/TALON-5.0-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'TALON' +version = '5.0' + +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 +(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'] +checksums = [ + 'aeb1c1f46a4c757a8bb866b9a4446186f0f280e9391933a040de9dad30453649', # v5.0.tar.gz +] + +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'), +] + +preinstallopts = "sed -i 's/pysam==/pysam>=/g' requirements.txt && " +preinstallopts += "sed -i 's/pysam==/pysam>=/g' setup.py && " + +sanity_check_commands = ['talon_label_reads -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb new file mode 100644 index 0000000000..508b9103e1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb @@ -0,0 +1,40 @@ +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', + '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 = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('molmod', '1.4.8'), +] + +# 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'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/TBA/TBA-1.0-foss-2020b.eb new file mode 100644 index 0000000000..1fa2407bbb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TBA/TBA-1.0-foss-2020b.eb @@ -0,0 +1,60 @@ +# 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', '3.3.3'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} + +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 ", +] + +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' diff --git a/easybuild/easyconfigs/__archive__/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9b46ca4cac --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 initially inspired by the user friendly CLAP library.""" + +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/__archive__/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/__archive__/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb new file mode 100644 index 0000000000..62453d378d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -0,0 +1,62 @@ +# 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', '3.3.3'), + ('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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb new file mode 100644 index 0000000000..08129698d7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -0,0 +1,79 @@ +# 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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..53a8eb3a50 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb @@ -0,0 +1,24 @@ +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'), +] + +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/__archive__/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 new file mode 100644 index 0000000000..2a70b5b676 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb @@ -0,0 +1,24 @@ +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'), +] + +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' diff --git a/easybuild/easyconfigs/__archive__/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9f5d55cc2a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TRF/TRF-4.09.1-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +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'] +checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] + +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' diff --git a/easybuild/easyconfigs/__archive__/t/TWL-NINJA/TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c754973398 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 +] + +maxparallel = 1 + +builddependencies = [ + ('binutils', '2.35'), + ('Pandoc', '2.10', '', SYSTEM), +] + +sanity_check_paths = { + 'dirs': [], + 'files': ['bin/tagdust'], +} + +sanity_check_commands = [('%(namelower)s', '--version')] +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5cd77d8338 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb new file mode 100644 index 0000000000..29bf154b7a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -0,0 +1,195 @@ +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'), +] + +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'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + }), + ('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-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', + ], + '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-bfloat16-alias-violation.patch + '6e845c44c27477740d16e9c525cdd4c2a96ac3deb2709ac62e21c3de79c4583b', + # 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' diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb new file mode 100644 index 0000000000..d10a63134e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 + ('UnZip', '6.0'), +] +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'), +] + +# 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'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + }), + ('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'], + }), + ('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'], + }), + ('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-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', + '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', + '-//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', + # 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', + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..e804f1d30d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -0,0 +1,237 @@ +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 + ('UnZip', '6.0'), +] +dependencies = [ + ('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 + ('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'), +] + +# 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'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + }), + ('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'], + }), + ('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'], + }), + ('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-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', + ], + '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/...', + # 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', + '-//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', + # 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 + 'f384cd97e004673ae530b6e5cc826f8fddb46646991f1a228fc07b2aac87ee80', + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb new file mode 100644 index 0000000000..160fa7f0ab --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -0,0 +1,215 @@ +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 + ('UnZip', '6.0'), +] +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'), +] + +# 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'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + }), + ('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_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-2.5.3_fix-aarch64-build.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_add-support-for-large-core-systems.patch + '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 + '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', + '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', + # 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, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb new file mode 100644 index 0000000000..ba53dc20ab --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -0,0 +1,232 @@ +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 + ('UnZip', '6.0'), +] +dependencies = [ + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), + ('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'), +] + +# 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'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + }), + ('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_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_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 + '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_add-support-for-large-core-systems.patch + '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 + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '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', + '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', + # 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 " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8880b56b40 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'TetGen' +version = '1.6.0' + +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'} + +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'), + ('binutils', '2.35'), +] + +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': [], +} + +sanity_check_commands = ["%(namelower)s -h"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb b/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb new file mode 100644 index 0000000000..10b775ad9c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.1.2-foss-2020b-PyMC.eb @@ -0,0 +1,34 @@ +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'), +] + +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 = [ + "python -c 'import theano.tensor' 2>&1 | grep '%s'; test $? != 0" % local_blas_warning, +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb b/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb new file mode 100644 index 0000000000..ee1184a31f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb @@ -0,0 +1,40 @@ +# Author: Denis Krišťák (INUITS) + +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'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), + ('SciPy-bundle', '2020.11'), +] + +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/__archive__/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb b/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb new file mode 100644 index 0000000000..b23c422240 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.1.2-intel-2020b-PyMC.eb @@ -0,0 +1,37 @@ +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'), +] + +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 $? != 0" % local_blas_warning, +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3c3f3db77b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.10' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + '63df418a859d0a463347f95ded5cd88a3dd3aaa1ceecaeee362194bc30f3e386', # tk8.6.10-src.tar.gz + '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch +] + +builddependencies = [('binutils', '2.35')] +dependencies = [ + ('Tcl', version), + ('X11', '20201008'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$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': [], +} + +modextrapaths = {'TCLLIBPATH': {'paths': 'lib', 'delimiter': ' '}} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-2.7.18-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b75688dff4 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c015497455 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +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'] +checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21'] + +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/__archive__/t/ToFu/ToFu-1.5.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/ToFu/ToFu-1.5.0-foss-2020b.eb new file mode 100644 index 0000000000..3203335051 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/ToFu/ToFu-1.5.0-foss-2020b.eb @@ -0,0 +1,41 @@ +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'), +] + +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_check_commands = ["python -c 'import tofu.geom'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/ToFu/ToFu-1.5.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/t/ToFu/ToFu-1.5.0-intel-2020b.eb new file mode 100644 index 0000000000..cfcc638deb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/ToFu/ToFu-1.5.0-intel-2020b.eb @@ -0,0 +1,41 @@ +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'), +] + +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_check_commands = ["python -c 'import tofu.geom'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/Togl/Togl-2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/Togl/Togl-2.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b764b7ccc1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/Togl/Togl-2.0-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +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/__archive__/t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.1.2-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..8b97539cf5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' + +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['tophat --version'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb new file mode 100644 index 0000000000..8c99143619 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TranscriptClean/TranscriptClean-2.0.2-foss-2020b.eb @@ -0,0 +1,36 @@ +# 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', '4.0.3'), + ('Python', '3.8.6'), + ('BEDTools', '2.30.0'), + ('SAMtools', '1.11'), + ('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' diff --git a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..36e7345465 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), + ('pigz', '2.6'), + ('Perl', '5.32.0'), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), + ('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' diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.9.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.9.1-foss-2020b.eb new file mode 100644 index 0000000000..fabca76f18 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Bowtie2', '2.4.2'), + ('HTSlib', '1.11'), + ('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' diff --git a/easybuild/easyconfigs/__archive__/t/tMAE/tMAE-1.0.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..442eed6ab0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/tabixpp/tabixpp-1.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/tabixpp/tabixpp-1.1.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..fc3261b743 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/taxator-tk/taxator-tk-1.3.3-GCC-10.2.0.eb new file mode 100644 index 0000000000..fa4ffd5008 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'), +] + +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/" + +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' diff --git a/easybuild/easyconfigs/__archive__/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ee01f36685 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb @@ -0,0 +1,19 @@ +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'), + ('CMake', '3.18.4'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b317cef498 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +## +# 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')] + +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + +sanity_check_paths = { + 'files': ["bin/tcsh", "bin/csh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/__archive__/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..0ba7aedbe6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/tensorboardX/tensorboardX-2.1-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,38 @@ +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'} + +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'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/__archive__/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..7c67aace7f --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/tensorboardX/tensorboardX-2.2-foss-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,38 @@ +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'} + +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'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/__archive__/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..e54e62f630 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/tensorboardX/tensorboardX-2.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,38 @@ +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'} + +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'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb new file mode 100644 index 0000000000..1fea1b5a53 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb @@ -0,0 +1,42 @@ +## +# 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_list = [ + ('cloudpickle', '1.6.0', { + '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/'], + 'checksums': ['1fe89e85fd053bf36e8645a5a1a53b729bc254cf1516bc224fcbd1e4ff50083a'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..2364e43ecf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb @@ -0,0 +1,42 @@ +## +# 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_list = [ + ('cloudpickle', '1.6.0', { + '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/'], + 'checksums': ['1fe89e85fd053bf36e8645a5a1a53b729bc254cf1516bc224fcbd1e4ff50083a'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/texinfo/texinfo-6.7-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..92671cd1e2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/time/time-1.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/time/time-1.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c8fda7a1c7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/t/tmux/tmux-3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/tmux/tmux-3.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..df0fc99300 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/__archive__/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..aed48cf251 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,28 @@ +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), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/__archive__/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..5c3fdce9f2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,28 @@ +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), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/__archive__/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 0000000000..afdcc67cd0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.10.0' +local_pytorch_version = '1.9.0' +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 &&" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/__archive__/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..98085d7ab2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/torchtext/torchtext-0.8.1-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,38 @@ +## +# 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', '4.56.2'), + ('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 &&" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/__archive__/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb new file mode 100644 index 0000000000..417f592c53 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb @@ -0,0 +1,42 @@ +## +# 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 &&" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/torchvision/torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/torchvision/torchvision-0.4.2-fosscuda-2020b-PyTorch-1.3.1.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/torchvision/torchvision-0.8.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/__archive__/t/torchvision/torchvision-0.8.2-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 0000000000..8d0b69baaf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/torchvision/torchvision-0.8.2-fosscuda-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': '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), +] + +# 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' diff --git a/easybuild/easyconfigs/__archive__/t/torchvision/torchvision-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/t/tox/tox-3.25.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/tox/tox-3.25.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1bfd6bcd46 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/tox/tox-3.25.1-GCCcore-10.2.0.eb @@ -0,0 +1,20 @@ +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')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..85258f3eb0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.56.2-GCCcore-10.2.0.eb @@ -0,0 +1,18 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['11d544652edbdfc9cc41aa4c8a5c166513e279f3f2d9f1a9e1c89935b51de6ff'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..574f1dde7c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.60.0-GCCcore-10.2.0.eb @@ -0,0 +1,18 @@ +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')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5e8501b1e5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-10.2.0.eb @@ -0,0 +1,18 @@ +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'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb new file mode 100644 index 0000000000..4f58f9acc8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.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 = '11.1.1' +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_IBVERBS_DEV] + +dependencies = [ + ('numactl', '2.0.13'), + ('CUDAcore', local_cudaversion, '', SYSTEM), + ('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=$EBROOTGDRCOPY ' + +prebuildopts = 'unset CUDA_CFLAGS && unset LIBS && ' +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb new file mode 100644 index 0000000000..11fabfc2ea --- /dev/null +++ b/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -0,0 +1,52 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.9.0' +local_cudaversion = '11.2.1' +versionsuffix = '-CUDA-%s' % local_cudaversion + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['a7a2c8841dc0d5444088a4373dc9b9cc68dbffcd917c1eba92ca8ed8e5e635fb'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('numactl', '2.0.13'), + ('CUDAcore', local_cudaversion, '', SYSTEM), + ('GDRCopy', '2.1', versionsuffix), +] + +configure_cmd = "contrib/configure-release" +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' +configopts += '--with-cuda=$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' diff --git a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..0c81fb441b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..765c13e793 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.2.26-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 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://artifacts.unidata.ucar.edu/repository/downloads-udunits/', + 'https://sources.easybuild.io/u/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'], +} + +maxparallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/u/UShER/UShER-0.4.1-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/u/UShER/UShER-0.4.1-gompi-2020b.eb new file mode 100644 index 0000000000..13dbafb70c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..07c853d36a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 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 ' +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' diff --git a/easybuild/easyconfigs/__archive__/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb new file mode 100644 index 0000000000..de2fa5f272 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb @@ -0,0 +1,37 @@ +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'), +] + +exts_list = [ + ('pynvml', '11.0.0', { + 'checksums': ['d5fc4a22d355b40c341d6ba0aa888a2d4d2253177d243900f8401b7e6cacb1bb'], + }), + (name, version, { + 'modulename': 'ucp', + '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': [ + '751da668ba43ad15b53cdb0bfd4084bd4b07200db57b604a9a09aa99d8a3bc1b', # v0.21.0.tar.gz + # ucx-py-0.21.0_setup-get-ucx-incpath.patch + 'faeb61c302ffb37e72221d18c83fc929e47a6c5cd84c4208b01c5a21f570f561', + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb new file mode 100644 index 0000000000..42b0ba96af --- /dev/null +++ b/easybuild/easyconfigs/__archive__/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb @@ -0,0 +1,27 @@ +# 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'), +] + +options = {'modulename': 'umap'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb new file mode 100644 index 0000000000..292ef5cd39 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/u/umap-learn/umap-learn-0.4.6-fosscuda-2020b.eb @@ -0,0 +1,27 @@ +# 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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('numba', '0.52.0'), +] + +options = {'modulename': 'umap'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb b/easybuild/easyconfigs/__archive__/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb new file mode 100644 index 0000000000..be1b827f91 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb @@ -0,0 +1,37 @@ +# 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'), +] + +exts_list = [ + ('pynndescent', '0.5.7', { + 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], + }), + (name, version, { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/u/unimap/unimap-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/u/unimap/unimap-0.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c03b77d5db --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..9081313486 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..280230633a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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=OFF', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/u/util-linux/util-linux-2.36-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/u/util-linux/util-linux-2.36-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..93640fcd1d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/v/VBZ-Compression/VBZ-Compression-1.0.1-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/v/VBZ-Compression/VBZ-Compression-1.0.1-gompi-2020b.eb new file mode 100644 index 0000000000..09c6e077ce --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb new file mode 100644 index 0000000000..4f24e03b47 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb @@ -0,0 +1,34 @@ +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'), +] + +dependencies = [ + ('Perl', '5.32.0'), + ('HTSlib', '1.12'), + ('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' diff --git a/easybuild/easyconfigs/__archive__/v/VEP/VEP-103.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/v/VEP/VEP-103.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..b53ccb6277 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/VEP/VEP-103.1-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +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'), + ('Archive-Zip', '1.68'), + ('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' diff --git a/easybuild/easyconfigs/__archive__/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/__archive__/v/VMD/VMD-1.9.4a51-foss-2020b.eb new file mode 100644 index 0000000000..26e658c5d6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -0,0 +1,60 @@ +## +# 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 + 'dc9fc419e2e938f42d2e4784b0c9c7429317893f08d3ed170f949c3ee3aec062', # VMD-1.9.4a51_configure.patch + '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4a51_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'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('POV-Ray', '3.7.0.8'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb new file mode 100644 index 0000000000..9037761dcb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -0,0 +1,61 @@ +## +# 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 + 'dc9fc419e2e938f42d2e4784b0c9c7429317893f08d3ed170f949c3ee3aec062', # VMD-1.9.4a51_configure.patch + '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4a51_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', '', SYSTEM), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('POV-Ray', '3.7.0.8'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb new file mode 100644 index 0000000000..0e0ca81463 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb new file mode 100644 index 0000000000..14ed6e6d97 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/v/VTK/VTK-9.0.1-foss-2020b.eb new file mode 100644 index 0000000000..b9847d81cc --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -0,0 +1,90 @@ +## +# 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'), + ('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 " +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' +# Other +configopts += "-DVTK_USE_MPI=ON " + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$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), +] + +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' % (x, SHLIB_EXT) for x 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' diff --git a/easybuild/easyconfigs/__archive__/v/VTK/VTK-9.0.1-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/v/VTK/VTK-9.0.1-fosscuda-2020b.eb new file mode 100644 index 0000000000..c4ae05ddd6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/VTK/VTK-9.0.1-fosscuda-2020b.eb @@ -0,0 +1,89 @@ +## +# 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 " + +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), +] + +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' % (x, SHLIB_EXT) for x 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 $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.16.1-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.16.1-gompi-2020b.eb new file mode 100644 index 0000000000..aa520b0bb1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.16.1-gompi-2020b.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.16.1' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'ftp://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Valgrind-3.15.0-no-MPI-1.patch'] +checksums = [ + 'c91f3a2f7b02db0f3bc99479861656154d241d2fdb265614ba918cc6720a33ca', # valgrind-3.16.1.tar.bz2 + 'e99464ad9f2d2e74c5c50d2fa1bcf8637295b11cd841102035f8601b01afd85f', # Valgrind-3.15.0-no-MPI-1.patch +] + +configopts = ' --with-mpicc="$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' diff --git a/easybuild/easyconfigs/__archive__/v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..edb6a8fe3b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/v/VisPy/VisPy-0.6.6-foss-2020b.eb b/easybuild/easyconfigs/__archive__/v/VisPy/VisPy-0.6.6-foss-2020b.eb new file mode 100644 index 0000000000..f2e533ad29 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/VisPy/VisPy-0.6.6-foss-2020b.eb @@ -0,0 +1,30 @@ +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'), +] + +exts_list = [ + ('freetype_py', '2.2.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-2.2.0.zip'], + 'checksums': ['cf43716bc5246cd54a64b2238b942e8dc80b79eda92f814c720286fa6fab387a'], + }), + ('vispy', version, { + 'checksums': ['6f3c4d00be9e6761c046d520a86693d78a0925d47eeb2fc095e95dac776f74ee'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/v/VisPy/VisPy-0.6.6-intel-2020b.eb b/easybuild/easyconfigs/__archive__/v/VisPy/VisPy-0.6.6-intel-2020b.eb new file mode 100644 index 0000000000..617ff51f77 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/VisPy/VisPy-0.6.6-intel-2020b.eb @@ -0,0 +1,30 @@ +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'), +] + +exts_list = [ + ('freetype_py', '2.2.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-2.2.0.zip'], + 'checksums': ['cf43716bc5246cd54a64b2238b942e8dc80b79eda92f814c720286fa6fab387a'], + }), + ('vispy', version, { + 'checksums': ['6f3c4d00be9e6761c046d520a86693d78a0925d47eeb2fc095e95dac776f74ee'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b23389e4e9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +## +# 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/', + 'https://download.lammps.org/thirdparty', +] +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' diff --git a/easybuild/easyconfigs/__archive__/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb new file mode 100644 index 0000000000..04e98360f2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb @@ -0,0 +1,35 @@ + +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'} + +builddependencies = [('binutils', '2.35')] +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' diff --git a/easybuild/easyconfigs/__archive__/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb new file mode 100644 index 0000000000..e6a30f8717 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -0,0 +1,68 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.2' + +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', + 'vcflib-1.0.2_fix-shared-linking.patch', +] +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 = [ + ('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 " +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 += r" -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': ['scripts'], +} + +sanity_check_commands = ["vcfremap"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/v/voltools/voltools-0.4.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/v/voltools/voltools-0.4.2-foss-2020b.eb new file mode 100644 index 0000000000..e556409d9a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/voltools/voltools-0.4.2-foss-2020b.eb @@ -0,0 +1,28 @@ +# 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'), +] + +exts_list = [ + ('GPUtil', '1.4.0', { + 'modulename': 'GPUtil', + 'checksums': ['099e52c65e512cdfa8c8763fca67f5a5c2afb63469602d5dcb4d296b3661efb9'], + }), + (name, version, { + 'checksums': ['4a5382e194a2769676e7ec67143055444072d140c19d9b24dbb5ce014ee7a603'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d3ffd1ef9c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +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'), +] + +local_bins = ['oggdec', 'oggenc', 'ogginfo', 'vorbiscomment'] +sanity_check_paths = { + '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' diff --git a/easybuild/easyconfigs/__archive__/v/vt/vt-0.57721-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/v/vt/vt-0.57721-GCC-10.2.0.eb new file mode 100644 index 0000000000..f5b37df4b6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb b/easybuild/easyconfigs/__archive__/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb new file mode 100644 index 0000000000..161a212ba3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb @@ -0,0 +1,49 @@ +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'), +] + +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' +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' diff --git a/easybuild/easyconfigs/__archive__/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb new file mode 100644 index 0000000000..55747ac92b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 = 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 +prebuildopts += "sed -i 's/ -O / -O -fallow-argument-mismatch /g' configure.wps && " + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/w/WPS/WPS-4.2-foss-2020b-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WPS/WPS-4.2-foss-2020b-dmpar.eb new file mode 100644 index 0000000000..7161c17020 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb new file mode 100644 index 0000000000..9fea5e7036 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-foss-2020b-dmpar.eb @@ -0,0 +1,51 @@ +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-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 +builddependencies = [ + ('tcsh', '6.22.03'), + ('time', '1.9'), +] + +dependencies = [ + ('libtirpc', '1.3.1'), + ('JasPer', '2.0.24'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb new file mode 100644 index 0000000000..44a0736663 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-intel-2020b-dmpar.eb @@ -0,0 +1,51 @@ +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-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 +builddependencies = [ + ('tcsh', '6.22.03'), + ('time', '1.9'), +] + +dependencies = [ + ('libtirpc', '1.3.1'), + ('JasPer', '2.0.24'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb new file mode 100644 index 0000000000..20b645cfdb --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/w/Wannier90/Wannier90-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/w/Wannier90/Wannier90-3.1.0-foss-2020b.eb new file mode 100644 index 0000000000..bad8326376 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/w/Wannier90/Wannier90-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/w/Wannier90/Wannier90-3.1.0-intel-2020b.eb new file mode 100644 index 0000000000..ada3e6966d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/w/Wannier90/Wannier90-3.1.0-intel-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb b/easybuild/easyconfigs/__archive__/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb new file mode 100644 index 0000000000..52ef2ed493 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/w/WannierTools/WannierTools-2.5.1-intel-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'WannierTools' +version = '2.5.1' + +homepage = 'http://www.wanniertools.com' +description = """WannierTools is an open source software that studies the physical properties of given tight-binding + model.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/quanshengwu/wannier_tools/archive'] +sources = ['V%(version)s.tar.gz'] +patches = ['WannierTools-2.5.1_fix_Makefile.patch'] +checksums = [ + '22aad8e95f2da07ac2dd892c2ca0438010779e6cc542e30f34ea5c3f580fd72c', # V2.5.1.tar.gz + '1752319cad40fc258c5b9753baa9db4ca1c5a4d931234164d66212c7ba92f7cb', # WannierTools-2.5.1_fix_Makefile.patch +] + +skipsteps = ['configure'] + +prebuildopts = 'cd src && ' +preinstallopts = prebuildopts + +# use -cpp -fallow-argument-mismatch -ffree-line-length-512 for GNU based compilers +# use -fpp for Intel based compilers +# We use the same Makefile regardless of toolchain due to the Makefile patch +buildopts = '-f Makefile.intel-mpi F90FLAGS="$F90FLAGS -fpp -DMPI" ' +installopts = '-f Makefile.intel-mpi PREFIX=%(installdir)s ' + +# No dependecies in the Makefile +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/wt.x'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb new file mode 100644 index 0000000000..684b63bf29 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/w/WhatsHap/WhatsHap-1.1-foss-2020b.eb @@ -0,0 +1,47 @@ +# 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'), + ('pyfaidx', '0.5.9.5'), +] + +exts_list = [ + ('isal', '0.10.0', { + 'checksums': ['3f89471065c2837d1235877dbdcdbd8b7649068723026b0582010fa106a71ff3'], + }), + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f'], + }), +] + +sanity_check_paths = { + 'files': ['bin/whatshap'], + 'dirs': ['bin', 'lib'], +} + +sanity_check_commands = [ + 'whatshap --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/w/wget/wget-1.20.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/w/wget/wget-1.20.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a32a03e427 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/w/wget/wget-1.20.3-GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +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'), + ('Perl', '5.32.0'), +] +dependencies = [ + ('PCRE', '8.44'), + ('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 + # ('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) +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] +# 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' diff --git a/easybuild/easyconfigs/__archive__/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/w/wgsim/wgsim-20111017-GCC-10.2.0.eb new file mode 100644 index 0000000000..4fc09775ac --- /dev/null +++ b/easybuild/easyconfigs/__archive__/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -0,0 +1,33 @@ +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." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_ZIP}] +checksums = ['1180fdd1d66691da5634e8c98b78c4742d0faf10042f35c2d17d26844d550f1c'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Perl', '5.32.0'), +] + +cmds_map = [('.*', "$CC $CFLAGS -o %(name)s %(name)s.c $LDFLAGS -lz -lm")] + +files_to_copy = [(['wgsim', 'wgsim_eval.pl'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/wgsim', 'bin/wgsim_eval.pl'], + 'dirs': [], +} + +sanity_check_commands = ["wgsim -h 2>&1 | grep 'Program: wgsim (short read simulator)'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..6e3ea0c67a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/w/wxWidgets/wxWidgets-3.1.4-GCC-10.2.0.eb @@ -0,0 +1,70 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.1.4' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f2698297b2d2c6d2372c23144c133e531248a64286c78ae17179155c94971d6f'] + +builddependencies = [ + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.1.0'), + ('expat', '2.2.9'), + ('GTK+', '3.24.23'), + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('SDL2', '2.0.14'), + ('cairo', '1.16.0'), + ('GST-plugins-base', '1.18.4'), + ('GLib', '2.66.1'), +] + +local_cpath_ext = '$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' diff --git a/easybuild/easyconfigs/__archive__/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/X11/X11-20201008-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c5a69cfdb8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -0,0 +1,216 @@ +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'), + ('Doxygen', '1.8.20'), +] + +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': ['ab68b25341c99f2218d7cf3dad459c1827f411219901ade05bbccbdb856b6c8d'], + '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 + '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'], + }), + ('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' diff --git a/easybuild/easyconfigs/__archive__/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b6179c2306 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +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') +] + +modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} + +sanity_check_paths = { + 'files': ['lib/libxcfun.%s' % SHLIB_EXT], + 'dirs': ['include/XCFun'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb new file mode 100644 index 0000000000..e0adab5b26 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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 +] + +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'), +] + +maxparallel = 1 + +prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..f290b9d2c9 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'PerlBundle' + +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_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'], + }), + ('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'], + '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'], + '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/'], + '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'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..633fc22773 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -0,0 +1,54 @@ +## +# 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-5.2.5_fix-symbols.patch', + 'xz-5.2.5-cve-2022-1271.patch', +] +checksums = [ + {'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 = [ + # 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'), +] + +# 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/__archive__/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..3d942f68bf --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1d3d0f33d8 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/XlsxWriter/XlsxWriter-1.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +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'), +] + +sanity_check_paths = { + 'files': ['bin/vba_extract.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['vba_extract.py --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..43d07a3d4e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb @@ -0,0 +1,112 @@ +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, + }), +] + +# 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'], + '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' diff --git a/easybuild/easyconfigs/__archive__/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b74cb1a349 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +# 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': [], +} + +sanity_check_commands = ["x13as --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/x/x264/x264-20201026-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/x264/x264-20201026-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..c7bbcc82b2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/x264/x264-20201026-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +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'), + ('pkg-config', '0.29.2'), + ('NASM', '2.15.05'), +] + +configopts = " --enable-shared --enable-static --disable-bashcompletion" + +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/__archive__/x/x265/x265-3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/x265/x265-3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..1a0bb416da --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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/__archive__/x/xESMF/xESMF-0.3.0-intel-2020b.eb b/easybuild/easyconfigs/__archive__/x/xESMF/xESMF-0.3.0-intel-2020b.eb new file mode 100644 index 0000000000..f311ed6b71 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/xESMF/xESMF-0.3.0-intel-2020b.eb @@ -0,0 +1,21 @@ +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'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.2-foss-2020b.eb b/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.2-foss-2020b.eb new file mode 100644 index 0000000000..7a57ff6c68 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.2-foss-2020b.eb @@ -0,0 +1,21 @@ +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 +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.2-fosscuda-2020b.eb b/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.2-fosscuda-2020b.eb new file mode 100644 index 0000000000..0d73906af0 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.2-fosscuda-2020b.eb @@ -0,0 +1,23 @@ +# Author: Denis Krišťák (INUITS) + +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['38e8439d6c91bcd5b7c0fca349daf8e0643ac68850c987262d53526e9d7d01e4'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, pandas +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.2-intel-2020b.eb b/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.2-intel-2020b.eb new file mode 100644 index 0000000000..b106b0275b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.2-intel-2020b.eb @@ -0,0 +1,21 @@ +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'} + +sources = [SOURCE_TAR_GZ] +checksums = ['38e8439d6c91bcd5b7c0fca349daf8e0643ac68850c987262d53526e9d7d01e4'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, pandas +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb new file mode 100644 index 0000000000..100e2c2696 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/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 new file mode 100644 index 0000000000..1e938b9be2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/x/xorg-macros/xorg-macros-1.19.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/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/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/x/xprop/xprop-1.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/xprop/xprop-1.2.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..b1256f2c81 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.31-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..56ff7cb84e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/x/xxHash/xxHash-0.8.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/xxHash/xxHash-0.8.1-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d659f1192d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5f89705193 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +# 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 serves to convert 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 +] + +builddependencies = [ + ('binutils', '2.35'), +] + +start_dir = 'src/xxd' + +files_to_copy = [ + (['xxd'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/xxd'], + 'dirs': [], +} + +sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..8039b6ee3e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/y/YACS/YACS-0.1.8-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +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'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/y/YAXT/YAXT-0.9.0-gompi-2020b.eb b/easybuild/easyconfigs/__archive__/y/YAXT/YAXT-0.9.0-gompi-2020b.eb new file mode 100644 index 0000000000..7febddd76e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/y/YAXT/YAXT-0.9.0-gompi-2020b.eb @@ -0,0 +1,26 @@ +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://swprojects.dkrz.de/redmine/attachments/download/498/', + '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' diff --git a/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..4614e5786e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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://github.com/yasm/yasm/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d6c493931c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.6.0-foss-2020b.eb new file mode 100644 index 0000000000..2539d3a9c5 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -0,0 +1,51 @@ +# 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 = 'PythonBundle' + +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'} + +builddependencies = [('pkgconfig', '1.5.1', '-python')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('molmod', '1.4.8'), +] + +local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +local_runtest += "python setup.py build_ext -i; nosetests -v" + +exts_list = [ + # yaff v1.6.0 does not work with h5py>=3.0, the default version in foss/2020b + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + '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'], + }), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb b/easybuild/easyconfigs/__archive__/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb new file mode 100644 index 0000000000..3b5d31e99a --- /dev/null +++ b/easybuild/easyconfigs/__archive__/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb @@ -0,0 +1,49 @@ +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'), +] + +_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_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/z/Z3/Z3-4.8.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/z/Z3/Z3-4.8.10-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..90cab60b94 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..a9ef2d5ea6 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/z/Zip/Zip-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/z/Zip/Zip-3.0-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..16af667205 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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' diff --git a/easybuild/easyconfigs/__archive__/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..d65bafa85e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +# 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': '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'] +checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF', +] + +sanity_check_paths = { + 'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["zopfli --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/z/zarr/zarr-2.8.1-foss-2020b.eb b/easybuild/easyconfigs/__archive__/z/zarr/zarr-2.8.1-foss-2020b.eb new file mode 100644 index 0000000000..9776bc7590 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/z/zarr/zarr-2.8.1-foss-2020b.eb @@ -0,0 +1,37 @@ +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'), +] + +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'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..860d74ceb2 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/z/zfp/zfp-0.5.5-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 +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 = [ + ('binutils', '2.35'), +] + +prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " +buildopts = 'ZFP_WITH_OPENMP=1' + +runtest = 'test' + +files_to_copy = ['bin', 'include', 'lib'] + +sanity_check_paths = { + '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' diff --git a/easybuild/easyconfigs/__archive__/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..bf962cbf1d --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'] +checksums = ['eca3fe72aea7036c31d00ca120493923c4d5b99fe02e6d3322f7c88dbdcd0085'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +configopts = ' -DZLIB_ENABLE_TESTS=True ' + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..5a346a38f1 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb new file mode 100644 index 0000000000..ad7e1f5e18 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/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'