From dddbc9d1147e7c6d2abb6e5d6695d73a2d9a2df1 Mon Sep 17 00:00:00 2001 From: meesters Date: Fri, 13 Dec 2019 10:48:12 +0100 Subject: [PATCH 1/4] adding easyconfigs: Varlociraptor-1.5.0-GCCcore-8.3.0.eb --- .../Varlociraptor-1.5.0-GCCcore-8.3.0.eb | 95 +++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb new file mode 100644 index 000000000000..f6b37930d88b --- /dev/null +++ b/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb @@ -0,0 +1,95 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'Binary' + +name = 'Varlociraptor' +version = "1.5.0" + +homepage = 'https://varlociraptor.github.io/' +description = """Varlociraptor is a Flexible, uncertainty-aware variant calling program +with parameter free filtration via FDR control. + +Key Features include: +- Calls SNVs and indels in all length ranges (from small to structural) with a unified statistical model. +- The statistical model entails all possible sources of uncertainty. +- Resulting variant calls can be filtered by false discovery rate. No parameter tuning necessary. +- Maximum a posteriori allele frequency estimates are provided with each call. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/varlociraptor/varlociraptor/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = [] +builddependencies = [ + ('binutils', '2.31.1'), + ('Rust', '1.37.0'), + ('Clang', '8.0.0'), + ('zlib', '1.2.11'), + ('XZ', '5.2.4'), +] + +dependencies = [ + ('GSL', '2.5'), +] + +extract_sources = True + +install_cmd = "cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio'buildstats = [ +{ + "build_time": 291.3, + "command_line": ['--add-dummy-to-minimal-toolchains', "--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--containerpath='/cluster/easybuild/containers'", "--filter-deps='adwaita-icon-theme,Autoconf,Autogen,Automake,Autotools,babl,binutils,Bison,byacc,bzip2,cairo,Coreutils,cURL,DBus,dbus-glib,Doxygen,Dyninst,Exiv2,expat,flex,FLTK,fontconfig,fontsproto,freeglut,freetype,FTGL,glibc,glib2,gc,Gdk-Pixbuf,GEGL,gettext,gexiv2,Ghostscript,GL2PS,GLEW,GLib,glproto,GObject-Introspection,GPC,gperfguile,GraphicsMagick,gsettings-desktop-schemas,GTI,GTK+,GtkSourceView,GTS,Guile,HarfBuzz,help2man,hwloc,inputproto,intltool,itstool,JasPer,jhbuild,kbproto,libcroco,libctl,libdap,libdrm,libdwarf,libelf,libepoxy,libevent,libffi,libfontenc,libgd,libgeotiff,libglade,libGLU,libICE,libidn,Libint,libjpeg-turbo,libmypaint,libpciaccess,libpng,libpthread-stubs,libreadline,librsvg,libSM,LibTIFF,libtool,libunistring,libunwind,LibUUID,libX11,libXau,libXaw,libxcb,libXcursor,libXdamage,libXdmcp,libXext,libXfixes,libXfont,libXft,libXi,libXinerama,libxkbcommon,libxml2,libXmu,libXpm,libXrandr,libXrender,libxslt,libXt,libXtst,libyaml,LittleCMS,M4,makedepend,Mesa,motif,ncurses,nettle,numactl,nvidia,Pango,Perl,PCRE,PDT,pixman,pkgconfig,pkg-config,popt,pscom,PyCairo,PyGObject,qt,Qt,Qt5,randrproto,recordproto,renderproto,S-Lang,SQLite,SWIG,Tcl,Tk,texinfo,UDUNITS,util-linux,wget,wxPropertyGrid,wxWidgets,xbitmaps,xcb-proto,xcb-util,xcb-util-image,xcb-util-keysyms,xcb-util-renderutil,xcb-util-wm,xextproto,xineramaproto,X11,XKeyboardConfig,XML-Parser,xorg-macros,XZ,Yasm,YAXT,zlib'", '--group-writable-installdir', "--hide-deps='x264,x265,LAME,g2lib,g2clib,libmatheval'", "--include-easyblocks='/cluster/easybuild/customeasyblocks/*.py'", "--installpath='/cluster/easybuild'", "--job-backend-config='/cluster/easybuild/gc3pie.cfg'", "--job-cores='64'", "--job-max-walltime='5'", "--job-target-resource='nodeshort'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--optarch='{\\'dummy\\': \\'march=corei7 -mtune=bdver1\\', \\'GCC\\': \\'march=nehalem -mtune=bdver1\\', \\'Intel\\': \\'msse4.2\\', \\'PGI\\': \\'tp=nehalem\\'}'", "--packagepath='/cluster/easybuild/packages'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/nehalem/easyconfigs_nehalem.git'", "--robot-paths='/cluster/easybuild/nehalem/easyconfigs_nehalem:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--subdir-modules='nehalem/modules'", "--subdir-software='nehalem/software'", "--testoutput='/gpfs/fs1/home/meesters/easyconfigs/easybuild-build/Varlociraptor-1.3.0-GCCcore-8.3.0'", "--tmpdir='/cluster/easybuild/tmp'", "--umask='002'", '/gpfs/fs1/home/meesters/easyconfigs/Varlociraptor-1.3.0-GCCcore-8.2.0.eb'], + "core_count": 64, + "cpu_model": "AMD Opteron(TM) Processor 6272", + "cpu_speed": 2099.915, + "cpu_vendor": "AMD", + "easybuild-easyblocks_version": "4.0.1", + "easybuild-framework_version": "4.0.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/gpfs/fs1/cluster/easybuild/nehalem/software/compiler/GCCcore/8.3.0/bin/../libexec/gcc/x86_64-pc-linux-gnu/8.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-plugins --enable-gold=default --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/nehalem/software/compiler/GCCcore/8.3.0 --with-local-prefix=/cluster/easybuild/nehalem/software/compiler/GCCcore/8.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/8.3.0/dummy-/gcc-8.3.0/stage2_stuff; Thread model: posix; gcc version 8.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "a0005.mogon", + "install_size": 5137217, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.6.1810", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Oct 30 2018, 23:45:53) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)]", + "system_gcc_path": "/cluster/easybuild/nehalem/software/compiler/GCCcore/8.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1573737336, + "total_memory": 257761, +}, +{ + "build_time": 194.12, + "command_line": ['--add-dummy-to-minimal-toolchains', "--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--containerpath='/cluster/easybuild/containers'", "--filter-deps='adwaita-icon-theme,Autoconf,Autogen,Automake,Autotools,babl,binutils,Bison,byacc,bzip2,cairo,Coreutils,cURL,DBus,dbus-glib,Doxygen,Dyninst,Exiv2,expat,flex,FLTK,fontconfig,fontsproto,freeglut,freetype,FTGL,glibc,glib2,gc,Gdk-Pixbuf,GEGL,gettext,gexiv2,Ghostscript,GL2PS,GLEW,GLib,GLPK,glproto,GMP,GObject-Introspection,GPC,gperfguile,GraphicsMagick,gsettings-desktop-schemas,GTI,GTK+,GtkSourceView,GTS,Guile,HarfBuzz,help2man,hwloc,inputproto,intltool,itstool,JasPer,jhbuild,kbproto,libcroco,libctl,libdap,libdrm,libdwarf,libelf,libepoxy,libevent,libffi,libfontenc,libgd,libgeotiff,libglade,libGLU,libICE,libidn,Libint,libjpeg-turbo,libmypaint,libpciaccess,libpng,libpthread-stubs,libreadline,librsvg,libSM,LibTIFF,libtool,libunistring,libunwind,LibUUID,libX11,libXau,libXaw,libxcb,libXcursor,libXdamage,libXdmcp,libXext,libXfixes,libXfont,libXft,libXi,libXinerama,libxkbcommon,libxml2,libXmu,libXpm,libXrandr,libXrender,libxslt,libXt,libXtst,libyaml,LittleCMS,M4,makedepend,Mesa,motif,NASM,ncurses,nettle,numactl,nvidia,PCRE,PDT,pixman,pkgconfig,pkg-config,popt,PROJ,pscom,PyCairo,PyGObject,qt,Qt,Qt5,randrproto,recordproto,renderproto,S-Lang,SQLite,SWIG,Tcl,texinfo,Tk,UDUNITS,util-linux,wxPropertyGrid,xbitmaps,xcb-proto,xcb-util,xcb-util-image,xcb-util-keysyms,xcb-util-renderutil,xcb-util-wm,xextproto,xineramaproto,X11,XKeyboardConfig,XML-Parser,xorg-macros,XZ,Yasm,YAXT,zlib'", '--group-writable-installdir', "--hide-deps='x264,x265,LAME,g2lib,g2clib,libmatheval'", "--include-easyblocks='/cluster/easybuild/customeasyblocks/*.py'", "--installpath='/cluster/easybuild'", "--job-backend-config='/cluster/easybuild/gc3pie.cfg'", "--job-cores='40'", "--job-max-walltime='5'", "--job-target-resource='parallel'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--optarch='{\\'dummy\\': \\'march=core-avx2\\', \\'GCC\\': \\'march=broadwell -mtune=broadwell\\', \\'Intel\\': \\'xCORE-AVX2\\', \\'PGI\\': \\'tp=haswell\\'}'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/broadwell/easyconfigs_broadwell.git'", "--robot-paths='/cluster/easybuild/broadwell/easyconfigs_broadwell:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--subdir-modules='broadwell/modules'", "--subdir-software='broadwell/software'", "--testoutput='/gpfs/fs1/home/meesters/easyconfigs/easybuild-build/Varlociraptor-1.5.0-GCCcore-8.3.0'", "--tmpdir='/cluster/easybuild/tmp'", "--umask='002'", '/cluster/easybuild/tmp/eb-cntuml/tweaked_easyconfigs/Varlociraptor-1.5.0-GCCcore-8.3.0.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 2201.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "4.0.1", + "easybuild-framework_version": "4.0.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/broadwell/software/compiler/GCCcore/8.3.0/libexec/gcc/x86_64-pc-linux-gnu/8.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-plugins --enable-gold=default --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/broadwell/software/compiler/GCCcore/8.3.0 --with-local-prefix=/cluster/easybuild/broadwell/software/compiler/GCCcore/8.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/8.3.0/dummy-/gcc-8.3.0/stage2_stuff; Thread model: posix; gcc version 8.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "z0630.mogonii", + "install_size": 5393029, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.6.1810", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Oct 30 2018, 23:45:53) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)]", + "system_gcc_path": "/cluster/easybuild/broadwell/software/compiler/GCCcore/8.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1576229590, + "total_memory": 128819, +}, +] From 80d9834965551aa815c9d78381650a82818279ed Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Tue, 17 Dec 2019 09:07:02 +0100 Subject: [PATCH 2/4] Update Varlociraptor-1.5.0-GCCcore-8.3.0.eb --- .../v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb index f6b37930d88b..fb43c9e40c4c 100644 --- a/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb @@ -1,4 +1,4 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +# This easyconfig was created by Christian Meesters of the HPC team at the Johannes Gutenberg University of Mainz. easyblock = 'Binary' name = 'Varlociraptor' @@ -43,7 +43,9 @@ sanity_check_paths = { sanity_check_commands = ["%(namelower)s --help"] -moduleclass = 'bio'buildstats = [ +moduleclass = 'bio' + +buildstats = [ { "build_time": 291.3, "command_line": ['--add-dummy-to-minimal-toolchains', "--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--containerpath='/cluster/easybuild/containers'", "--filter-deps='adwaita-icon-theme,Autoconf,Autogen,Automake,Autotools,babl,binutils,Bison,byacc,bzip2,cairo,Coreutils,cURL,DBus,dbus-glib,Doxygen,Dyninst,Exiv2,expat,flex,FLTK,fontconfig,fontsproto,freeglut,freetype,FTGL,glibc,glib2,gc,Gdk-Pixbuf,GEGL,gettext,gexiv2,Ghostscript,GL2PS,GLEW,GLib,glproto,GObject-Introspection,GPC,gperfguile,GraphicsMagick,gsettings-desktop-schemas,GTI,GTK+,GtkSourceView,GTS,Guile,HarfBuzz,help2man,hwloc,inputproto,intltool,itstool,JasPer,jhbuild,kbproto,libcroco,libctl,libdap,libdrm,libdwarf,libelf,libepoxy,libevent,libffi,libfontenc,libgd,libgeotiff,libglade,libGLU,libICE,libidn,Libint,libjpeg-turbo,libmypaint,libpciaccess,libpng,libpthread-stubs,libreadline,librsvg,libSM,LibTIFF,libtool,libunistring,libunwind,LibUUID,libX11,libXau,libXaw,libxcb,libXcursor,libXdamage,libXdmcp,libXext,libXfixes,libXfont,libXft,libXi,libXinerama,libxkbcommon,libxml2,libXmu,libXpm,libXrandr,libXrender,libxslt,libXt,libXtst,libyaml,LittleCMS,M4,makedepend,Mesa,motif,ncurses,nettle,numactl,nvidia,Pango,Perl,PCRE,PDT,pixman,pkgconfig,pkg-config,popt,pscom,PyCairo,PyGObject,qt,Qt,Qt5,randrproto,recordproto,renderproto,S-Lang,SQLite,SWIG,Tcl,Tk,texinfo,UDUNITS,util-linux,wget,wxPropertyGrid,wxWidgets,xbitmaps,xcb-proto,xcb-util,xcb-util-image,xcb-util-keysyms,xcb-util-renderutil,xcb-util-wm,xextproto,xineramaproto,X11,XKeyboardConfig,XML-Parser,xorg-macros,XZ,Yasm,YAXT,zlib'", '--group-writable-installdir', "--hide-deps='x264,x265,LAME,g2lib,g2clib,libmatheval'", "--include-easyblocks='/cluster/easybuild/customeasyblocks/*.py'", "--installpath='/cluster/easybuild'", "--job-backend-config='/cluster/easybuild/gc3pie.cfg'", "--job-cores='64'", "--job-max-walltime='5'", "--job-target-resource='nodeshort'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--optarch='{\\'dummy\\': \\'march=corei7 -mtune=bdver1\\', \\'GCC\\': \\'march=nehalem -mtune=bdver1\\', \\'Intel\\': \\'msse4.2\\', \\'PGI\\': \\'tp=nehalem\\'}'", "--packagepath='/cluster/easybuild/packages'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/nehalem/easyconfigs_nehalem.git'", "--robot-paths='/cluster/easybuild/nehalem/easyconfigs_nehalem:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--subdir-modules='nehalem/modules'", "--subdir-software='nehalem/software'", "--testoutput='/gpfs/fs1/home/meesters/easyconfigs/easybuild-build/Varlociraptor-1.3.0-GCCcore-8.3.0'", "--tmpdir='/cluster/easybuild/tmp'", "--umask='002'", '/gpfs/fs1/home/meesters/easyconfigs/Varlociraptor-1.3.0-GCCcore-8.2.0.eb'], From e4b08e6810fa7dbddc9b3c9f91bdf1547016c0ed Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Tue, 17 Dec 2019 09:17:24 +0100 Subject: [PATCH 3/4] Update Varlociraptor-1.5.0-GCCcore-8.3.0.eb Well, if the build-stats give issues with the style requirements, they are now dropped. --- .../Varlociraptor-1.5.0-GCCcore-8.3.0.eb | 51 ------------------- 1 file changed, 51 deletions(-) diff --git a/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb index fb43c9e40c4c..0949076ed450 100644 --- a/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb @@ -44,54 +44,3 @@ sanity_check_paths = { sanity_check_commands = ["%(namelower)s --help"] moduleclass = 'bio' - -buildstats = [ -{ - "build_time": 291.3, - "command_line": ['--add-dummy-to-minimal-toolchains', "--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--containerpath='/cluster/easybuild/containers'", "--filter-deps='adwaita-icon-theme,Autoconf,Autogen,Automake,Autotools,babl,binutils,Bison,byacc,bzip2,cairo,Coreutils,cURL,DBus,dbus-glib,Doxygen,Dyninst,Exiv2,expat,flex,FLTK,fontconfig,fontsproto,freeglut,freetype,FTGL,glibc,glib2,gc,Gdk-Pixbuf,GEGL,gettext,gexiv2,Ghostscript,GL2PS,GLEW,GLib,glproto,GObject-Introspection,GPC,gperfguile,GraphicsMagick,gsettings-desktop-schemas,GTI,GTK+,GtkSourceView,GTS,Guile,HarfBuzz,help2man,hwloc,inputproto,intltool,itstool,JasPer,jhbuild,kbproto,libcroco,libctl,libdap,libdrm,libdwarf,libelf,libepoxy,libevent,libffi,libfontenc,libgd,libgeotiff,libglade,libGLU,libICE,libidn,Libint,libjpeg-turbo,libmypaint,libpciaccess,libpng,libpthread-stubs,libreadline,librsvg,libSM,LibTIFF,libtool,libunistring,libunwind,LibUUID,libX11,libXau,libXaw,libxcb,libXcursor,libXdamage,libXdmcp,libXext,libXfixes,libXfont,libXft,libXi,libXinerama,libxkbcommon,libxml2,libXmu,libXpm,libXrandr,libXrender,libxslt,libXt,libXtst,libyaml,LittleCMS,M4,makedepend,Mesa,motif,ncurses,nettle,numactl,nvidia,Pango,Perl,PCRE,PDT,pixman,pkgconfig,pkg-config,popt,pscom,PyCairo,PyGObject,qt,Qt,Qt5,randrproto,recordproto,renderproto,S-Lang,SQLite,SWIG,Tcl,Tk,texinfo,UDUNITS,util-linux,wget,wxPropertyGrid,wxWidgets,xbitmaps,xcb-proto,xcb-util,xcb-util-image,xcb-util-keysyms,xcb-util-renderutil,xcb-util-wm,xextproto,xineramaproto,X11,XKeyboardConfig,XML-Parser,xorg-macros,XZ,Yasm,YAXT,zlib'", '--group-writable-installdir', "--hide-deps='x264,x265,LAME,g2lib,g2clib,libmatheval'", "--include-easyblocks='/cluster/easybuild/customeasyblocks/*.py'", "--installpath='/cluster/easybuild'", "--job-backend-config='/cluster/easybuild/gc3pie.cfg'", "--job-cores='64'", "--job-max-walltime='5'", "--job-target-resource='nodeshort'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--optarch='{\\'dummy\\': \\'march=corei7 -mtune=bdver1\\', \\'GCC\\': \\'march=nehalem -mtune=bdver1\\', \\'Intel\\': \\'msse4.2\\', \\'PGI\\': \\'tp=nehalem\\'}'", "--packagepath='/cluster/easybuild/packages'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/nehalem/easyconfigs_nehalem.git'", "--robot-paths='/cluster/easybuild/nehalem/easyconfigs_nehalem:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--subdir-modules='nehalem/modules'", "--subdir-software='nehalem/software'", "--testoutput='/gpfs/fs1/home/meesters/easyconfigs/easybuild-build/Varlociraptor-1.3.0-GCCcore-8.3.0'", "--tmpdir='/cluster/easybuild/tmp'", "--umask='002'", '/gpfs/fs1/home/meesters/easyconfigs/Varlociraptor-1.3.0-GCCcore-8.2.0.eb'], - "core_count": 64, - "cpu_model": "AMD Opteron(TM) Processor 6272", - "cpu_speed": 2099.915, - "cpu_vendor": "AMD", - "easybuild-easyblocks_version": "4.0.1", - "easybuild-framework_version": "4.0.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/gpfs/fs1/cluster/easybuild/nehalem/software/compiler/GCCcore/8.3.0/bin/../libexec/gcc/x86_64-pc-linux-gnu/8.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-plugins --enable-gold=default --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/nehalem/software/compiler/GCCcore/8.3.0 --with-local-prefix=/cluster/easybuild/nehalem/software/compiler/GCCcore/8.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/8.3.0/dummy-/gcc-8.3.0/stage2_stuff; Thread model: posix; gcc version 8.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "a0005.mogon", - "install_size": 5137217, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.6.1810", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Oct 30 2018, 23:45:53) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)]", - "system_gcc_path": "/cluster/easybuild/nehalem/software/compiler/GCCcore/8.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1573737336, - "total_memory": 257761, -}, -{ - "build_time": 194.12, - "command_line": ['--add-dummy-to-minimal-toolchains', "--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--containerpath='/cluster/easybuild/containers'", "--filter-deps='adwaita-icon-theme,Autoconf,Autogen,Automake,Autotools,babl,binutils,Bison,byacc,bzip2,cairo,Coreutils,cURL,DBus,dbus-glib,Doxygen,Dyninst,Exiv2,expat,flex,FLTK,fontconfig,fontsproto,freeglut,freetype,FTGL,glibc,glib2,gc,Gdk-Pixbuf,GEGL,gettext,gexiv2,Ghostscript,GL2PS,GLEW,GLib,GLPK,glproto,GMP,GObject-Introspection,GPC,gperfguile,GraphicsMagick,gsettings-desktop-schemas,GTI,GTK+,GtkSourceView,GTS,Guile,HarfBuzz,help2man,hwloc,inputproto,intltool,itstool,JasPer,jhbuild,kbproto,libcroco,libctl,libdap,libdrm,libdwarf,libelf,libepoxy,libevent,libffi,libfontenc,libgd,libgeotiff,libglade,libGLU,libICE,libidn,Libint,libjpeg-turbo,libmypaint,libpciaccess,libpng,libpthread-stubs,libreadline,librsvg,libSM,LibTIFF,libtool,libunistring,libunwind,LibUUID,libX11,libXau,libXaw,libxcb,libXcursor,libXdamage,libXdmcp,libXext,libXfixes,libXfont,libXft,libXi,libXinerama,libxkbcommon,libxml2,libXmu,libXpm,libXrandr,libXrender,libxslt,libXt,libXtst,libyaml,LittleCMS,M4,makedepend,Mesa,motif,NASM,ncurses,nettle,numactl,nvidia,PCRE,PDT,pixman,pkgconfig,pkg-config,popt,PROJ,pscom,PyCairo,PyGObject,qt,Qt,Qt5,randrproto,recordproto,renderproto,S-Lang,SQLite,SWIG,Tcl,texinfo,Tk,UDUNITS,util-linux,wxPropertyGrid,xbitmaps,xcb-proto,xcb-util,xcb-util-image,xcb-util-keysyms,xcb-util-renderutil,xcb-util-wm,xextproto,xineramaproto,X11,XKeyboardConfig,XML-Parser,xorg-macros,XZ,Yasm,YAXT,zlib'", 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"--subdir-modules='broadwell/modules'", "--subdir-software='broadwell/software'", "--testoutput='/gpfs/fs1/home/meesters/easyconfigs/easybuild-build/Varlociraptor-1.5.0-GCCcore-8.3.0'", "--tmpdir='/cluster/easybuild/tmp'", "--umask='002'", '/cluster/easybuild/tmp/eb-cntuml/tweaked_easyconfigs/Varlociraptor-1.5.0-GCCcore-8.3.0.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 2201.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "4.0.1", - "easybuild-framework_version": "4.0.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/broadwell/software/compiler/GCCcore/8.3.0/libexec/gcc/x86_64-pc-linux-gnu/8.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-plugins --enable-gold=default --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/broadwell/software/compiler/GCCcore/8.3.0 --with-local-prefix=/cluster/easybuild/broadwell/software/compiler/GCCcore/8.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/8.3.0/dummy-/gcc-8.3.0/stage2_stuff; Thread model: posix; gcc version 8.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "z0630.mogonii", - "install_size": 5393029, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.6.1810", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Oct 30 2018, 23:45:53) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)]", - "system_gcc_path": "/cluster/easybuild/broadwell/software/compiler/GCCcore/8.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1576229590, - "total_memory": 128819, -}, -] From 1f3fded793a1fb41dd9ecad7fa680d2fca1c9d5a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 18:42:03 +0100 Subject: [PATCH 4/4] update (build) dependencies in Varlociraptor easyconfig to match easyconfigs already in `develop` branch --- .../v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb index 0949076ed450..524ec3da0d77 100644 --- a/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/v/Varlociraptor/Varlociraptor-1.5.0-GCCcore-8.3.0.eb @@ -21,15 +21,15 @@ source_urls = ['https://github.com/varlociraptor/varlociraptor/archive'] sources = ['v%(version)s.tar.gz'] checksums = [] builddependencies = [ - ('binutils', '2.31.1'), + ('binutils', '2.32'), ('Rust', '1.37.0'), - ('Clang', '8.0.0'), + ('Clang', '9.0.1'), ('zlib', '1.2.11'), ('XZ', '5.2.4'), ] dependencies = [ - ('GSL', '2.5'), + ('GSL', '2.6'), ] extract_sources = True