diff --git a/.gitignore b/.gitignore index ed706988e3a820cd998275e2c62e9d2c7bb4a7d5..03b321d42a13463aecdc627e57380795114ad853 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,7 @@ .project LICENSE_HEADER *.pyc +*.pyo *.nja build/ dist/ diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000000000000000000000000000000000000..127edacd18f78a497ee4043a8a596b93812079ad --- /dev/null +++ b/.travis.yml @@ -0,0 +1,38 @@ +language: python +python: 2.6 +env: + matrix: + - ENV_MOD_VERSION=3.2.10 + - LMOD_VERSION=5.6.3 EASYBUILD_MODULES_TOOL=Lmod + - LMOD_VERSION=6.3.1 EASYBUILD_MODULES_TOOL=Lmod EASYBUILD_MODULE_SYNTAX=Lua +matrix: + # mark build as finished as soon as job has failed + fast_finish: true + include: + # also test default configuration with Python 2.7 + - python: 2.7 + env: ENV_MOD_VERSION=3.2.10 +addons: + apt: + packages: + - tcl8.5 +install: + # required for test_dep_graph + - pip install python-graph-core python-graph-dot + # install easybuild-framework/easybuild-easyblocks (and dependencies) + # use 'develop' branch of framework/easyblocks, except when testing 'master' + - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - cd $HOME + - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-framework.git + - cd easybuild-framework; git log -n 1; cd - + - easy_install $PWD/easybuild-framework + - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-easyblocks.git + - cd easybuild-easyblocks; git log -n 1; cd - + - easy_install $PWD/easybuild-easyblocks + # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework + - if [ ! -z $ENV_MOD_VERSION ]; then source $(which install_eb_dep.sh) modules-${ENV_MOD_VERSION} $HOME; fi + - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi + - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) Lmod-${LMOD_VERSION} $HOME; fi +script: + - export PYTHONPATH=$TRAVIS_BUILD_DIR + - python -O -m test.easyconfigs.suite diff --git a/README.rst b/README.rst index becdc63ccbda9e17041091f9c49c75724cbea14c..b6fcf302e98c2dbb4b3f29e119d21cb445f7a37d 100644 --- a/README.rst +++ b/README.rst @@ -34,22 +34,12 @@ Related Python packages: *Build status overview:* -* **master** branch *(Python 2.4, Python 2.6, Python 2.7)* +* **master** branch: - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python24/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python24/ + .. image:: https://travis-ci.org/hpcugent/easybuild-easyconfigs.svg?branch=master + :target: https://travis-ci.org/hpcugent/easybuild-easyconfigs/branches - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master/ +* **develop** branch: - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python27/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python27/ - -* **develop** branch *(Python 2.4, Python 2.6, Python 2.7)* - - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python24/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python24/ - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop/ - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python27/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python27/ + .. image:: https://travis-ci.org/hpcugent/easybuild-easyconfigs.svg?branch=develop + :target: https://travis-ci.org/hpcugent/easybuild-easyconfigs/branches diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b5c225454e3fd529cccc356c15a7db34c82a0d7a..2b32873f47d07c495a09f592041bdacdbe96f10c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,89 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 5,580 easyconfig files, for 862 different software packages, -34 different (compiler) toolchains, 12 software bundles and 1 meta-package. +The latest version of easybuild-easyconfig provides 6,193 easyconfig files, for 944 different software packages, +37 different (compiler) toolchains, 12 software bundles and 1 meta-package. + + +v2.8.1 (May 30th 2016) +---------------------- + +- added example easyconfig files for 13 new software packages: + drFAST (#906), git-lfs (#2478), grabix (#3127), JWM (#3007), libcroco (#3007), librsvg (#3007), MaCH (#3136), + mayavi (#3106), OpenMM (#2762), Pysam (#3080), SeqPrep (#3097), vt (#3128), wkhtmltopdf (#3098) +- added new easyconfigs for existing toolchains: intel/2016.03-GCC-4.9 (#3088) +- added additional easyconfigs for various supported software packages, including: + Boost 1.61.0, ESMF 7.0.0, Inspector 2016 update 3, IPython 4.2, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, Perl 5.22.2, VTune 2016 update 3 +- various bug fixes, including: + - apply libreadline patch to fix bug triggering segmentation fault (#3086) + + +v2.8.0 (May 18th 2016) +---------------------- + +feature + bugfix release +- added example easyconfig files for 69 new software packages: + ALPS (#2888), annovar (#3010), BayeScEnv (#2765), BayesAss (#2870), BerkeleyGW (#2925), Blitz++ (#2784, #3004), + bam-readcount (#2850), Commet (#2938), CrossTalkZ (#2939), cuDNN (#2882), DBus (#2855), DFT-D3 (#2107), + DIAL (#3056), dask (#2885), dbus-glib (#2855), FFLAS-FFPACK (#2793), FLAC (#2824), FLANN (#3015, #3029), + FLEUR (#3043), GConf (#2855), GROMOS++ (#1297), GST-plugins-base (#2855), GStreamer (#2855), GTOOL (#2805), + Givaro (#2793), gdist (#2935), gromosXX (#1297), HISAT2 (#2809), i-PI (#2940), Kraken (#3037, #3041), LAME (#2823), + LASTZ (#3002), LinBox (#2793), Loki (#2839), libQGLViewer (#2923, #3008), libXxf86vm (#2855), + MDSplus (#2787, #2838, #3027), MRIcron (#2831), Mawk (#2732), minieigen (#2839), mpmath (#3058), NBO (#3047, 3048), + NGS (#2803), NGS-Python (#2810), ncbi-vdb (#2808), OptiX (#2795), PCL (#3024), PEAR (#2731), PLplot (#2990), + Postgres-XL (#2891), PyGTS (#2969), RSeQC (#2788), Rust (#2920, #2943), rainbow (#2730), SHAPEIT (#2806), + SIONlib (#2908), Saxon-HE (#2773), Singularity (#2901), SoX (#2825), Subread (#2790), SuperLU (#2665), + travis (#2953), VASP (#2950), Wannier90 (#2906, #3042), wget (#3041), wxPython (#2855), xf86vidmodeproto (#2855), + Yade (#2839), Yambo (#2932) +- add test configuration for Travis (#2942, #2944, #2954, #3061) +- added easyconfigs for new PGI-based toolchains + - pomkl/2016.03 (#2899, #2900, #3046), pomkl/2016.04 (#3044), CrayPGI/2016.04 (#2927) +- added new easyconfigs for existing toolchains: + foss/2016.04 (#3013), intel/2016.02-GCC-5.3 (#2523), intel/2016.03-GCC-5.3 (#3009) +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + incl. CGAL 4.8, Clang 3.8.0, icc/ifort 2016.2.181 & 2016.3.210, imkl 11.3.2.181 & 11.3.3.210, impi 5.1.3.181, + LLVM 3.8.0, OpenCV 2.4.12, pandas 0.18.0, Qt 5.6.0, Scalasca 2.3, Score-P 2.0.1, SuiteSparse 4.5.2, WRF 3.8 +- various other enhancements, including: + - enhance ORCA easyconfig for compatibility with SLURM (#1819) + - enable -fPIC in GraphicsMagick easyconfig, required by Octave (#2764) + - clean up binutils easyconfigs to use binutils easyblock (#3006) + - add include/GraphicsMagick to $CPATH in GraphicsMagick easyconfigs (#3034) + - update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (#3050) +- various bug fixes, including: + - fix Perl extensions download urls (#2738) + - add Autoconf as build dep for GCCcore (#2772) + - fix versions of extensions in Bioconductor 3.2 bundles (#2769) + - fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender (#2785, #2874) + - use 'env' wherever preconfig/build/installopts is used to set environmental variables (#2807, #2811, #2812) + - add zlib as explicit dep in Tk easyconfigs (#2815) + - consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#2774, #2779, #2816) + - fix homepage and description in Pygments easyconfigs (#2822) + - include pkg-config as build dependencies for libXau, libXdmcp, libxcb (#2827) + - consistently use XORG_*_SOURCE constants (#2829, #2830, #2848) + - update source URLs in ScientificPython easyconfig files (#2847) + - add checksums in SuiteSparse easyconfigs (#2849) + - fix build deps for GObject-Introspection (#2852) + - correctly specify Perl location in git easyconfig (#2866) + - fix bitstring 3.1.3 download URL in Python easyconfigs, source tarball on PyPI disappeared (#2880) + - fix Perl dependency in worker easyconfig, it requires non-standard Perl modules (#2884) + - add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma (#2887) + - fix download URL for packmol (#2902) + - drop usempi toolchain in numexpr easyconfigs, not needed (#2937) + - fix use of resolve_dependencies in tests according to changes in framework (#2952) + - add dependency extensions for MarkupSafe and jsonscheme in IPython 3.2.3 easyconfigs (#2967) + - add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being used (#2971) + - add xproto build dependency for makedepend v1.0.5 (#2982) + - disable parallel build for Doxygen (#2986) + - fix source URLs for FreezeThaw and Tie::Function extensions for Perl v5.22.1 (#2988) + - add sed command in worker easyconfig files to fix module_path in conf/worker.conf (#2997, #3000) + - drop toolchainopts from Eigen easyconfigs, since it is headers-only (#3025) + - clean up dummy bzip2 easyconfig, define buildopts rather than defining $CC and $CFLAGS via os.environ (#3036) + - use %(pyshortver)s template rather than hardcoding 2.7 in VTK easyconfigs (#3052) + - correct install location of OpenCV Python bindings (#3054) + - include XZ as dependency for libunwind (#3055) + - add patch to fix broken OpenSSL tests due to expired certificates (#3057) + - fix broken link to VSC website in license headers (#3062) + v2.7.0 (March 20th 2016) ------------------------ diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb new file mode 100644 index 0000000000000000000000000000000000000000..9651451f5dea4dfe36455f49d671a8eef4537da1 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = "7.10.5" +versionsuffix = "-libxc" + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# ensure mpi and intel toolchain +configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' +configopts += '--with-fft-flavor=fftw3-mkl ' +configopts += '--with-fft-libs="$LIBFFT" ' + +# libxc variant +configopts += '--with-dft-flavor=libxc ' + +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/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..d13b10cfefc211c5453329c298bddcb32c7e0ff8 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = "7.10.5" + +homepage = 'http://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': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# ensure mpi and intel toolchain +configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' +configopts += '--with-fft-flavor=fftw3-mkl ' +configopts += '--with-fft-libs="$LIBFFT"' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb index 20c30c8e6291466a063743c95a346c88a54af5b8..6b5c1c6d525616ee6854448663e4077c8042721d 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb @@ -31,7 +31,7 @@ dependencies = [ ('Boost', '1.58.0', versionsuffix), ] -preconfigopts = 'CPPFLAGS=-I$EBROOTSPARSEHASH/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTSPARSEHASH/include' sanity_check_paths = { 'files': ["bin/ABYSS", "bin/ABYSS-P"], diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa09a6e789d150412b669eeede3fcf142adbe66d --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Maxime Schmitt , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.9.0' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] + +dependencies = [ + ('Boost', '1.60.0'), + ('sparsehash', '2.0.2'), + ('SQLite', '3.9.2'), +] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20160329-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20160329-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..f69d4cd5999f79d6d6ceed458cffcef06b53a087 --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20160329-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,64 @@ +easyblock = 'ConfigureMake' + +name = 'AFNI' +version = '20160329' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://afni.nimh.nih.gov/' +description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - + a technique for mapping human brain activity.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True, 'pic': True} + +# download afni_src.tgz manually from http://afni.nimh.nih.gov/pub/dist/tgz/, and rename to include datestamp +# detailed release notes are available at http://afni.nimh.nih.gov/pub/dist/doc/misc/history/afni_hist_level1_all.html +# but last update doesn't match datestamp of most recent afni_src.tgz? +sources = ['afni_src-%(version)s.tgz'] +checksums = ['f6a1fd2893ad9963ffd4356ccdc1ae4b'] + +patches = ['AFNI-20150717_omp-pragma-statement-fix.patch'] + +dependencies = [ + ('tcsh', '6.19.00'), + ('Python', '2.7.11'), + ('libXp', '1.0.3'), + ('libXt', '1.1.5'), + ('libXpm', '3.5.11'), + ('libXmu', '1.1.2'), + ('motif', '2.3.5'), + ('R', '3.2.3'), + ('PyQt', '4.11.4', versionsuffix), + ('expat', '2.1.0'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('GSL', '2.1'), + ('GLib', '2.47.5'), # must match version used in Qt (via PyQt) + ('zlib', '1.2.8'), +] + +skipsteps = ['configure', 'install'] + +prebuildopts = "cp Makefile.linux_openmp_64 Makefile && " +buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%(pyshortver)s" ' +buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' +buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%(pyshortver)s ' +buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"' +buildopts += ' INSTALLDIR=%(installdir)s' + +parallel = 1 + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['afni'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..74ee42be3ad41f0b23d37952c1422e7f681e2808 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'ALPS' +version = '2.2.b4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.example.com' +description = """ The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort +aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ +libraries for simplifying the development of such code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://alps.comp-phys.org/static/software/releases'] + +patches = ['ALPS-%(version)s-python-embedding.patch'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), + ('Python', '2.7.11'), + ('Boost', '1.58.0', versionsuffix), + ('HDF5', '1.8.16'), + ('matplotlib', '1.5.1', versionsuffix), +] + +configopts = '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/alpspython', 'lib/libalps.%s' % SHLIB_EXT], + 'dirs': ['include/alps', 'lib/python'] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch new file mode 100644 index 0000000000000000000000000000000000000000..5927e2e7847e78efa9fafdc6bf23efe27faf9a2b --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch @@ -0,0 +1,14 @@ +# To embed python, it must return a list of needed libraries with `;` instead of whitespace +# Ward Poelmans +diff -ur alps-2.2.b4-src.orig/alps/config/FindPython.cmake alps-2.2.b4-src/alps/config/FindPython.cmake +--- alps-2.2.b4-src.orig/alps/config/FindPython.cmake 2015-09-20 21:21:42.000000000 +0200 ++++ alps-2.2.b4-src/alps/config/FindPython.cmake 2016-04-20 11:28:18.828407677 +0200 +@@ -160,7 +160,7 @@ + # + # libraries which must be linked in when embedding + # +- EXEC_PYTHON_SCRIPT ("from distutils.sysconfig import * ;print (str(get_config_var('LOCALMODLIBS')) + ' ' + str(get_config_var('LIBS'))).strip()" ++ EXEC_PYTHON_SCRIPT ("from distutils.sysconfig import * ;print (str(get_config_var('LOCALMODLIBS')) + ' ' + str(get_config_var('LIBS'))).strip().replace(' ', ';')" + PYTHON_EXTRA_LIBS) + MESSAGE(STATUS "PYTHON_EXTRA_LIBS =${PYTHON_EXTRA_LIBS}" ) + mark_as_advanced(PYTHON_EXTRA_LIBS) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..ddbfe7c0922a88321be2052c0e0095df494923ac --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = "2.7.7" +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +source_urls = ['http://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_includes.patch'] + +dependencies = [ + ('Java', '1.8.0_74', '', True), + ('Python', '2.7.11'), +] + +configopts = '--disable-examples --disable-csharp ' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..a8183634de3fccf5e81ba18107e3bfb35e35490d --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2c8911864b07d3faaad3700b8db2b80efc349c6f --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.20.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +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': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb new file mode 100644 index 0000000000000000000000000000000000000000..9eab720e748108f354c9cb5b97af2eeefe336b03 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb @@ -0,0 +1,41 @@ +# +# modified by Stephane Thiell (Stanford University) for Amber v14 +# +# author: Benjamin P. Roberts (University of Auckland) +# +# based on work by Marios Constantinou (University of Cyprus) +# +name = 'Amber' +version = '14' + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': False, 'usempi': True} + +ambertools_ver = '15' +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%(version)s_fix-hardcoding.patch', + 'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver, +] + +dependencies = [ + ('CUDA', '7.5.18', '', True), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +patchlevels = (13, 13) +patchruns = 1 + +versionsuffix = '-AmberTools-%s-patchlevel-%d-%d' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-14_fix-hardcoding.patch b/easybuild/easyconfigs/a/Amber/Amber-14_fix-hardcoding.patch new file mode 100644 index 0000000000000000000000000000000000000000..6f4b9b5047fb4597c09086597c706e1e0233af74 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-14_fix-hardcoding.patch @@ -0,0 +1,173 @@ +fix hardcoding of compilers & MKL lib dir, add support for separate netCDF-Fortran installation & recent CUDA +author: Stephane Thiell (Stanford University) +--- amber14/AmberTools/src/cpptraj/configure.orig 2015-11-25 21:25:27.219014394 -0800 ++++ amber14/AmberTools/src/cpptraj/configure 2015-11-25 21:26:36.935069823 -0800 +@@ -676,9 +676,9 @@ fi + if [[ $USEMPI -eq 1 ]] ; then + echo "Using MPI" + DIRECTIVES="$DIRECTIVES -DMPI" +- CC=mpicc +- CXX=mpicxx +- FC=mpif90 ++ CC=${CC} ++ CXX=${CXX} ++ FC=${F90} + SFX=".MPI" + fi + +--- amber14/AmberTools/src/configure2.orig 2015-11-25 21:18:37.473056279 -0800 ++++ amber14/AmberTools/src/configure2 2015-11-27 00:05:54.009556748 -0800 +@@ -385,6 +385,7 @@ mpinab='' + mpi='no' + mtkpp='install_mtkpp' + netcdf_dir='' ++netcdf_fort_dir='' + netcdf_flag='' + netcdfstatic='no' + noX11='false' +@@ -442,6 +443,7 @@ while [ $# -gt 0 ]; do + -lio) lio='yes' ;; + --with-python) shift; python="$1";; + --with-netcdf) shift; netcdf_dir="$1";; ++ --with-netcdf-fort) shift; netcdf_fort_dir="$1";; + -netcdfstatic) netcdfstatic='yes' ;; + -dragonegg) shift; dragonegg="$1";; + -g95) g95='yes' ;; +@@ -594,7 +596,7 @@ flibs="-larpack -llapack -lblas " + # Fortran versions, if compiled from source: + flibsf="-larpack -llapack -lblas" + # only used when the user requests a static build: +-staticflag='-static' ++staticflag='-static-intel' + omp_flag= + mpi_flag= + lex=flex +@@ -861,13 +863,13 @@ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPXP + echo "CUDA Version $cudaversion detected" + echo "Configuring for SM2.0 and SM3.0 - warning does not support Maxwell (GM200/GM204) cards [e.g. GTX970/980]" + nvccflags="$sm20flags $sm30flags" +- elif [ "$cudaversion" = "6.5" ]; then ++ elif [ "$cudaversion" = "6.5" -o "$cudaversion" = "7.0" -o "$cudaversion" = "7.5" ]; then + echo "CUDA Version $cudaversion detected" + echo "Configuring for SM2.0, SM3.0 and SM5.0" + nvccflags="$sm20flags $sm30flags $sm50flags" + else + echo "Error: Unsupported CUDA version $cudaversion detected." +- echo " AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5" ++ echo " AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.0 .or. 7.5" + exit 1 + fi + nvcc="$nvcc $nvccflags" +@@ -1058,7 +1060,7 @@ gnu) + fi + if [ "$mpi" = 'yes' -a "$intelmpi" = 'no' ]; then + if [ "$intelmpi" = 'no' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + fi + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" +@@ -1354,7 +1356,7 @@ intel) + fi + + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$pmemd_coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1630,7 +1632,7 @@ EOF + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1880,7 +1882,7 @@ clang) + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1947,17 +1949,17 @@ if [ -n "$MKL_HOME" ]; then + blas=skip + flibs="-larpack " + flibsf="-larpack " +- mkll="$MKL_HOME/lib/32" ++ mkll="$MKL_HOME/mkl/lib/32" + mkl_processor="32" + mkl_procstring="ia32" + mklinterfacelayer='libmkl_intel.a' + if [ "$x86_64" = 'yes' ]; then +- if [ -d "$MKL_HOME/lib/em64t" ]; then +- mkll="$MKL_HOME/lib/em64t" ++ if [ -d "$MKL_HOME/mkl/lib/em64t" ]; then ++ mkll="$MKL_HOME/mkl/lib/em64t" + mkl_processor="em64t" + mkl_procstring="em64t" + else +- mkll="$MKL_HOME/lib/intel64" ++ mkll="$MKL_HOME/mkl/lib/intel64" + mkl_processor="intel64" + mkl_procstring="intel64" + fi +@@ -2374,8 +2376,13 @@ if [ "$bintraj" = 'yes' ]; then + else + # A NetCDF directory was specified. Check that library exists and compiles + printf "\tUsing external NetCDF in '$netcdf_dir'\n" ++ # Support separate NetCDF-Fortran installation with --with-netcdf-fort ++ if [ ! -e "$netcdf_fort_dir" ]; then ++ netcdf_fort_dir="$netcdf_dir" ++ fi ++ printf "\tUsing external NetCDF-Fortran in '$netcdf_fort_dir'\n" + netcdf_flag="-L${netcdf_dir}/lib $netcdf_flag" +- netcdf=$netcdf_dir"/include/netcdf.mod" ++ netcdf=$netcdf_fort_dir"/include/netcdf.mod" + if [ ! -e "$netcdf" ]; then + echo "Error: '$netcdf' not found." + exit 1 +@@ -2385,7 +2392,7 @@ if [ "$bintraj" = 'yes' ]; then + netcdfflagc="-L${netcdf_dir}/lib -lnetcdf" + # Newer versions of NetCDF have a separate fortran library. + # If not found default to libnetcdf.a +- netcdfflagf=$netcdf_dir"/lib/libnetcdff" ++ netcdfflagf=$netcdf_fort_dir"/lib/libnetcdff" + if [ ! -e "${netcdfflagf}.a" -a ! -e "${netcdfflagf}.so" ]; then + echo "Does not exist!" + netcdfflagf=$netcdfflagc +@@ -2399,7 +2406,7 @@ if [ "$bintraj" = 'yes' ]; then + echo "Error: '$netcdfflagc' not found." + exit 1 + fi +- netcdfflagf=$netcdf_dir"/lib/libnetcdff.a" ++ netcdfflagf=$netcdf_fort_dir"/lib/libnetcdff.a" + if [ ! -e "$netcdfflagf" ]; then + netcdfflagf=$netcdfflagc + fi +@@ -2814,14 +2821,14 @@ if [ "$mpi" = 'yes' ]; then + cplusplus="CC" + mpi_flag="-DMPI " + elif [ "$intelmpi" = 'yes' ]; then +- cc="mpiicc" +- fc="mpiifort" +- cplusplus="mpiicpc" +- mpi_flag="-DMPI " ++ cc=${CC} ++ fc=${F90} ++ cplusplus=${CXX} ++ mpi_flag="-DMPI " + else +- cc="mpicc" +- cplusplus="mpicxx" +- fc="mpif90" ++ cc=${CC} ++ fc=${F90} ++ cplusplus=${CXX} + mpi_flag="-DMPI " + + # Catch a corner-case of unusually setup intel compilers. diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-15_fix-mdgx-print-bug.patch b/easybuild/easyconfigs/a/Amber/AmberTools-15_fix-mdgx-print-bug.patch new file mode 100644 index 0000000000000000000000000000000000000000..20f849b0561528690fff33a38083aae0f97511b8 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/AmberTools-15_fix-mdgx-print-bug.patch @@ -0,0 +1,16 @@ +fix for hanging mdgx test (Test.1p7e) on long installation paths, backported from AmberTools 16 +author: David Cerutti +--- amber14/AmberTools/src/mdgx/Manual.c.orig 2016-06-10 11:39:47.719576723 +0200 ++++ amber14/AmberTools/src/mdgx/Manual.c 2016-06-10 11:41:16.670677715 +0200 +@@ -142,9 +142,10 @@ + endfound = 0; + j = 0; + while (endfound == 0) { ++ vpivot = j + width; + for (i = 0; i < width; i++) { + if (vpar[j+i] == ' ') { +- i++; ++ i++; + vpivot = j+i; + } + if (vpar[j+i] == '\0') { diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..e627b672b4451bad6041a56059c51a52bba44605 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://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': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..cc76e86a614a0d17a50fa30e2acc6c5304ee3025 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..84750fffa92820d228e1f43b4f9dfbc5cb4fc9c4 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..36c5a28f14d66d20ead85ae92b06d5dda2e3182c --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..65fd1e93a3296a9428c993408ca51828287febc8 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb index 13ae69456f14f9b397dee2e18014a038485d63fc..916fcd7e489fe5b0f1ca868922f66c92f0eca2c2 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb index 5144a9afc901faa64dee9d0f7f8b97e9d19d113a..97e5c8330bb93f9f763c58fa72f552580a4ca366 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb index 3b963e0d7e42a1d6dd9636c168d29da03b83a077..74f9dffca6ad13347f80125b7c61acc369eb7231 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb index f6a35a3dc06198a1d27febe9d36da9ae1e35768d..efd5845e70b2ae97f41ef3d71024890ea99d77d6 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..e14e02289183e6aa2497c43b99987f83f91784e2 --- /dev/null +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'annovar' +# Unconventional version is taken from the upstream site +# http://annovar.openbioinformatics.org/en/latest/user-guide/download/ +version = '2016Feb01' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://annovar.openbioinformatics.org/en/latest/' +description = """ ANNOVAR is an efficient software tool to utilize update-to-date information + to functionally annotate genetic variants detected from diverse genomes (including human + genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# Registration required for download +# http://www.openbioinformatics.org/annovar/annovar_download_form.php +# rename after download to %(name)s-%(version)s.tar.gz +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['2b26e514c54a847bfdcf4ce57e43f95c'] + +dependencies = [('Perl', '5.22.1')] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'dirs': ["example", "humandb"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6d469bdd3bfdf8170b2cbb1329fd00c1b6e73eda --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.3' + +homepage = 'http://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': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [ + ('HTSlib', '1.3'), + ('zlib', '1.2.8'), + ('GSL', '2.1'), +] + +parallel = 1 + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1' +installopts = ' prefix=%(installdir)s' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/plugins', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['lib/plugins'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..056a4ca4d8b15e63885702028f62781a1b04d084 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BCFtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """BCFtools is a set of utilities that manipulate variant calls in the + Variant Call Format (VCF) and its binary counterpart BCF""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '1.16'), +] + +buildopts = " USE_GPL=1 GSL_LIBS='-lgsl -lgslcblas'" + +runtest = 'test' + +files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"), + "doc", "plugins", "test", "LICENSE", "README", "AUTHORS"] + +sanity_check_paths = { + 'files': ["bin/bcftools"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..50f76cdae7065ab6b201133efa8e0b9d005bf7d3 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb @@ -0,0 +1,33 @@ +# 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 = '2.25.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """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': 'foss', 'version': '2015b'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..89147e0b2075048bb79ed7c0827f6229e61417df --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.25.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..88e524cd9dfc39177028a262b3c02da8cac42f2a --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.15' + +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': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..7a976185d2b1cde165fca93e9e87cbe80335db4e --- /dev/null +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BayeScEnv' +version = '1.1' + +homepage = 'https://github.com/devillemereuil/bayescenv' +description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/devillemereuil/bayescenv/archive/'] +sources = ['v%(version)s.tar.gz'] + +start_dir = 'source' + +files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/bayescenv'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0dc4a540af75aeeb1671168000928c0badaa7da6 --- /dev/null +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'BayesAss' +version = '3.0.4' + +homepage = 'http://www.rannala.org/?page_id=245' +description = """ +BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes +""" + +toolchain = {'name': 'foss','version': '2016a'} +sources = ['BA3-%(version)s.tar.gz'] + +source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/'] + +dependencies = [ + ('GSL','2.1') +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/BA3'], + 'dirs' : ['bin', 'include'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..484da63909cf76bf4f8ad53154161fe0b0f837e8 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'Beast' +version = '2.4.0' + +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': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%(version)s.Linux.tgz'] + +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', '2.1.2'), +] + +sanity_check_paths = { + 'files': ["bin/beast"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..5afb842c806f0011366ad25d2fd7544e65143a85 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'BerkeleyGW' +version = "1.0.6" + +homepage = 'http://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': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] +sources = ['BGW-%(version)s.tar.gz'] +checksums = ['8740562da41e87a62eb8d457675e4bfd'] + +skipsteps = ['configure'] + +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' + +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' +buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' + +installopts = 'INSTDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/'+prog+'.'+flavor+'.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] + for flavor in ['real', 'cplx']], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..9d064dae20430ed745791509ebf355d9d5b0b99c --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'BerkeleyGW' +version = "1.1-beta2" + +homepage = 'http://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] +sources = ['BGW-%(version)s.tar.gz'] +checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] + +skipsteps = ['configure'] + +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' + +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' +buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' + +installopts = 'INSTDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/'+prog+'.'+flavor+'.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] + for flavor in ['real', 'cplx']], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..d62e2cbb8823c0787bf2bc24c9cf66135246bc84 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,40 @@ +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.6.924' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.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': 'foss', 'version': '2016a'} + +# this is a bundle of Perl modules +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +dependencies = [ + ('Perl', '5.22.1'), + ('DB_File', '1.835', versionsuffix), +] + +exts_list = [ + # CGI has been removed from the Perl core since version 5.22 + ('CGI', '4.28', { + 'source_tmpl': 'CGI-4.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + }), + (name, version, { + 'modulename': 'Bio::Perl', + 'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'), + 'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..a42f248efeb46bf4dd8e0f662f640fcf7dc6273d --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = "PythonPackage" + +name = 'Biopython' +version = '1.65' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://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': '2016a'} + +source_urls = ['http://biopython.org/DIST'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.11') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..159751eac59fc77d31b944be15bb14f24266359c --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://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': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..b7cebec0495d7b7c81ee8147da87d345f1bfa6b1 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://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': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.26', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..5aa4ce571e95c66d52c0b3299346d3bf45c27fcc --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://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': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.26', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..64d95d529f92c97987703edd0948463cac584918 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://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': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f5aaed761cd6084d890f13e684db42b3bacb0d07 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Blitz++' +version = '0.10' + +homepage = 'http://blitz.sourceforge.net/' +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': 'foss', 'version': '2016a'} + +sources = ['blitz-%(version)s.tar.gz'] +source_urls = [('https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', 'download')] + +sanity_check_paths = { + 'files': ['lib/libblitz.a'], + 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], +} + +configopts = '--enable-shared' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..e75ab2de98e8d1c7e8463035955b5cd7456f93e8 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Blitz++' +version = '0.10' + +homepage = 'http://blitz.sourceforge.net/' +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': 'goolf', 'version': '1.5.16'} + +sources = ['blitz-%(version)s.tar.gz'] +source_urls = [('https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', 'download')] + +sanity_check_paths = { + 'files': ['lib/libblitz.a'], + 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], +} + +configopts = '--enable-shared' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f63a76fa69259c7e8077d4eebb005e0a4c496fa1 --- /dev/null +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'Bonnie++' +version = '1.97' + +homepage = 'http://www.coker.com.au/bonnie++/' +description = """Bonnie++-1.97: Enhanced performance Test of Filesystem I/O""" + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://www.coker.com.au/bonnie++/experimental'] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['sbin/bonnie++'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-GCC-4.7.3-serial.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-GCC-4.7.3-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..98fbdcdb13e8b62c0b497dcf1d797be9f0ed254b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-GCC-4.7.3-serial.eb @@ -0,0 +1,20 @@ +name = 'Boost' +version = '1.53.0' +versionsuffix = '-serial' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +configopts = '--with-libraries=serialization' + +sanity_check_paths = { + 'files': ["lib/libboost_serialization.a"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..621e1934a4f440176973f1b6bfdb849be4109c2c --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.53.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [('bzip2', '1.0.6')] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel', 'zlib1g-dev')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..e7642e0b5ff8ae2383fd123c921c5855f8388fb1 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goolf-1.7.20.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.53.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.9.2-serial.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.9.2-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..a23a6b98964b76fb93dc483afb29c3b7ec2032ed --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.9.2-serial.eb @@ -0,0 +1,29 @@ +name = 'Boost' +version = '1.58.0' +versionsuffix = '-serial' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source +libraries.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--with-libraries=serialization' + +toolset = 'gcc' + +sanity_check_paths = { + 'files': ["lib/libboost_serialization.a"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..d764ab9fbfd2d491569c681d9e6258a2b6247a76 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.58.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..f392ae7ad43de789e65a530d800f515652b94256 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.58.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..18a7a4b74458a4b3750b6162faf0665cf40002fe --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb @@ -0,0 +1,30 @@ +# @author: Luca Marsella (CSCS) +# @author: Guilherme Peretti-Pezzi (CSCS) +# @author: Petar Forai (IMP/IMBA) + +name = 'Boost' +version = "1.60.0" + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'CrayGNU', 'version': '2016.03'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.bz2' % '_'.join(version.split('.'))] + +pythonversion = '2.7.11' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6' ), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b079d2cebd36e70ea92b6c2294f1e15aab481ee --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.60.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015b.eb index 6319781076f5254aea6c6dd4989cc4b1b1469d39..ffc05c737eb8eb6a11246244defc0d65dfd5e5f1 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015b.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True, 'usempi': True} sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] source_urls = [SOURCEFORGE_SOURCE] +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7e8085b5c4fe626abbb551660abbbb2f38e7c897 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.60.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb index c50510711dba9e3d0833c53637a8cb56915a465e..e6a66c8f3d2f27ca6610414552c8a429b7ef3222 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True, 'usempi': True} sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] source_urls = [SOURCEFORGE_SOURCE] +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb index 5a42251165e3c2c62dcf1d031fad3e12dd34d96e..15e0b3204eef070aca9e1e1416285088795eeaea 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe909ab861b69be64bd59f784854199777527bb8 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.60.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0_fix-auto-pointer-reg.patch b/easybuild/easyconfigs/b/Boost/Boost-1.60.0_fix-auto-pointer-reg.patch new file mode 100644 index 0000000000000000000000000000000000000000..74e13d96056b08c50be1d9f149b06e6a567a80fc --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0_fix-auto-pointer-reg.patch @@ -0,0 +1,31 @@ +see https://github.com/boostorg/python/issues/56 and https://github.com/boostorg/python/pull/59 +diff --git a/include/boost/python/object/class_metadata.hpp b/include/boost/python/object/class_metadata.hpp +index c71cf67..5009c17 100644 +--- a/include/boost/python/object/class_metadata.hpp ++++ b/include/boost/python/object/class_metadata.hpp +@@ -164,7 +164,7 @@ struct class_metadata + >::type held_type; + + // Determine if the object will be held by value +- typedef is_convertible use_value_holder; ++ typedef mpl::bool_::value> use_value_holder; + + // Compute the "wrapped type", that is, if held_type is a smart + // pointer, we're talking about the pointee. +@@ -175,10 +175,12 @@ struct class_metadata + >::type wrapped; + + // Determine whether to use a "back-reference holder" +- typedef mpl::or_< +- has_back_reference +- , is_same +- , is_base_and_derived ++ typedef mpl::bool_< ++ mpl::or_< ++ has_back_reference ++ , is_same ++ , is_base_and_derived ++ >::value + > use_back_reference; + + // Select the holder. diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..d705f5fffbf8ca5f858e95e79b4894cfe00ed0d2 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.61.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..822d74b107331b20a796e205a66e4f05538da643 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.61.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7840698ed46ea38b18c1383ba8780af0f2aad86b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.61.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7979ba4e23291604f891e983d5c280eec51368b0 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb @@ -0,0 +1,18 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +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': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..29bf068b6a79690b5e927f38a324b10edd666115 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.8' + +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': 'foss', 'version': '2015b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e48888855ecec82e7a43ed845c0965f2e2390ab1 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.8' + +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': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..63080d8ef9d20b9ef66d6a5c02446dfb368cea2f --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.9' + +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': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab9ee385d74b9a703f0820e4e71d0ea923a42afa --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = "2.2.9" + +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': 'goolf', 'version': '1.7.20'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..95d2b2fb64d59d69068ce6424ce27d9083f7750e --- /dev/null +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Bullet' +version = '2.83.7' + +homepage = "http://bulletphysics.org/" +description = """Bullet professional 3D Game Multiphysics Library provides state + of the art collision detection, soft body and rigid body dynamics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://github.com/bulletphysics/bullet3/archive/'] +sources = ["%(version)s.tar.gz"] + +builddependencies = [('CMake', '3.5.2')] + +# build shared libraries +configopts = "-DBUILD_SHARED_LIBS=ON" + +sanity_check_paths = { + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + ['lib/libBullet%s.%s' % (x,SHLIB_EXT) for x in ['Collision', 'Dynamics']], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/bullet'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d23fa88f5772ac64dd8e2190914cfe2365747c83 --- /dev/null +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Bullet' +version = '2.83.7' + +homepage = "http://bulletphysics.org/" +description = """Bullet professional 3D Game Multiphysics Library provides state + of the art collision detection, soft body and rigid body dynamics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://github.com/bulletphysics/bullet3/archive/'] +sources = ["%(version)s.tar.gz"] + +builddependencies = [('CMake', '3.5.2')] + +# build shared libraries +configopts = "-DBUILD_SHARED_LIBS=ON" + +sanity_check_paths = { + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + ['lib/libBullet%s.%s' % (x,SHLIB_EXT) for x in ['Collision', 'Dynamics']], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/bullet'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch new file mode 100644 index 0000000000000000000000000000000000000000..aecba22db8fb2b7b37824de6b34efbf436c84194 --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch @@ -0,0 +1,16 @@ +# patch to remove hard-coded installation prefix +# Adam Huffman +# The Francis Crick Institute + +diff -u bam-readcount-0.7.4/CMakeLists.txt bam-readcount-0.7.4.new/CMakeLists.txt +--- bam-readcount-0.7.4/CMakeLists.txt 2014-12-07 19:45:03.000000000 +0000 ++++ bam-readcount-0.7.4.new/CMakeLists.txt 2016-04-06 22:06:12.336807391 +0100 +@@ -2,7 +2,7 @@ + + project(bam-readcount) + +-set(CMAKE_INSTALL_PREFIX "/usr") ++#set(CMAKE_INSTALL_PREFIX "/usr") + set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake;${CMAKE_SOURCE_DIR}/build-common/cmake") + include(TestHelper) + include(VersionHelper) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9f5b2f295cd32806339f9446da158198d4dbf08a --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'CMakeMake' + +name = 'bam-readcount' +version = '0.7.4' + +homepage = 'https://github.com/genome/bam-readcount' +description = """Count DNA sequence reads in BAM files""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/genome/%(name)s/archive'] + +patches = ['%(name)s-%(version)s-cmake_install_prefix.patch'] + +builddependencies = [ + ('CMake', '3.4.1'), +] + +dependencies = [ + ('SAMtools', '1.3'), + ('zlib', '1.2.8'), +] + +prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&" + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/bam-readcount"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..29785ed5e61f15120787c76c6b0da2b7d58fc09e --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '2.1.2' +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': 'foss', 'version': '2016a'} + +# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] + +dependencies = [('Java', '1.8.0_74', '', True)] + +builddependencies = [('Autotools', '20150215')] + +# parallel build does not work (to test) +parallel = 1 + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba27dc855d3aab79bdaa1090fc8c16f2705a0ea7 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '2.1.2' + +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': 'goolf', 'version': '1.7.20'} + +# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] + +dependencies = [('Java', '1.7.0_80', '', True)] + +builddependencies = [('Autotools', '20150215', '', True)] + +# parallel build does not work (to test) +parallel = 1 + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index bfc339020fbd2b5f416984daa12cbb53c402e10f..af12b0472e56e4b6b22fc9073144dc3d7a14d4c2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,15 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 437f04c2a6fc8e9622950e760f51e26a99b1a307..8035182b62245ac3c4b8a514b4f17b0492dd2949 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,15 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index 5f76d89a06764d873b39e83f81320f12e7e8f66c..de87300f7c45a4deeb13fbc0d2a2279c625d41a3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -23,15 +20,4 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb index 5dae8ebe27dc03e4c75dc3c7bdc380e8e2823f76..d989a00acf10d062f6ab7be1a7064278b136888e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,12 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%(version)s.tar.bz2'] source_urls = [GNU_SOURCE] -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb index 3d49fdcf03a6d201b6de0aaad2b6fb363160402d..9683cfc7289740b52aed8a666eeb95bba67b635e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.24' @@ -15,15 +13,4 @@ dependencies = [ ('zlib', '1.2.8'), ] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 77fb03962bf0ff81f50096e33d3cc63e99def20f..7598e76c0730b11c331fb482479d25903de038e8 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.24' @@ -15,18 +13,7 @@ dependencies = [ ('zlib', '1.2.8'), ] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - # disable warning/error #175 ("subscript out of range") buildopts = 'CFLAGS="$CFLAGS -wd175"' -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 608c44a15521cde30eec5ba9c49943893f9c0e17..08e10d150ca088971d37c0e9f9d9b8b0e88d11db 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 17ecd5c19008a011fb0180ea8bc6f8c4d342ab97..ea9a13974b4fef4514d3dc59c1fcf84bc310289f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -11,30 +9,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -# zlib required, but being linked instatically, so not a runtime dep builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 61254037e0396e5d63659b3e4c854e5aacb3403e..9709696cf5d799e6a07dbba291c31adcf8029718 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index 0007322f1fb51af25c3045f33ec9ce537e831076..7ccace850154f2a1081ff7cab8cdee3f4aa51e42 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -11,30 +9,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -# zlib required, but being linked instatically, so not a runtime dep builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index e6f5a84c78781fe6e551cdee1befa1c521116c05..d6e68008e5b74f3b7b37e5c24b59f2fad41a83a7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..9ec7a3f3f32c857c08cdceb68bb64cccdf58be86 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -0,0 +1,22 @@ +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 8efdae380a3276dbcf09a912fcc6f2dabe6af209..f411442d12171e8f694182b97b8c6ede94946df0 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,28 +13,10 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index b6d188a41b1513a8888fb8e9b020022b67894154..e3f5b15724b3c824f9f42a3b0f1bd93b43df255d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25.1' @@ -14,26 +12,8 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 40e3ccc1a8a1d21b734167a244140b98ac4ab08c..e08cd975ad8390ca71b24ccc2327ca7ce761515b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,26 +13,8 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7c829040f282bbcca731450c140f8fb6f46dd28 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..0461a3563b635b64b16313315f07388f4cb85e7c --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..702b4131204ea3a3ad1e00a352867735673631eb --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb @@ -0,0 +1,19 @@ +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb b/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a80f721d5ed5a1f94d3b86b2ed9072c8b8b080f2 --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '20160324' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TGZ] +source_urls = ['ftp://invisible-island.net/byacc'] + +checksums = ['bde0463c6c03f059b1e6e9c5579cbe49'] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..276f46cd3c4dcfcbe3be8b4f767754f59ff57a93 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +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': 'CrayGNU', 'version': '2016.03'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..1f608a116f8799fea788891a894d0a9c5112e48e --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +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': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s/'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..d048641ea527b171eeccebf91de6ea202c4d367b --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +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': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb index 4d95eeaef28755957f4e842c930738ec3f87dd2a..46b2debed46dbac17d6f423b8382d965772d60a8 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb @@ -12,8 +12,9 @@ toolchainopts = {'pic': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.bzip.org/%(version)s/'] -import os -os.environ['CC'] = 'gcc' -os.environ['CFLAGS'] = '-O3 -fPIC' +buildopts = "CC=gcc CFLAGS='-Wall -Winline -O3 -fPIC -g $(BIGFILES)'" + +# building of shared libraries doesn't work on OS X (where 'gcc' is actually Clang...) +with_shared_libs = OS_TYPE == 'Linux' moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..f4633df3983106f014a0f0945e76d324e68e9a07 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +name = 'CGAL' +version = '4.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['e31e7039b5cdc74ac7b106db8ba644f3'] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('MPFR', '3.1.4'), + ('Qt5', '5.6.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.5.2'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd4219e20618e9c2c7b77f255d4a2f3a2823d232 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +name = 'CGAL' +version = '4.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['e31e7039b5cdc74ac7b106db8ba644f3'] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('MPFR', '3.1.4'), + ('Qt5', '5.6.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.5.2'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..189d703582249f6ae527ac1845723bb66e832ff3 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '2.8.12' + +homepage = 'http://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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..130d3553bdf799008ba38f34dfb603f1ed489d6e --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.3' + +homepage = 'http://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': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..df5823de42217612725d39f3c8cf7901504e638f --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +homepage = 'http://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': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..7deb175b910b133e3379d1db0991272376d43082 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.3' + +homepage = 'http://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': 'ictce', 'version': '7.3.5'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a70441375c0e4016fb4660ae26409b92fa93be4b --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.1' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..619aaa3ab8aa293ee5a423bca49653d6debe769d --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://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': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), + # 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', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9075c094fb9dddf47a7d3a7d009235ce8088034e --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..1f3daa3224c58476a6109ba6ba8ca96a5f162c5a --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6d07f31ebd4b1a43e755b2083b42e9d8d54c391d --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..412e055df687a82606c730b5edd4c317f7958305 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://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': 'dummy', 'version': ''} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-proteins.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-proteins.eb new file mode 100644 index 0000000000000000000000000000000000000000..b60083b2b25384326d5e375064d468eeafb77621 --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-proteins.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'CONTRAlign' +version = '2.01' +versionsuffix = '-proteins' + +homepage = 'http://contra.stanford.edu/contralign/' +description = """CONditional TRAining for Protein Sequence Alignment""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] + +patches = ['CONTRAlign-%(version)s_gcc47.patch'] + +start_dir = 'src' + +# this option determines whether the program is being compiled for protein or RNA sequence input. +# Here we are compiling for protein input. Check docs for details +buildopts = 'MODEL_TYPE="-DRNA=0"' + +files_to_copy = [(['contralign', 'score_directory.pl', 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/contralign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-rna.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-rna.eb new file mode 100644 index 0000000000000000000000000000000000000000..41ffea3e50b9484c18167e39191d078fbf5bb66e --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-rna.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'CONTRAlign' +version = '2.01' +versionsuffix = '-rna' + +homepage = 'http://contra.stanford.edu/contralign/' +description = """CONditional TRAining for Protein Sequence Alignment""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] + +patches = ['CONTRAlign-%(version)s_gcc47.patch'] + +start_dir = 'src' + +# this option determines whether the program is being compiled for protein or RNA sequence input. +# Here we are compiling for RNA input. Check docs for details +buildopts = 'MODEL_TYPE="-DRNA=1"' + +files_to_copy = [(['contralign', 'score_directory.pl', 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/contralign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01_gcc47.patch b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01_gcc47.patch new file mode 100644 index 0000000000000000000000000000000000000000..f2647d776330dda1cc76fb92a776b81287c18b09 --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01_gcc47.patch @@ -0,0 +1,24 @@ +this patch adds flag -fpermissive which is needed to build with GCC-4.7.x +and also adds a missing include +Pablo Escobar - sciCORE +--- contralign.orig/src/Makefile 2008-08-15 03:06:30.000000000 +0200 ++++ contralign/src/Makefile 2014-02-04 17:25:31.364788280 +0100 +@@ -23,7 +23,7 @@ + -ffast-math -funroll-all-loops -funsafe-math-optimizations \ + -fpeel-loops -Winline --param large-function-growth=100000 \ + --param max-inline-insns-single=100000 \ +- --param inline-unit-growth=100000 ++ --param inline-unit-growth=100000 -fpermissive + + OTHER_FLAGS = + +--- contralign.orig/src/Utilities.cpp 2008-08-14 02:08:30.000000000 +0200 ++++ contralign/src/Utilities.cpp 2014-02-04 17:25:05.483971266 +0100 +@@ -2,6 +2,7 @@ + // Utilities.cpp + ////////////////////////////////////////////////////////////////////// + ++#include + #include "Utilities.hpp" + + bool toggle_error = false; diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb index 428626aef1f0a454e076498929067aeb1cdc9c55..3b5ab3bb9d0c5d4ab77ab9b4a8bf980814c8eb83 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb @@ -24,6 +24,7 @@ dependencies = [ ] builddependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), ('flex', '2.5.39'), ('Bison', '3.0.2'), ] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb index 1b2b44d855a3c9c4abcfccb015719ef6cfaa115f..4d855a0429cebbab4606523f13c12feab5720208 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb @@ -19,6 +19,7 @@ patches = [ ] dependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), ('Libint', '1.1.4'), ('libxc', '2.2.1'), ] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d4b88847698e17f484531db6e557e13126a53a0 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb @@ -0,0 +1,41 @@ +name = 'CP2K' +version = '3.0' + +homepage = 'http://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': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.3'), + ('PLUMED', '2.2.2'), + ('libxsmm', '1.4'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True +plumed = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab24e09cd3a0bc66da7cc4c57f0e4a5eb6bb9c6f --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -0,0 +1,18 @@ +name = 'CUDA' +version = '7.0.28' + +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': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/Prod/local_installers/', +] + +sources = ['%(namelower)s_%(version)s_linux.run'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb index aab739ed1901a03e0aa2af38f5e0159a956672e6..c318ed2f596c1e1f2d931542650ac4c027484648 100644 --- a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb @@ -19,8 +19,6 @@ dependencies = [ ('HDF5', '1.8.16') ] -buildopts = 'VERBOSE=1' - runtest = 'test' separate_build_dir = True diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7f97d6e59de8ef48ce74b16345dd8e4c631495b --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.7-rc2' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('GSL', '2.1'), + ('HDF5', '1.8.16') +] + +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..23fe1ddcc97c66d723718c6137f9dc6f202d24fe --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 = "3.8.0" + +homepage = "http://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': 'GCC', 'version': '4.9.3-2.25'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", + "openmp-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.0'), + ('ISL', '0.16'), +] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Python', '2.7.11', '-bare'), + ('libxml2', '2.9.3'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20160106-intel-2016a.eb b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20160106-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..009a6c205795e637c8f16f9f2f2d4f9e3313d2ec --- /dev/null +++ b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20160106-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'CmdCp' + +name = 'Cluster-Buster' +version = '20160106' + +homepage = 'https://github.com/weng-lab/cluster-buster/' +description = """Cluster-Buster: Finding dense clusters of motifs in DNA sequences""" + +source_urls = ['https://github.com/weng-lab/cluster-buster/archive/'] +sources = ['a343491.tar.gz'] + +toolchain = {'name': 'intel', 'version': '2016a'} + +start_dir = 'cbust-src' + +cmds_map = [('.*', "$CXX $CXXFLAGS -DNDEBUG -o cbust *.cpp")] + +files_to_copy = [(['cbust'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cbust'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..549296f08e8118a595916f2a733b3415255e9de9 --- /dev/null +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'Commet' +version = '20150415' +commit = '4ef0705' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://colibread.inria.fr/software/commet/' +description = """ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of + a large metagenomic project. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/pierrepeterlongo/commet/archive'] +sources = ['%s.tar.gz' % commit] + +checksums = ['19cba09ca7a92eaed75ed6af820d9451'] + +dependencies = [ + ('Python', '2.7.11'), +] + +files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', + 'extract_reads', 'filter_reads', 'index_and_search']], + 'dirs' : ['doc', 'include'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.03.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..eeedf98b762503c576fdeeaf47d9e5505f7858c4 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.03.eb @@ -0,0 +1,19 @@ +easyblock = 'CrayToolchain' + +name = 'CrayGNU' +version = '2016.03' + +homepage = 'http://docs.cray.com/books/S-9408-1603/' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: March 2016).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-gnu', EXTERNAL_MODULE), + ('gcc/4.9.3', EXTERNAL_MODULE), + ('cray-libsci/16.03.1', EXTERNAL_MODULE), + ('cray-mpich/7.3.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..112a9312bced57dab986f2f79a1173329d09ab43 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb @@ -0,0 +1,19 @@ +easyblock = 'CrayToolchain' + +name = 'CrayPGI' +version = '2016.04' + +homepage = 'http://www.pgroup.com/' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-pgi module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-pgi', EXTERNAL_MODULE), + ('pgi/16.3.0' , EXTERNAL_MODULE), + ('cray-mpich/7.3.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2facea57d93b5384a34e9b880f0c3713c743f78c --- /dev/null +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'CrossTalkZ' +version = '1.4' + +homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +description = """ +CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment +between pairs of gene or protein groups in large biological networks. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +] +sources = ['%(name)s_%(version)s.tgz'] + +dependencies = [('Boost', '1.60.0')] + +builddependencies = [('CMake', '3.4.3',)] + + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" + +sanity_check_paths = { + 'files': ['bin/CrossTalkZ'], + 'dirs': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2ac3b5a935547750a024749a71bed1356b662225 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb @@ -0,0 +1,44 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2016 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 = 'Cube' +version = '4.3.4' + +homepage = 'http://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.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + '50f73060f55311cb12c5b3cb354d59fa', # cube-4.3.4.tar.gz +] + +dependencies = [ + ('Qt', '4.8.7'), +] + +sanity_check_paths = { + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), + ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index 501824903b421ad611701a06a6531280b6c7dfe4..7b8dca855454b089db498ab87d21136757cb1d8b 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -34,7 +34,7 @@ patches = [ 'cufflinks-1.x-ldflags.patch' ] -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb index d25853769963dfb67b91b97772ad77a39117c74a..2ef873d2da07e979d4a67c4bcf473d137ee0be67 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb @@ -30,7 +30,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb index 645f94a8337430d99428ef59d3908aff3b5a98a1..25b9208f0e418c4eb25e097bca73df4ad93d3c5e 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb @@ -32,7 +32,7 @@ dependencies = [ patches = ['Cufflinks_GCC-4.7.patch'] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb index 799e9172ba2fc4690f20879733c158d8af239901..9c37cd717b93588153399ef57f9e729dccc63e73 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb @@ -34,7 +34,7 @@ dependencies = [ configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' configopts += ' --enable-intel64 ' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb index 991b5a4c8bfc3039af562bada4809817feb358dc..6751cec53076cba6266b1fd8a819dbede980bb93 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb @@ -33,7 +33,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb index d0372e6f7036ef03b18931e96882e5a5a80096ed..6ac33d77d411c4d88b5696c7f00fa86ccef9f2b7 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb index 2741497a4d1b8df3330585dc6d778caa15b2520e..e368245a6cd43bd3e3d29cd2519b1a7c6e724db3 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb index 0a4b6fa7ab65249235b7e6e3b74ef54514d92ae4..fe15c228e170cd48c58f13f63458bd0438baa1bb 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb @@ -18,7 +18,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb index 43da714323fdde6ed1031d9eb95f25a6c4a469b6..50fce481a6c8bdf4963cb7296c1eb6e3faefe778 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb @@ -19,7 +19,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb index 38e9d1ce03cfd65a4af1be442d39f9b620ef711b..8360322002f7e357ac4410234990fb67f42b9cdd 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb @@ -21,7 +21,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I${EBROOTEIGEN}/include' +preconfigopts = 'env CPPFLAGS=-I${EBROOTEIGEN}/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..45e6650292aaf7f5fc881a0fa122c503615f4219 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.47.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1s')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8d8841ea433ecf9b8afc58262eeb86a1980eee5e --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +glibver = '2.47.5' + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] +builddependencies = [ + ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +# 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 " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['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/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..ecd56f916623676b053f4ad8a8e0f5392585eeff --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' +glibver = '2.48.0' +versionsuffix = '-GLib-%s' % glibver + +homepage = 'http://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': 'intel', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.3'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.95'), + ('expat', '2.1.1'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] +builddependencies = [ + ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +# 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 " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['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/c/cairo/cairo-1.14.6-intel-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb index 2966a85fa7cad2f61e253380f87fb857c937e0df..a289e5fb021f8e19bd1b4fc2fec9298ef3447170 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb @@ -28,9 +28,13 @@ dependencies = [ ('libxcb', '1.11.1'), ('libXrender', '0.9.9'), ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), ] builddependencies = [ ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..d00a912e71a5b69f94d1ffa3613d19925b4b10d1 --- /dev/null +++ b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'cramtools' +version = '3.0' +versionsuffix = "-Java-%(javaver)s" + +homepage = 'https://github.com/enasequence/cramtools/' +description = """CRAMTools is a set of Java tools and APIs for efficient compression of sequence +read data. Although this is intended as a stable version the code is released as +early access. Parts of the CRAMTools are experimental and may not be supported +in the future.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/enasequence/%(name)s/archive/'] + +dependencies = [('Java', '1.7.0_80')] + +modloadmsg = "To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" + +sanity_check_paths = { + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': ["lib"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..5bcd0e1aa3b8e9cb6ad86b7d7fc2298851393a97 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '4.0' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-7.0-linux-x64-v%(version)s-prod.tgz'] + +dependencies = [('CUDA', '7.5.18')] + +checksums = [ + '845ead4b37f1a2a243d7d1b4d42d1d8b', # cudnn-7.0-linux-x64-v4.0-prod.tgz +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb new file mode 100644 index 0000000000000000000000000000000000000000..536c2f33c677c08b16964966b0a22da92b2e17cf --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '5.0-rc' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-7.5-linux-x64-v%(version)s.tgz'] + +dependencies = [('CUDA', '7.5.18')] + +checksums = [ + '0febee3f11276218668857191514b7e0', # cudnn-7.5-linux-x64-v5.0-rc.tgz +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..5c57e5846c2a39d70bd372c02702812bcd8d4c7e --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cutadapt/'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fcf1bd769617b093b3eb1824ad17539b52004e91 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '6.2.23' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["include/db.h"], + 'dirs': [], +} + +moduleclass = 'tools' \ No newline at end of file diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..6491ebe755614488ed5bca43b4265b1e3da6b7f6 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb @@ -0,0 +1,36 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.032' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~capttofu/DBD-mysql-%(version)s/' +description = """Perl binding for MySQL""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cpan.metacpan.org/authors/id/C/CA/CAPTTOFU/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.2'), + ('MariaDB', '10.1.13'), + ('zlib', '1.2.8'), + # OS dependency should be preferred if the os version is more recent then this version + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1q'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# force static linking of libmysqlclient to dance around problem with unresolved symbols +configopts = '--libs="-L$EBROOTMARIADB/lib -Wl,-Bstatic -lmysqlclient -Wl,-Bdynamic -lpthread -lz -lrt -lssl -lcrypto"' + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..8c069fec945235589e0467118777b76be9742c9e --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.835' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1'), + ('DB', '6.2.23'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' + diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f322881382fc4ad293ba4d60f7249dc3baf08b41 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.10.8' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +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': 'intel', 'version': '2016a'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cpu.eb b/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cpu.eb similarity index 100% rename from easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cpu.eb rename to easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cpu.eb diff --git a/easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cuda.eb b/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cuda.eb similarity index 100% rename from easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cuda.eb rename to easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cuda.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..99e680c26db2e91d3c7e82a59a71ab8d66deb3e4 --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.1.1' + +homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] +# 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: 15 April 2016 +# Date tarball was reported to have been modified: 11 January 2016 +sources = ['dftd3-%(version)s.tgz'] +checksums = [('md5', 'c9d6a92c43bb2ba71ad75f388fdce216')] + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0edd0228ed665f100ce875affd1624aff6992c73 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'DIAL' +version = '2011.06.06' + +homepage = 'http://www.bx.psu.edu/miller_lab/' +description = """DIAL (De novo Identification of Alleles) is a collection of programs + to automate the discovery of alleles for a species where we lack a reference sequence. + The SNPs/alleles are specifically selected for a low error rate in genotyping assays. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] + +patches = ['DIAL-%(version)s_Makefile.in.patch'] + +dependencies = [ + ('LASTZ', '1.02.00'), +] + +binaries = [ 'assemble', 'assemble1', 'assemble_illumina', 'build_sff_index', 'convertFastqFasta', + 'cull_components', 'DIAL', 'filter', 'filter_clusters', 'fish_clusters', 'make_template', + 'masker', 'partition', 'remove_clones', 'remove_clusters', 'update', 'update_clusters', + 'update_status',] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in binaries], + 'dirs': ['bin'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch new file mode 100644 index 0000000000000000000000000000000000000000..0f365be126b8f7235fb62413b47433ac5a038308 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch @@ -0,0 +1,13 @@ +# Remove use of -Werror because Werror is not used (discussed in http://seqanswers.com/forums/showthread.php?t=20113). +# Using -Werror gives warnings which result in a failure of the installation. +# Author: Fokke Dijkstra - Rijksuniversiteit Groningen (RUG)--- DIAL/src/Makefile.in 2015-02-10 14:10:33.143293723 +0100 ++++ DIAL/src/Makefile.in 2015-02-10 14:10:39.462384572 +0100 +@@ -246,7 +246,7 @@ + @DEBUG_FALSE@@PROFILE_FALSE@@TESTING_TRUE@OPTIMIZATIONS = -ggdb + @DEBUG_FALSE@@PROFILE_TRUE@OPTIMIZATIONS = -ggdb -pg -DNDEBUG -O2 -funroll-all-loops $(ARCH) + @DEBUG_TRUE@OPTIMIZATIONS = -ggdb -DDEBUG +-AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall -Werror \ ++AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall \ + -Wunused-variable -Wunused-parameter -Wreturn-type -Wswitch \ + -Wcast-align -Winline -Wnested-externs -Wextra $(OPTIMIZATIONS) \ + -std=c99 diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..6c27df0850942f371670c22f0085ee9f65c7aed2 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.10' + +homepage = 'http://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': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.1'), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb index 5adccf48d70476aee19c14ae1596e1fb79b5676d..9af65e4593e31e084a8d6901f7f2277fa3cd18dc 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb index 1db648e43da586836ab0c3363835af1f96228f92..5b5d5f06cdfdb264c93dfc91fd059ce07d44554c 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb index fea350b75565a0e9bf692634e37b3fd33d8d9ee0..45e774b0e381a8b6a5bc693fc87371bf23ecc3fd 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb index 2d5dc8597f3f6417bf228fc27656f6292b38ede9..a63ff80fea99963b24142537f73563091eb9397b 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..10a9f3bf3627be8228d9911e5770f0cb9a29d672 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..7dcf741ab4c8763b294ecc35375c4ee19b2d8e29 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..321204b24485cd0ee7ac1bc8ecf88b6f6d50a658 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.106' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GLib', '2.47.5'), + ('DBus', '1.10.8'), + ('expat', '2.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..ed4f3f692d8b98149c0fef35c4b0d9df3e8a939a --- /dev/null +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'drFAST' +version = '1.0.0.0' + +homepage = 'http://drfast.sourceforge.net/' +description = """ drFAST is designed to map di-base reads (SOLiD color space reads) + to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [('zlib', '1.2.8')] + +buildopts = ' CC="$CC"' + +parallel = 1 + +files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] + +sanity_check_paths = { + 'files': ["bin/drfast", "README.txt"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f01a8dfb96f0a4516cdd5e3f21260cca03174aa --- /dev/null +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'drFAST' +version = '1.0.0.0' + +homepage = 'http://drfast.sourceforge.net/' +description = """ drFAST is designed to map di-base reads (SOLiD color space reads) + to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [('zlib', '1.2.8')] + +buildopts = ' CC="$CC"' + +parallel = 1 + +files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] + +sanity_check_paths = { + 'files': ["bin/drfast", "README.txt"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..fc4103fecb21aee28f9300fa180848f7afad048e --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Provided binaries required OpenBLAS and GSL libraries + +easyblock = 'Tarball' + +name = 'EIGENSOFT' +version = '6.1.1' + +homepage = 'http://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': 'goolf', 'version': '1.7.20'} + +dependencies = [ + ('GSL', '1.16'), +] + +source_urls = [ + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/', + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/'] +sources = ['EIG%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d7fea90a9e6deb4b2cd49178fca270fb3c3426a --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb @@ -0,0 +1,28 @@ +name = 'ESMF' +version = '7.0.0' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] + +patches = ['ESMF-6.1.1_libopts.patch'] + +dependencies = [ + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.3'), + ('netCDF-C++', '4.2'), +] + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`ncconfig --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..07bb77b4539a9a97e657ef7ec5105ae40381ed84 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.8.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/1d/9e/9a69f54d7bdb4a75e78530d1ccdd66be5fd61e31ef289f167cf007e11089/', + 'https://pypi.python.org/packages/e9/c2/db36d5a92ddcb68645a64f9017a7056438aa40f224e09c3b6af374d58ebc/', + 'https://pypi.python.org/packages/c0/84/ebe0a2fc169370db663d82caf7c0224771028c79ec9a324b46d029840773/', + 'https://pypi.python.org/packages/ea/f2/a5556cc4e7f3dd4059d890b56a6af9ca80e9210993db65303aa0163806fd/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.4.18.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..f166a5d5875478d6a27faba9136d6e4ddb18fc34 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.8.1' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/18/7a/c983e61bb91687ad74faab0edd7471b5e78f12cf3c71087581eedc6dd9e5/', + # vsc-base + 'https://pypi.python.org/packages/c2/b9/8686ca09c21d59d49ce5964cea035d158d84447fdd0c7d1bfc1d2701c17d/', + # easybuild-framework + 'https://pypi.python.org/packages/22/66/21c21c0f1770ba240a3ef37ed7ba20eb0af0ff08be1f522c849310444ee3/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/93/7a/0d89cfde1530fc6932b9a474bd23808fef40ffcce03b99a7907700612371/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/22/22/ecabee7c42a676a195301251bdc486c8b25fb4422963a0daab2184afed8f/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.6.tar.gz', + 'vsc-base-2.5.1.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb index a9cf3457671e383e781c4df906461f81cd4135fc..447fdcc2f14fed2853196a19c997772ac88ba321 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb index 57fad2e4e7e074765592ee1ea27458b10c134ba5..3cc61b864372d3299c7b17d084cc0401bd104679 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb index 04a48d1f609f90ea81f460110119dba6c8c4ddb1..f64ca17dc1cb76865df99fd6134328879eafb2eb 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb index 34c32694d7333835906879dde48afd1176033b20..ad92c7352d47a758d5f873e1e657fa8050ade12e 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb index eda95916d09d66092fd23b490b1db6ec88872bc8..c2159638f240dd527660d01ad202029b9f019ed4 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb @@ -19,7 +19,6 @@ description = """Eigen is a C++ template library for linear algebra: toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb index ab4f378feb1ea3191188fd4b8b6a83d12209bbac..0db2cb2232438d36ef168245fa871a56e412a881 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb index 92042e0a82004dd369dfe3921d2de6fe67f1ad38..ad65bdfc92e9490b91fbb3e0201d58bb57d87cb0 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb index 5e8553cde74c6c267527a535cb144be11d2a2eb2..8868b07c8240c5d73b6cc0e131809415f26ac592 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb index bf8140941835814debfcfe826f8d272ab1e31dfb..0a2271f0359a8924a7e75f1d9c3d9902e1c29311 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb index 934d581d377f9514463314da63fd12775c751977..0dd48816d2d2d9f930bb212cc97e7d151029a16d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb index 890a8a48390f86db428dfd7c0f2fef71d071e4cd..9e7b9cf60de7cdcb32e742410320195b21078ffb 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb index 024205f8b6ba005855a3e96cb6518728ad49a7a6..7cbefdf8ab1fe2181989e23d49163a1690a71875 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb index bca769f27d8d7115a6d5a9f6c6ae000a9b16daaa..81edc7d68bfa13d788db47f922fcbb14c5409382 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb index ab03a385a5b063bcadbee86c2d3a365ce269f129..b3c186165b6652facb329316b158ec46e1b07955 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb index 9cca953ebc6cc2b9652bb63d0d44c727845fc488..d9a3a23dd02e5d414de5fe6f2ccfb28be38c36f7 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'foss', 'version': '2015a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb index d9ce74d1cfac69e2491f7f37c867760cb49b4609..fcb13a817fb7063a99fdfab3b80f7bbbf35ec58b 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb index 5ec6f45b74a642c3db3a6590956641b161cda7af..8648dbd440ce004e46bbc5645b6655e6f5e1ada6 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'dummy', 'version': ''} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb index ec09959b7403acd969cdc628ceed8e42282601be..59832233f0ee52f020a433bcaed6c9938dc81378 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb index 6d4de9bbd8952ccecb80ae1c4e53f42e1834e4f2..d79ef2b7af35124dba3d18ee18d26b9da9a88076 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'dummy', 'version': ''} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7d8ebf1a320bbb63eec255d66f50902ecd3897b9 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.7' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb index 16eecd14b86a00f9318963bc0ec2a58bc5b92ae3..499d24c76ff95d135875279cf9847e1b99f2fdc0 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb index 5e2d4fc5a2ba7d3fbe50fa0dc37dd237a7b3cfd1..f02fff458c02c637054c21ce00fcb1f4706f707d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3ba31dc38dc9df798ab73b28dda978b461d081ea --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.8' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..34ee5e6ea4967b1a07773ba7de18fedf49c50b7a --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.8' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0cfe11f239af086b8b24e92e4ca93c329bb0dfcc --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'http://www.ebi.ac.uk/~guy/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': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/nathanweeks/exonerate/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GLib', '2.47.5')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..b3d4b5ae5a81c57a982ddc2392369fdaf16d2bd3 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = 'Extrae' +version = '2.4.1' + +homepage = 'http://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': '1.4.12-no-OFED'} +toolchainopts = {'usempi': True} + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['Extrae-%(version)s_configure-no-shared-binutils.patch'] + +# compiler toolchain depencies +dependencies = [ + ('zlib', '1.2.7'), + ('binutils', '2.22'), + ('Boost', '1.53.0'), + ('libunwind', '1.1'), + ('libxml2', '2.9.1'), + ('PAPI', '5.2.0'), +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1_configure-no-shared-binutils.patch b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1_configure-no-shared-binutils.patch new file mode 100644 index 0000000000000000000000000000000000000000..c2fc719e06365bdccd09363a17b28186f01f51c6 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1_configure-no-shared-binutils.patch @@ -0,0 +1,16 @@ +fix configure tests for libbfd.a +author: Bernd Mohr (Juelich Supercomputing Centre, Germany) +--- configure.orig 2013-11-11 16:38:11.872367495 +0100 ++++ configure 2013-11-11 16:38:32.872767289 +0100 +@@ -27477,9 +27477,9 @@ + BFD_LIBSDIR="${binutils_home_dir}/lib${BITS}" + elif test -r "${binutils_home_dir}/lib/libbfd.so" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" +- elif test -r "${binutils_home_dir}/lib${BITS}/libbfd.a" -a "${binutils_require_shared}" = "no" ; then ++ elif test -r "${binutils_home_dir}/lib${BITS}/libbfd.a"; then #-a "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib${BITS}" +- elif test -r "${binutils_home_dir}/lib/libbfd.a" -a "${binutils_require_shared}" = "no" ; then ++ elif test -r "${binutils_home_dir}/lib/libbfd.a"; then # -a "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" + else + if test -d ${binutils_home_dir}/lib${BITS} ; then diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4e0f98d635d634fa4cf2aa3a64bd778789ccea6f --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = 'Extrae' +version = '3.0.1' + +homepage = 'http://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': 'foss', 'version': '2015a'} +toolchainopts = {'usempi': True} + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = [SOURCELOWER_TAR_BZ2] + +compname = 'GCC' +compver = '4.9.2' + +# compiler toolchain depencies +dependencies = [ + ('zlib', '1.2.8', '', (compname, compver)), + ('Boost', '1.58.0', '-serial', (compname, compver)), + ('libunwind', '1.1', '', (compname, compver)), + ('libxml2', '2.9.2', '', (compname, compver)), + ('libdwarf', '20150310', '', (compname, compver)), + ('PAPI', '5.4.1'), +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3265e4fdb489fb73974e09fa0fa0cf642c9b61e8 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.1.5' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-3.1.2_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1a58effe3dde3eee8d8bad81bae06a8ed6be60d2 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.1' + +homepage = 'http://expat.sourceforge.net/' +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': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6e5b60c35f5bc631d1d58285916029d1d81f6e2b --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.1' + +homepage = 'http://expat.sourceforge.net/' +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': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a69a7b9e2fd4a380b4fce2c047576d8ba0e2eec7 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , 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 = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['fastx_toolkit-%(version)s.tar.bz2'] + +builddependencies = [('libgtextutils', '0.7')] + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']], + 'dirs': ['.'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb index 24f4ba27ec42e20fc26af691a91d2a8c222a93f6..7278d23d80b703dd82a2dec30188728b4ed9bf53 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb @@ -23,7 +23,7 @@ start_dir = 'FDS_Compilation' skipsteps = ['configure', 'install'] buildininstalldir = True -prebuildopts = 'FFLAGS="$FFLAGS -fpp"' +prebuildopts = 'env FFLAGS="$FFLAGS -fpp"' modextrapaths = {'PATH': 'FDS_Compilation'} diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..da99f9d5b8eaa97f82ef9d0c9732d003d60d8a29 --- /dev/null +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'FFLAS-FFPACK' +version = '2.2.0' + +homepage = 'https://linbox-team.github.io/fflas-ffpack/' +description = "Finite Field Linear Algebra Subroutines / Package" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/fflas-ffpack/archive'] + +builddependencies = [ + ('Autotools', '20150215'), +] +dependencies = [ + ('GMP', '6.1.0'), + ('Givaro', '4.0.1'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' +configopts += ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' + +sanity_check_paths = { + 'files': ['bin/fflas-ffpack-config', 'include/fflas-ffpack/fflas-ffpack.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..aeee54992ebd580acae2f557ef22c1d3955247f9 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +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': '2016.04'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.06.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..274c8d2e7c9dc742b757f1d8d0580420029af148 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.06.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +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': '2016.06'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..09d52dd7555024329d8a4456ed623babc8e6340e --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +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': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +# no quad precision, requires GCC v4.6 or higher +# see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0badebf4eb9eac06b609ce7704baaf1e3293e081 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.7' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('x264', '20160430'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..05478ccadaa7fcaad792c1fee2c2dd065061c646 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.7' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('x264', '20160430'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fb0c75a29bf506b5f2c2f3bc0c2fa9bead429a0a --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.0.2' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('x264', '20160430'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..d0e91ca7e72df37e5f794b080db823521f180ca0 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '1.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/fenics-project/fiat' +description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order + instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating + arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('sympy', '1.0', versionsuffix), +] + +options = {'modulename': name} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..76be36ffc6f0dcfa6d1288cd42bd333a52d99e7c --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.3.1' + +homepage = 'https://xiph.org/flac/' +description = """Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://downloads.xiph.org/releases/flac/'] + +# use of assembly routines requires a recent binutils +builddependencies = [('binutils', '2.25', '', ('GCC', '4.9.2'))] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..82bf05536dcaeecf1caf9f94faca9cf00619a0ea --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.8.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cs.ubc.ca/research/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www.cs.ubc.ca/research/flann/uploads/FLANN/'] +sources = ['flann-%(version)s-src.zip'] + +builddependencies = [('CMake', '3.5.2')] +dependencies = [ + ('Python', '2.7.11'), +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/doc/flann', 'share/flann/python'], +} +sanity_check_commands = [('python', '-c "import pyflann"')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb b/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5212c8b65816b4a10f49c486d5f30dbafa47ec62 --- /dev/null +++ b/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'FLASH' +version = '1.2.11' + +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': '2016a'} + +source_urls = ['http://download.sourceforge.net/%(namelower)spage'] +sources = [SOURCE_TAR_GZ] + +files_to_copy = [(['flash'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/flash'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7d711211d473aafbd04bb0bf2a34fd72fd3e4cd --- /dev/null +++ b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'FLEUR' +version = '0.26e' + +homepage = 'http://www.flapw.de/' +description = """FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, + based on density-functional theory.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'r8': True} + +# dowload requires registration, see http://www.flapw.de/pm/index.php?n=FLEUR.Downloads +sources = ['v%s.tgz' % version.split('.')[1]] + +builddependencies = [('imake', '1.0.7')] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), + ('HDF5', '1.8.16'), +# ('Wannier90', '2.0.1'), # only needed if '#define wann' is added to Imakefile +] + +# define hardware platform to be 'parallel intel compiler, 64 bit, use scalapack') +prebuildopts = "sed -i 's/^#define jureca/#define linux_evp_64/g' Imakefile && " +# don't specialize for systems with structural symmetry +prebuildopts += "sed -i 's/^#define inversion//g' Imakefile && " +# no need to jump through hoops to make compilation work with older Fortran compilers +prebuildopts += "sed -i 's/^#define f_90//g' Imakefile && " + +prebuildopts += "imake && " +buildopts = 'FC="$FC" FFLAGS="$FFLAGS" HDFROOT=$EBROOTHDF5 fleur.x inpgen.x' + +# parallel build tends to fail +parallel = 1 + +files_to_copy = [(['fleur.x', 'inpgen.x'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fleur.x', 'bin/inpgen.x'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0056b1139192bd5799d888a349a75faf2c3c2398 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb @@ -0,0 +1,39 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.3' + +homepage = 'http://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': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('libX11', '1.6.3'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('xprop', '1.2.2'), + ('libXft', '2.3.2'), +] + +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/f/FLTK/FLTK-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb index 97b3b63c16c30463331ef76e5b82bc8e996cb37f..d88b64d96a2da3e6b80862b404dd8d9b8273843d 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb @@ -17,6 +17,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +configopts = '--enable-shared --enable-threads --enable-xft' dependencies = [ ('libX11', '1.6.3'), @@ -27,10 +28,11 @@ dependencies = [ ('libpng', '1.6.21'), ('libjpeg-turbo', '1.4.2'), ('xprop', '1.2.2'), + ('libXft', '2.3.2'), ] sanity_check_paths = { - 'files': ['bin/fltk-config', 'bin/fluid'], + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], 'dirs': ['lib'], } diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-centos6_64.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-centos6_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..a98d2244dbe0b45d845451bf8044aa9fe03c645d --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-centos6_64.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'FSL' +version = '5.0.9' +versionsuffix = '-centos6_64' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://fsl.fmrib.ox.ac.uk/fsldownloads/'] +sources = ['fsl-%(version)s%(versionsuffix)s.tar.gz'] + +modextravars = {'FSLDIR': '%(installdir)s'} + +# eddy_openmp is not available anymore when compiling FSL 5.0.9 from source +# fslview (& others incl. atlasquery) are more difficult via compiling from source due to required dependencies +sanity_check_paths = { + 'files': ['bin/atlasquery', 'bin/basil', 'bin/bet', 'bin/eddy_openmp', 'bin/fabber', 'bin/fast', 'bin/Fdt', + 'bin/feat', 'bin/first', 'bin/flirt', 'bin/fnirt', 'bin/fsl', 'bin/fsl_anat', 'bin/fslview', + 'bin/melodic', 'bin/pngappend', 'bin/siena', 'bin/tbss_fill', 'bin/topup'], + 'dirs': ['data', 'etc', 'extras', 'include', 'lib'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..0b3248c5dd5d984ba37f03359f1afe20608265b4 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,26 @@ +name = 'FSL' +version = '5.0.9' +versionsuffix = '-Mesa-11.2.1' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] + +patches = [ + 'FSL-%(version)s_makefile_fixes.patch', + 'FSL-%(version)s_missing_lib.patch', + 'FSL_icc_nan-inf_fix.patch', +] + +dependencies = [ + ('freeglut', '3.0.0', versionsuffix), + ('expat', '2.1.0'), + ('libX11', '1.6.3'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b9dfba11bf116530866c8e54737ce2c5f3cc506 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb @@ -0,0 +1,25 @@ +name = 'FSL' +version = '5.0.9' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] + +patches = [ + 'FSL-%(version)s_makefile_fixes.patch', + 'FSL-%(version)s_missing_lib.patch', + 'FSL_icc_nan-inf_fix.patch', +] + +dependencies = [ + ('freeglut', '3.0.0'), + ('expat', '2.1.0'), + ('libX11', '1.6.3'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch new file mode 100644 index 0000000000000000000000000000000000000000..40e5baff2f0ff261643eeefae732f55f28e7b651 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch @@ -0,0 +1,14 @@ +# On RHEL 7 and friends, you need to link to libglapi too +# Ward Poelmans +diff -ur fsl.oirg/src/fslsurface/Makefile fsl/src/fslsurface/Makefile +--- fsl.oirg/src/fslsurface/Makefile 2014-02-24 12:09:05.000000000 +0100 ++++ fsl/src/fslsurface/Makefile 2016-04-21 18:03:50.246117983 +0200 +@@ -37,7 +37,7 @@ + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} + + +-LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass ++LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass -lglapi + + APPLY_ZLIB = -DHAVE_ZLIB + diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..f6dbacc9e2aa15de1cbc18f69adfdfedb7c27cad --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] + +patches = ['FastQC_shebang.patch'] + +dependencies = [('Java', '1.7.0_80')] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] + +sanity_check_paths = { + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb new file mode 100644 index 0000000000000000000000000000000000000000..7b8be6500dd186f2c784666549a8a718522010e8 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] + +patches = ['FastQC_shebang.patch'] + +dependencies = [('Java', '1.8.0_74')] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] + +sanity_check_paths = { + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb b/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb index 63db8305d5a81ee034b3a260ab80a7dfbe24355a..bca5d6950841fc77e87458ed55016f32fd63784c 100644 --- a/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb @@ -12,14 +12,14 @@ homepage = 'http://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': 'GCC', 'version': '4.8.2'} + source_urls = ['ftp://ftp.astron.com/pub/file/'] sources = [SOURCE_TAR_GZ] -toolchain = {'name': 'GCC', 'version': '4.8.2'} - sanity_check_paths = { - 'files': ['bin/file'], - 'dirs': [] + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] } moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb b/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..61f8e29397861eb43ff3b2ec6d7e5ae2b49a7062 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.25' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b04efa3b3acc51b4f2b283745cf71e6db42672ce --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb index 88fa55c14db33d01979e69594722e051c7c0366d..1deb262347d6cec0b6b1daa4ce3fad21644c23d8 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb index 80e72c01e5bb3b8b04659e2067134a22e720b622..574d6d02de60f8acae56a1410fe186783d7d5104 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb index c52db08f490f4e4e4d1dcdc398943c33a72e4684..15154dbbea85ea9a5b64fd770dd2c1323dfd3c9e 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb index 06e3d71fbaec6a89a48ba660d029649d15a409d7..4df2be2be9ab59e57e748bfb0245722c1b817f7e 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb index 5d430a5301ff2097bd77b34744024402eba4b2a2..8b11789fcafe67943b1d888619934c8d6a24554a 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb index 3fe841d973935304390ec3285222255a7ec09ff2..fd373c373ac0b18c8db9c4fd48c59003d950f6f6 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb index 33951308af68a4f506e2ed0c727bc31482a23d58..f26ed2df7ac7bb5e12118867ec0c210a1827721c 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..71675a8b5cf7215ebdc4aa4a09783a1e834e7e93 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb @@ -0,0 +1,19 @@ +name = 'flex' +version = '2.5.39' + +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': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.25', '', True) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..154963c1c85cc6f2b946d83fb270a96e19cb018c --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +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': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..e1a943777464a69db10ab7b224b2bd5116257f58 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -0,0 +1,21 @@ +name = 'flex' +version = '2.6.0' + +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': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +parallel = 1 + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..299747415ee51dbf81f0ed048d0d9bb390c5560f --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb @@ -0,0 +1,21 @@ +name = 'flex' +version = '2.6.0' + +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': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +parallel = 1 + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..e7580df4ae2d27389ac5ad52e49caf6295a1b414 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +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': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d955835431314f03ef5685bb23f6c1f469b2f4c3 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.94' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.6.2'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..93a5699fb5577bd4970d78c8fa48441098162698 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.95' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.1'), + ('freetype', '2.6.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..09b5a490888d0c0a3cba1a72e3bf82a737c292db --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.95' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.1'), + ('freetype', '2.6.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1fbffb27588efc6c82d37f505ba0e96a0ed0aef6 --- /dev/null +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'fontsproto' +version = '2.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X11 font extension wire protocol" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb index 0719ec51f469e4f1bac78111cbf5ff491e5c907d..8e577e277b2e6ff595f523fe19ef4eed3facb7c9 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb index 6c5ce993873e7f5c7bc3475680d36e78c998aae5..47f2d3c961f7262b6053e69bd5ca0d223e9580a7 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb index 5c83a62b97f110f575b7046df964205e3d44cd96..062cfdbcf85c80d376e4e66b02c79577ec814d73 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb index 5b1c1517ba9fd32526c995e76cc4e99ef739d60c..9c00b32506d3366db2c62d0738c75afeb56cfc02 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/foss/foss-2016.04.eb b/easybuild/easyconfigs/f/foss/foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..b70b879a23795ec2976966775c479b4ff14f06a9 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016.04.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016.04' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.3.0-2.26' + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('OpenMPI', '1.10.2', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.06.eb b/easybuild/easyconfigs/f/foss/foss-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..66d73ecb4aeba0d724a19ca014ec642d261df9b7 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016.06.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016.06' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.4.0-2.26' + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('OpenMPI', '1.10.3', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..1965349120d771320ee1751d89bbd458efd15b57 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', mesa_ver), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/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/f/freeglut/freeglut-3.0.0-foss-2016a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa4fa34ea22d6438c43103e1a29f66429bf0e9b6 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', '11.1.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..fceaa15cbb9c99657d6bf9a720f0267c437d4731 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', mesa_ver), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/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/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7f9b603bc65faa52d8b46126a50bcee29ffc269e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://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': 'CrayGNU', 'version': '2015.11'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +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/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3111a314be1d335be306892eb54230a67e4fb812 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +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/f/freetype/freetype-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bc610c637e09e0c08336acbbe80fe5837022c229 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.3' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +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/f/freetype/freetype-2.6.3-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6245460dc23afc9577f6deaf6f3f21d4296c981d --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.3' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..34bf1f36a8eb137e603623c0b622df2ff8c7ed17 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '5.3.0' + +binutilsver = '2.26' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://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 = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/g/GCC/GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..5be824a1d7d6291807c148b8d5d400fea253096b --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.4.0-2.26.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '5.4.0' + +binutilsver = '2.26' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://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 = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..01f4776c64c4627f65b18f7407d6c2bc3d3c22ab --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb @@ -0,0 +1,48 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '4.9.2' + +homepage = 'http://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 = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.2' +gcc_name = 'GCC' + +source_urls = [ + 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + '%s-%s.tar.bz2' % (gcc_name.lower(), version), + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('binutils', '2.25'), +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index 268b0526876636af0c7f5e6de8a2e6e7aba2f7d7..a4f11a8fbdad1938453a02d2e5f7b788de3cdc5b 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -10,7 +10,6 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' -gcc_name = 'GCC' source_urls = [ 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror @@ -19,13 +18,16 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ - '%s-%s.tar.bz2' % (gcc_name.lower(), version), + 'gcc-%(version)s.tar.bz2', 'gmp-6.0.0a.tar.bz2', 'mpfr-%s.tar.gz' % mpfr_version, 'mpc-1.0.2.tar.gz', ] -builddependencies = [('binutils', '2.25')] +builddependencies = [ + ('Autotools', '20150215'), + ('binutils', '2.25'), +] patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..1f2fc04edbe382762c3f9effff81cf3c4d7f1c5e --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '5.3.0' + +homepage = 'http://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 = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.3' + +source_urls = [ + 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.0.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.15.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20151029.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [ + ('binutils', '2.26'), + ('M4', '1.4.17'), +] + +checksums = [ + 'c9616fd448f980259c31de613e575719', # gcc-5.3.0.tar.bz2 + '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 + '7b650781f0a7c4a62e9bc8bdaaa0018b', # mpfr-3.1.3.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + '8428efbbc6f6e2810ce5c1ba73ecf98c', # isl-0.15.tar.bz2 + '6476b450c3db177b2250f3549362380e', # mpfr-3.1.3-allpatches-20151029.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b9a17485e0b1e0ea8b55fe34c5700270ae8a7dc --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '5.4.0' + +homepage = 'http://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 = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.4' + +source_urls = [ + 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.0.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.15.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20160601.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [ + ('binutils', '2.26'), + ('M4', '1.4.17'), +] + +checksums = [ + '4c626ac2a83ef30dfb9260e6f59c2b30', # gcc-5.4.0.tar.bz2 + '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 + '482ab3c120ffc959f631b4ba9ec59a46', # mpfr-3.1.4.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + '8428efbbc6f6e2810ce5c1ba73ecf98c', # isl-0.15.tar.bz2 + '22164533561142b70fda09af4e775acc', # mpfr-3.1.4-allpatches-20150603.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch new file mode 100644 index 0000000000000000000000000000000000000000..891831f521e3fc32e59adb76f4dfe42083df1538 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch @@ -0,0 +1,1830 @@ +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:49:23.950112879 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:49:24.042113845 +0000 +@@ -0,0 +1 @@ ++lngamma-and-doc +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-06-19 19:55:09.000000000 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:49:24.042113845 +0000 +@@ -1 +1 @@ +-3.1.3 ++3.1.3-p1 +diff -Naurd mpfr-3.1.3-a/doc/mpfr.texi mpfr-3.1.3-b/doc/mpfr.texi +--- mpfr-3.1.3-a/doc/mpfr.texi 2015-06-19 19:55:11.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.texi 2015-07-02 10:49:24.018113593 +0000 +@@ -810,13 +810,17 @@ + When the input point is in the closure of the domain of the mathematical + function and an input argument is +0 (resp.@: @minus{}0), one considers + the limit when the corresponding argument approaches 0 from above +-(resp.@: below). If the limit is not defined (e.g., @code{mpfr_log} on +-@minus{}0), the behavior is specified in the description of the MPFR function. ++(resp.@: below), if possible. If the limit is not defined (e.g., ++@code{mpfr_sqrt} and @code{mpfr_log} on @minus{}0), the behavior is ++specified in the description of the MPFR function, but must be consistent ++with the rule from the above paragraph (e.g., @code{mpfr_log} on @pom{}0 ++gives @minus{}Inf). + + When the result is equal to 0, its sign is determined by considering the + limit as if the input point were not in the domain: If one approaches 0 + from above (resp.@: below), the result is +0 (resp.@: @minus{}0); +-for example, @code{mpfr_sin} on +0 gives +0. ++for example, @code{mpfr_sin} on @minus{}0 gives @minus{}0 and ++@code{mpfr_acos} on 1 gives +0 (in all rounding modes). + In the other cases, the sign is specified in the description of the MPFR + function; for example @code{mpfr_max} on @minus{}0 and +0 gives +0. + +@@ -832,8 +836,8 @@ + @c that advantages in practice), like for any bug fix. + Example: @code{mpfr_hypot} on (NaN,0) gives NaN, but @code{mpfr_hypot} + on (NaN,+Inf) gives +Inf (as specified in @ref{Special Functions}), +-since for any finite input @var{x}, @code{mpfr_hypot} on (@var{x},+Inf) +-gives +Inf. ++since for any finite or infinite input @var{x}, @code{mpfr_hypot} on ++(@var{x},+Inf) gives +Inf. + + @node Exceptions, Memory Handling, Floating-Point Values on Special Numbers, MPFR Basics + @comment node-name, next, previous, up +@@ -1581,7 +1585,8 @@ + @deftypefunx int mpfr_add_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_add_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} + @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) + 0 = (+0) and (@minus{}0) + 0 = (@minus{}0)). + The @code{mpfr_add_d} function assumes that the radix of the @code{double} type + is a power of 2, with a precision at most that declared by the C implementation +@@ -1599,7 +1604,8 @@ + @deftypefunx int mpfr_sub_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sub_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} - @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) @minus{} 0 = (+0), (@minus{}0) @minus{} 0 = (@minus{}0), + 0 @minus{} (+0) = (@minus{}0) and 0 @minus{} (@minus{}0) = (+0)). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_sub} +@@ -1615,7 +1621,7 @@ + Set @var{rop} to @math{@var{op1} @GMPtimes{} @var{op2}} rounded in the + direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_mul_d}. + @end deftypefun + +@@ -1635,7 +1641,7 @@ + @deftypefunx int mpfr_div_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1}/@var{op2}} rounded in the direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_div} + and @code{mpfr_div_d}. + @end deftypefun +@@ -1643,15 +1649,18 @@ + @deftypefun int mpfr_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sqrt_ui (mpfr_t @var{rop}, unsigned long int @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{\sqrt{@var{op}}, the square root of @var{op}} +-rounded in the direction @var{rnd} (set @var{rop} to @minus{}0 if @var{op} is +-@minus{}0, to be consistent with the IEEE 754 standard). ++rounded in the direction @var{rnd}. Set @var{rop} to @minus{}0 if ++@var{op} is @minus{}0, to be consistent with the IEEE 754 standard. + Set @var{rop} to NaN if @var{op} is negative. + @end deftypefun + + @deftypefun int mpfr_rec_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{1/\sqrt{@var{op}}, the reciprocal square root of @var{op}} +-rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is +-@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. ++rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is ++@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. Warning! ++Therefore the result on @minus{}0 is different from the one of the rSqrt ++function recommended by the IEEE 754-2008 standard (Section 9.2.1), which ++is @minus{}Inf instead of +Inf. + @end deftypefun + + @deftypefun int mpfr_cbrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -1832,7 +1841,9 @@ + @m{\log_2 @var{op}, log2(@var{op})} or + @m{\log_{10} @var{op}, log10(@var{op})}, respectively, + rounded in the direction @var{rnd}. +-Set @var{rop} to @minus{}Inf if @var{op} is @minus{}0 ++Set @var{rop} to +0 if @var{op} is 1 (in all rounding modes), ++for consistency with the ISO C99 and IEEE 754-2008 standards. ++Set @var{rop} to @minus{}Inf if @var{op} is @pom{}0 + (i.e., the sign of the zero has no influence on the result). + @end deftypefun + +@@ -2003,8 +2014,11 @@ + @deftypefun int mpfr_lngamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to the value of the logarithm of the Gamma function on @var{op}, + rounded in the direction @var{rnd}. +-When @math{@minus{}2@var{k}@minus{}1 @le{} @var{op} @le{} @minus{}2@var{k}}, +-@var{k} being a non-negative integer, @var{rop} is set to NaN. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf, ++following the general rules on special values. ++When @math{@minus{}2@var{k}@minus{}1 < @var{op} < @minus{}2@var{k}}, ++@var{k} being a nonnegative integer, set @var{rop} to NaN@. + See also @code{mpfr_lgamma}. + @end deftypefun + +@@ -2012,10 +2026,11 @@ + Set @var{rop} to the value of the logarithm of the absolute value of the + Gamma function on @var{op}, rounded in the direction @var{rnd}. The sign + (1 or @minus{}1) of Gamma(@var{op}) is returned in the object pointed to +-by @var{signp}. When @var{op} is an infinity or a non-positive integer, set +-@var{rop} to +Inf. When @var{op} is NaN, @minus{}Inf or a negative integer, +-*@var{signp} is undefined, and when @var{op} is @pom{}0, *@var{signp} is +-the sign of the zero. ++by @var{signp}. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf. ++When @var{op} is NaN, @minus{}Inf or a negative integer, *@var{signp} is ++undefined, and when @var{op} is @pom{}0, *@var{signp} is the sign of the zero. + @end deftypefun + + @deftypefun int mpfr_digamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -2064,7 +2079,10 @@ + @deftypefunx int mpfr_fms (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_t @var{op3}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{(@var{op1} @GMPtimes{} @var{op2}) + @var{op3}} + (resp.@: @math{(@var{op1} @GMPtimes{} @var{op2}) - @var{op3}}) +-rounded in the direction @var{rnd}. ++rounded in the direction @var{rnd}. Concerning special values (signed zeros, ++infinities, NaN), these functions behave like a multiplication followed by a ++separate addition or subtraction. That is, the fused operation matters only ++for rounding. + @end deftypefun + + @deftypefun int mpfr_agm (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_rnd_t @var{rnd}) +@@ -2089,8 +2107,8 @@ + i.e., $\sqrt{x^2+y^2}$, + @end tex + rounded in the direction @var{rnd}. +-Special values are handled as described in Section F.9.4.3 of +-the ISO C99 and IEEE 754-2008 standards: ++Special values are handled as described in the ISO C99 (Section F.9.4.3) ++and IEEE 754-2008 (Section 9.2.1) standards: + If @var{x} or @var{y} is an infinity, then +Inf is returned in @var{rop}, + even if the other number is NaN. + @end deftypefun +diff -Naurd mpfr-3.1.3-a/doc/mpfr.info mpfr-3.1.3-b/doc/mpfr.info +--- mpfr-3.1.3-a/doc/mpfr.info 2015-06-19 19:55:53.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.info 2015-07-02 10:49:38.718267817 +0000 +@@ -1,4 +1,4 @@ +-This is mpfr.info, produced by makeinfo version 5.2 from mpfr.texi. ++This is mpfr.info, produced by makeinfo version 6.0 from mpfr.texi. + + This manual documents how to install and use the Multiple Precision + Floating-Point Reliable Library, version 3.1.3. +@@ -55,7 +55,7 @@ + MPFR Copying Conditions + *********************** + +-The GNU MPFR library (or MPFR for short) is "free"; this means that ++The GNU MPFR library (or MPFR for short) is “free”; this means that + everyone is free to use it and free to redistribute it on a free basis. + The library is not in the public domain; it is copyrighted and there are + restrictions on its distribution, but these restrictions are designed to +@@ -418,7 +418,7 @@ + 4.2 Nomenclature and Types + ========================== + +-A "floating-point number", or "float" for short, is an arbitrary ++A “floating-point number”, or “float” for short, is an arbitrary + precision significand (also called mantissa) with a limited precision + exponent. The C data type for such objects is ‘mpfr_t’ (internally + defined as a one-element array of a structure, and ‘mpfr_ptr’ is the C +@@ -432,7 +432,7 @@ + to the other functions supported by MPFR. Unless documented otherwise, + the sign bit of a NaN is unspecified. + +-The "precision" is the number of bits used to represent the significand ++The “precision” is the number of bits used to represent the significand + of a floating-point number; the corresponding C data type is + ‘mpfr_prec_t’. The precision can be any integer between ‘MPFR_PREC_MIN’ + and ‘MPFR_PREC_MAX’. In the current implementation, ‘MPFR_PREC_MIN’ is +@@ -446,7 +446,7 @@ + may abort, crash or have undefined behavior (depending on your C + implementation). + +-The "rounding mode" specifies the way to round the result of a ++The “rounding mode” specifies the way to round the result of a + floating-point operation, in case the exact result can not be + represented exactly in the destination significand; the corresponding C + data type is ‘mpfr_rnd_t’. +@@ -499,14 +499,14 @@ + representable numbers, it is rounded to the one with the least + significant bit set to zero. For example, the number 2.5, which is + represented by (10.1) in binary, is rounded to (10.0)=2 with a precision +-of two bits, and not to (11.0)=3. This rule avoids the "drift" ++of two bits, and not to (11.0)=3. This rule avoids the “drift” + phenomenon mentioned by Knuth in volume 2 of The Art of Computer + Programming (Section 4.2.2). + + Most MPFR functions take as first argument the destination variable, + as second and following arguments the input variables, as last argument + a rounding mode, and have a return value of type ‘int’, called the +-"ternary value". The value stored in the destination variable is ++“ternary value”. The value stored in the destination variable is + correctly rounded, i.e., MPFR behaves as if it computed the result with + an infinite precision, then rounded it to the precision of this + variable. The input variables are regarded as exact (in particular, +@@ -572,15 +572,18 @@ + When the input point is in the closure of the domain of the + mathematical function and an input argument is +0 (resp. −0), one + considers the limit when the corresponding argument approaches 0 from +-above (resp. below). If the limit is not defined (e.g., ‘mpfr_log’ on +-−0), the behavior is specified in the description of the MPFR function. ++above (resp. below), if possible. If the limit is not defined (e.g., ++‘mpfr_sqrt’ and ‘mpfr_log’ on −0), the behavior is specified in the ++description of the MPFR function, but must be consistent with the rule ++from the above paragraph (e.g., ‘mpfr_log’ on ±0 gives −Inf). + + When the result is equal to 0, its sign is determined by considering + the limit as if the input point were not in the domain: If one + approaches 0 from above (resp. below), the result is +0 (resp. −0); for +-example, ‘mpfr_sin’ on +0 gives +0. In the other cases, the sign is +-specified in the description of the MPFR function; for example +-‘mpfr_max’ on −0 and +0 gives +0. ++example, ‘mpfr_sin’ on −0 gives −0 and ‘mpfr_acos’ on 1 gives +0 (in all ++rounding modes). In the other cases, the sign is specified in the ++description of the MPFR function; for example ‘mpfr_max’ on −0 and +0 ++gives +0. + + When the input point is not in the closure of the domain of the + function, the result is NaN. Example: ‘mpfr_sqrt’ on −17 gives NaN. +@@ -590,8 +593,8 @@ + numbers; such a case is always explicitly specified in *note MPFR + Interface::. Example: ‘mpfr_hypot’ on (NaN,0) gives NaN, but + ‘mpfr_hypot’ on (NaN,+Inf) gives +Inf (as specified in *note Special +-Functions::), since for any finite input X, ‘mpfr_hypot’ on (X,+Inf) +-gives +Inf. ++Functions::), since for any finite or infinite input X, ‘mpfr_hypot’ on ++(X,+Inf) gives +Inf. + +  + File: mpfr.info, Node: Exceptions, Next: Memory Handling, Prev: Floating-Point Values on Special Numbers, Up: MPFR Basics +@@ -1253,8 +1256,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_add_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 + OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) + 0 = ++ Set ROP to OP1 + OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) + 0 = + (+0) and (−0) + 0 = (−0)). The ‘mpfr_add_d’ function assumes that + the radix of the ‘double’ type is a power of 2, with a precision at + most that declared by the C implementation (macro +@@ -1280,8 +1284,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_sub_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 - OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) − 0 = ++ Set ROP to OP1 - OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) − 0 = + (+0), (−0) − 0 = (−0), 0 − (+0) = (−0) and 0 − (−0) = (+0)). The + same restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_sub’ and + ‘mpfr_sub_d’. +@@ -1300,7 +1305,7 @@ + mpfr_rnd_t RND) + Set ROP to OP1 times OP2 rounded in the direction RND. When a + result is zero, its sign is the product of the signs of the +- operands (for types having no signed zero, it is considered ++ operands (for types having no signed zeros, 0 is considered + positive). The same restrictions than for ‘mpfr_add_d’ apply to + ‘mpfr_mul_d’. + +@@ -1327,21 +1332,24 @@ + mpfr_rnd_t RND) + Set ROP to OP1/OP2 rounded in the direction RND. When a result is + zero, its sign is the product of the signs of the operands (for +- types having no signed zero, it is considered positive). The same ++ types having no signed zeros, 0 is considered positive). The same + restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_div’ and + ‘mpfr_div_d’. + + -- Function: int mpfr_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_sqrt_ui (mpfr_t ROP, unsigned long int OP, + mpfr_rnd_t RND) +- Set ROP to the square root of OP rounded in the direction RND (set +- ROP to −0 if OP is −0, to be consistent with the IEEE 754 +- standard). Set ROP to NaN if OP is negative. ++ Set ROP to the square root of OP rounded in the direction RND. Set ++ ROP to −0 if OP is −0, to be consistent with the IEEE 754 standard. ++ Set ROP to NaN if OP is negative. + + -- Function: int mpfr_rec_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the reciprocal square root of OP rounded in the + direction RND. Set ROP to +Inf if OP is ±0, +0 if OP is +Inf, and +- NaN if OP is negative. ++ NaN if OP is negative. Warning! Therefore the result on −0 is ++ different from the one of the rSqrt function recommended by the ++ IEEE 754-2008 standard (Section 9.2.1), which is −Inf instead of ++ +Inf. + + -- Function: int mpfr_cbrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_root (mpfr_t ROP, mpfr_t OP, unsigned long int K, +@@ -1515,8 +1523,10 @@ + -- Function: int mpfr_log2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_log10 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the natural logarithm of OP, log2(OP) or log10(OP), +- respectively, rounded in the direction RND. Set ROP to −Inf if OP +- is −0 (i.e., the sign of the zero has no influence on the result). ++ respectively, rounded in the direction RND. Set ROP to +0 if OP is ++ 1 (in all rounding modes), for consistency with the ISO C99 and ++ IEEE 754-2008 standards. Set ROP to −Inf if OP is ±0 (i.e., the ++ sign of the zero has no influence on the result). + + -- Function: int mpfr_exp (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_exp2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) +@@ -1649,17 +1659,21 @@ + + -- Function: int mpfr_lngamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the Gamma function on OP, +- rounded in the direction RND. When −2K−1 <= OP <= −2K, K being a +- non-negative integer, ROP is set to NaN. See also ‘mpfr_lgamma’. ++ rounded in the direction RND. When OP is 1 or 2, set ROP to +0 (in ++ all rounding modes). When OP is an infinity or a nonpositive ++ integer, set ROP to +Inf, following the general rules on special ++ values. When −2K−1 < OP < −2K, K being a nonnegative integer, set ++ ROP to NaN. See also ‘mpfr_lgamma’. + + -- Function: int mpfr_lgamma (mpfr_t ROP, int *SIGNP, mpfr_t OP, + mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the absolute value of the + Gamma function on OP, rounded in the direction RND. The sign (1 or + −1) of Gamma(OP) is returned in the object pointed to by SIGNP. +- When OP is an infinity or a non-positive integer, set ROP to +Inf. +- When OP is NaN, −Inf or a negative integer, *SIGNP is undefined, +- and when OP is ±0, *SIGNP is the sign of the zero. ++ When OP is 1 or 2, set ROP to +0 (in all rounding modes). When OP ++ is an infinity or a nonpositive integer, set ROP to +Inf. When OP ++ is NaN, −Inf or a negative integer, *SIGNP is undefined, and when ++ OP is ±0, *SIGNP is the sign of the zero. + + -- Function: int mpfr_digamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the Digamma (sometimes also called Psi) +@@ -1703,7 +1717,10 @@ + -- Function: int mpfr_fms (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, mpfr_t + OP3, mpfr_rnd_t RND) + Set ROP to (OP1 times OP2) + OP3 (resp. (OP1 times OP2) - OP3) +- rounded in the direction RND. ++ rounded in the direction RND. Concerning special values (signed ++ zeros, infinities, NaN), these functions behave like a ++ multiplication followed by a separate addition or subtraction. ++ That is, the fused operation matters only for rounding. + + -- Function: int mpfr_agm (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, + mpfr_rnd_t RND) +@@ -1717,9 +1734,10 @@ + RND) + Set ROP to the Euclidean norm of X and Y, i.e., the square root of + the sum of the squares of X and Y, rounded in the direction RND. +- Special values are handled as described in Section F.9.4.3 of the +- ISO C99 and IEEE 754-2008 standards: If X or Y is an infinity, then +- +Inf is returned in ROP, even if the other number is NaN. ++ Special values are handled as described in the ISO C99 (Section ++ F.9.4.3) and IEEE 754-2008 (Section 9.2.1) standards: If X or Y is ++ an infinity, then +Inf is returned in ROP, even if the other number ++ is NaN. + + -- Function: int mpfr_ai (mpfr_t ROP, mpfr_t X, mpfr_rnd_t RND) + Set ROP to the value of the Airy function Ai on X, rounded in the +@@ -2670,7 +2688,7 @@ + 5.16 Internals + ============== + +-A "limb" means the part of a multi-precision number that fits in a ++A “limb” means the part of a multi-precision number that fits in a + single word. Usually a limb contains 32 or 64 bits. The C data type + for a limb is ‘mp_limb_t’. + +@@ -3140,7 +3158,7 @@ + 0. PREAMBLE + + The purpose of this License is to make a manual, textbook, or other +- functional and useful document "free" in the sense of freedom: to ++ functional and useful document “free” in the sense of freedom: to + assure everyone the effective freedom to copy and redistribute it, + with or without modifying it, either commercially or + noncommercially. Secondarily, this License preserves for the +@@ -3655,9 +3673,9 @@ + * Menu: + + * mpfr_abs: Basic Arithmetic Functions. +- (line 160) +-* mpfr_acos: Special Functions. (line 51) +-* mpfr_acosh: Special Functions. (line 115) ++ (line 165) ++* mpfr_acos: Special Functions. (line 53) ++* mpfr_acosh: Special Functions. (line 117) + * mpfr_add: Basic Arithmetic Functions. + (line 6) + * mpfr_add_d: Basic Arithmetic Functions. +@@ -3670,15 +3688,15 @@ + (line 8) + * mpfr_add_z: Basic Arithmetic Functions. + (line 14) +-* mpfr_agm: Special Functions. (line 210) +-* mpfr_ai: Special Functions. (line 226) +-* mpfr_asin: Special Functions. (line 52) +-* mpfr_asinh: Special Functions. (line 116) ++* mpfr_agm: Special Functions. (line 219) ++* mpfr_ai: Special Functions. (line 236) ++* mpfr_asin: Special Functions. (line 54) ++* mpfr_asinh: Special Functions. (line 118) + * mpfr_asprintf: Formatted Output Functions. + (line 193) +-* mpfr_atan: Special Functions. (line 53) +-* mpfr_atan2: Special Functions. (line 63) +-* mpfr_atanh: Special Functions. (line 117) ++* mpfr_atan: Special Functions. (line 55) ++* mpfr_atan2: Special Functions. (line 65) ++* mpfr_atanh: Special Functions. (line 119) + * mpfr_buildopt_decimal_p: Miscellaneous Functions. + (line 162) + * mpfr_buildopt_gmpinternals_p: Miscellaneous Functions. +@@ -3690,7 +3708,7 @@ + * mpfr_can_round: Rounding Related Functions. + (line 39) + * mpfr_cbrt: Basic Arithmetic Functions. +- (line 108) ++ (line 113) + * mpfr_ceil: Integer Related Functions. + (line 7) + * mpfr_check_range: Exception Related Functions. +@@ -3735,18 +3753,18 @@ + (line 27) + * mpfr_cmp_z: Comparison Functions. + (line 11) +-* mpfr_const_catalan: Special Functions. (line 237) +-* mpfr_const_euler: Special Functions. (line 236) +-* mpfr_const_log2: Special Functions. (line 234) +-* mpfr_const_pi: Special Functions. (line 235) ++* mpfr_const_catalan: Special Functions. (line 247) ++* mpfr_const_euler: Special Functions. (line 246) ++* mpfr_const_log2: Special Functions. (line 244) ++* mpfr_const_pi: Special Functions. (line 245) + * mpfr_copysign: Miscellaneous Functions. + (line 109) +-* mpfr_cos: Special Functions. (line 29) +-* mpfr_cosh: Special Functions. (line 95) +-* mpfr_cot: Special Functions. (line 47) +-* mpfr_coth: Special Functions. (line 111) +-* mpfr_csc: Special Functions. (line 46) +-* mpfr_csch: Special Functions. (line 110) ++* mpfr_cos: Special Functions. (line 31) ++* mpfr_cosh: Special Functions. (line 97) ++* mpfr_cot: Special Functions. (line 49) ++* mpfr_coth: Special Functions. (line 113) ++* mpfr_csc: Special Functions. (line 48) ++* mpfr_csch: Special Functions. (line 112) + * mpfr_custom_get_exp: Custom Interface. (line 75) + * mpfr_custom_get_kind: Custom Interface. (line 65) + * mpfr_custom_get_significand: Custom Interface. (line 70) +@@ -3756,47 +3774,47 @@ + * mpfr_custom_move: Custom Interface. (line 82) + * MPFR_DECL_INIT: Initialization Functions. + (line 74) +-* mpfr_digamma: Special Functions. (line 166) ++* mpfr_digamma: Special Functions. (line 172) + * mpfr_dim: Basic Arithmetic Functions. +- (line 166) ++ (line 171) + * mpfr_div: Basic Arithmetic Functions. +- (line 72) ++ (line 74) + * mpfr_divby0_p: Exception Related Functions. + (line 134) + * mpfr_div_2exp: Compatibility with MPF. + (line 49) + * mpfr_div_2si: Basic Arithmetic Functions. +- (line 181) ++ (line 186) + * mpfr_div_2ui: Basic Arithmetic Functions. +- (line 179) ++ (line 184) + * mpfr_div_d: Basic Arithmetic Functions. +- (line 84) ++ (line 86) + * mpfr_div_q: Basic Arithmetic Functions. +- (line 88) ++ (line 90) + * mpfr_div_si: Basic Arithmetic Functions. +- (line 80) ++ (line 82) + * mpfr_div_ui: Basic Arithmetic Functions. +- (line 76) ++ (line 78) + * mpfr_div_z: Basic Arithmetic Functions. +- (line 86) ++ (line 88) + * mpfr_d_div: Basic Arithmetic Functions. +- (line 82) ++ (line 84) + * mpfr_d_sub: Basic Arithmetic Functions. +- (line 35) +-* mpfr_eint: Special Functions. (line 133) ++ (line 36) ++* mpfr_eint: Special Functions. (line 135) + * mpfr_eq: Compatibility with MPF. + (line 28) + * mpfr_equal_p: Comparison Functions. + (line 59) + * mpfr_erangeflag_p: Exception Related Functions. + (line 137) +-* mpfr_erf: Special Functions. (line 177) +-* mpfr_erfc: Special Functions. (line 178) +-* mpfr_exp: Special Functions. (line 23) +-* mpfr_exp10: Special Functions. (line 25) +-* mpfr_exp2: Special Functions. (line 24) +-* mpfr_expm1: Special Functions. (line 129) +-* mpfr_fac_ui: Special Functions. (line 121) ++* mpfr_erf: Special Functions. (line 183) ++* mpfr_erfc: Special Functions. (line 184) ++* mpfr_exp: Special Functions. (line 25) ++* mpfr_exp10: Special Functions. (line 27) ++* mpfr_exp2: Special Functions. (line 26) ++* mpfr_expm1: Special Functions. (line 131) ++* mpfr_fac_ui: Special Functions. (line 123) + * mpfr_fits_intmax_p: Conversion Functions. + (line 150) + * mpfr_fits_sint_p: Conversion Functions. +@@ -3815,20 +3833,20 @@ + (line 147) + * mpfr_floor: Integer Related Functions. + (line 8) +-* mpfr_fma: Special Functions. (line 203) ++* mpfr_fma: Special Functions. (line 209) + * mpfr_fmod: Integer Related Functions. + (line 92) +-* mpfr_fms: Special Functions. (line 205) ++* mpfr_fms: Special Functions. (line 211) + * mpfr_fprintf: Formatted Output Functions. + (line 157) + * mpfr_frac: Integer Related Functions. + (line 76) +-* mpfr_free_cache: Special Functions. (line 244) ++* mpfr_free_cache: Special Functions. (line 254) + * mpfr_free_str: Conversion Functions. + (line 137) + * mpfr_frexp: Conversion Functions. + (line 45) +-* mpfr_gamma: Special Functions. (line 148) ++* mpfr_gamma: Special Functions. (line 150) + * mpfr_get_d: Conversion Functions. + (line 7) + * mpfr_get_decimal64: Conversion Functions. +@@ -3887,7 +3905,7 @@ + (line 56) + * mpfr_greater_p: Comparison Functions. + (line 55) +-* mpfr_hypot: Special Functions. (line 218) ++* mpfr_hypot: Special Functions. (line 227) + * mpfr_inexflag_p: Exception Related Functions. + (line 136) + * mpfr_inf_p: Comparison Functions. +@@ -3922,21 +3940,21 @@ + (line 31) + * mpfr_integer_p: Integer Related Functions. + (line 119) +-* mpfr_j0: Special Functions. (line 182) +-* mpfr_j1: Special Functions. (line 183) +-* mpfr_jn: Special Functions. (line 184) ++* mpfr_j0: Special Functions. (line 188) ++* mpfr_j1: Special Functions. (line 189) ++* mpfr_jn: Special Functions. (line 190) + * mpfr_lessequal_p: Comparison Functions. + (line 58) + * mpfr_lessgreater_p: Comparison Functions. + (line 64) + * mpfr_less_p: Comparison Functions. + (line 57) +-* mpfr_lgamma: Special Functions. (line 157) +-* mpfr_li2: Special Functions. (line 143) +-* mpfr_lngamma: Special Functions. (line 152) ++* mpfr_lgamma: Special Functions. (line 162) ++* mpfr_li2: Special Functions. (line 145) ++* mpfr_lngamma: Special Functions. (line 154) + * mpfr_log: Special Functions. (line 16) + * mpfr_log10: Special Functions. (line 18) +-* mpfr_log1p: Special Functions. (line 125) ++* mpfr_log1p: Special Functions. (line 127) + * mpfr_log2: Special Functions. (line 17) + * mpfr_max: Miscellaneous Functions. + (line 22) +@@ -3947,29 +3965,29 @@ + * mpfr_modf: Integer Related Functions. + (line 82) + * mpfr_mul: Basic Arithmetic Functions. +- (line 51) ++ (line 53) + * mpfr_mul_2exp: Compatibility with MPF. + (line 47) + * mpfr_mul_2si: Basic Arithmetic Functions. +- (line 174) ++ (line 179) + * mpfr_mul_2ui: Basic Arithmetic Functions. +- (line 172) ++ (line 177) + * mpfr_mul_d: Basic Arithmetic Functions. +- (line 57) ++ (line 59) + * mpfr_mul_q: Basic Arithmetic Functions. +- (line 61) ++ (line 63) + * mpfr_mul_si: Basic Arithmetic Functions. +- (line 55) ++ (line 57) + * mpfr_mul_ui: Basic Arithmetic Functions. +- (line 53) ++ (line 55) + * mpfr_mul_z: Basic Arithmetic Functions. +- (line 59) ++ (line 61) + * mpfr_nanflag_p: Exception Related Functions. + (line 135) + * mpfr_nan_p: Comparison Functions. + (line 39) + * mpfr_neg: Basic Arithmetic Functions. +- (line 159) ++ (line 164) + * mpfr_nextabove: Miscellaneous Functions. + (line 15) + * mpfr_nextbelow: Miscellaneous Functions. +@@ -3983,13 +4001,13 @@ + * mpfr_overflow_p: Exception Related Functions. + (line 133) + * mpfr_pow: Basic Arithmetic Functions. +- (line 116) ++ (line 121) + * mpfr_pow_si: Basic Arithmetic Functions. +- (line 120) ++ (line 125) + * mpfr_pow_ui: Basic Arithmetic Functions. +- (line 118) ++ (line 123) + * mpfr_pow_z: Basic Arithmetic Functions. +- (line 122) ++ (line 127) + * mpfr_prec_round: Rounding Related Functions. + (line 13) + * ‘mpfr_prec_t’: Nomenclature and Types. +@@ -3999,7 +4017,7 @@ + * mpfr_print_rnd_mode: Rounding Related Functions. + (line 71) + * mpfr_rec_sqrt: Basic Arithmetic Functions. +- (line 103) ++ (line 105) + * mpfr_regular_p: Comparison Functions. + (line 43) + * mpfr_reldiff: Compatibility with MPF. +@@ -4021,11 +4039,11 @@ + * ‘mpfr_rnd_t’: Nomenclature and Types. + (line 34) + * mpfr_root: Basic Arithmetic Functions. +- (line 109) ++ (line 114) + * mpfr_round: Integer Related Functions. + (line 9) +-* mpfr_sec: Special Functions. (line 45) +-* mpfr_sech: Special Functions. (line 109) ++* mpfr_sec: Special Functions. (line 47) ++* mpfr_sech: Special Functions. (line 111) + * mpfr_set: Assignment Functions. + (line 9) + * mpfr_setsign: Miscellaneous Functions. +@@ -4100,57 +4118,57 @@ + (line 49) + * mpfr_signbit: Miscellaneous Functions. + (line 99) +-* mpfr_sin: Special Functions. (line 30) +-* mpfr_sinh: Special Functions. (line 96) +-* mpfr_sinh_cosh: Special Functions. (line 101) +-* mpfr_sin_cos: Special Functions. (line 35) ++* mpfr_sin: Special Functions. (line 32) ++* mpfr_sinh: Special Functions. (line 98) ++* mpfr_sinh_cosh: Special Functions. (line 103) ++* mpfr_sin_cos: Special Functions. (line 37) + * mpfr_si_div: Basic Arithmetic Functions. +- (line 78) ++ (line 80) + * mpfr_si_sub: Basic Arithmetic Functions. +- (line 31) ++ (line 32) + * mpfr_snprintf: Formatted Output Functions. + (line 180) + * mpfr_sprintf: Formatted Output Functions. + (line 170) + * mpfr_sqr: Basic Arithmetic Functions. +- (line 69) ++ (line 71) + * mpfr_sqrt: Basic Arithmetic Functions. +- (line 96) ++ (line 98) + * mpfr_sqrt_ui: Basic Arithmetic Functions. +- (line 97) ++ (line 99) + * mpfr_strtofr: Assignment Functions. + (line 80) + * mpfr_sub: Basic Arithmetic Functions. +- (line 25) ++ (line 26) + * mpfr_subnormalize: Exception Related Functions. + (line 60) + * mpfr_sub_d: Basic Arithmetic Functions. +- (line 37) ++ (line 38) + * mpfr_sub_q: Basic Arithmetic Functions. +- (line 43) ++ (line 44) + * mpfr_sub_si: Basic Arithmetic Functions. +- (line 33) ++ (line 34) + * mpfr_sub_ui: Basic Arithmetic Functions. +- (line 29) ++ (line 30) + * mpfr_sub_z: Basic Arithmetic Functions. +- (line 41) +-* mpfr_sum: Special Functions. (line 252) ++ (line 42) ++* mpfr_sum: Special Functions. (line 262) + * mpfr_swap: Assignment Functions. + (line 150) + * ‘mpfr_t’: Nomenclature and Types. + (line 6) +-* mpfr_tan: Special Functions. (line 31) +-* mpfr_tanh: Special Functions. (line 97) ++* mpfr_tan: Special Functions. (line 33) ++* mpfr_tanh: Special Functions. (line 99) + * mpfr_trunc: Integer Related Functions. + (line 10) + * mpfr_ui_div: Basic Arithmetic Functions. +- (line 74) ++ (line 76) + * mpfr_ui_pow: Basic Arithmetic Functions. +- (line 126) ++ (line 131) + * mpfr_ui_pow_ui: Basic Arithmetic Functions. +- (line 124) ++ (line 129) + * mpfr_ui_sub: Basic Arithmetic Functions. +- (line 27) ++ (line 28) + * mpfr_underflow_p: Exception Related Functions. + (line 132) + * mpfr_unordered_p: Comparison Functions. +@@ -4181,61 +4199,61 @@ + (line 182) + * mpfr_vsprintf: Formatted Output Functions. + (line 171) +-* mpfr_y0: Special Functions. (line 193) +-* mpfr_y1: Special Functions. (line 194) +-* mpfr_yn: Special Functions. (line 195) ++* mpfr_y0: Special Functions. (line 199) ++* mpfr_y1: Special Functions. (line 200) ++* mpfr_yn: Special Functions. (line 201) + * mpfr_zero_p: Comparison Functions. + (line 42) +-* mpfr_zeta: Special Functions. (line 171) +-* mpfr_zeta_ui: Special Functions. (line 172) ++* mpfr_zeta: Special Functions. (line 177) ++* mpfr_zeta_ui: Special Functions. (line 178) + * mpfr_z_sub: Basic Arithmetic Functions. +- (line 39) ++ (line 40) + + +  + Tag Table: + Node: Top775 + Node: Copying2007 +-Node: Introduction to MPFR3766 +-Node: Installing MPFR5880 +-Node: Reporting Bugs11323 +-Node: MPFR Basics13353 +-Node: Headers and Libraries13669 +-Node: Nomenclature and Types16828 +-Node: MPFR Variable Conventions18874 +-Node: Rounding Modes20418 +-Ref: ternary value21544 +-Node: Floating-Point Values on Special Numbers23526 +-Node: Exceptions26572 +-Node: Memory Handling29749 +-Node: MPFR Interface30894 +-Node: Initialization Functions33008 +-Node: Assignment Functions40318 +-Node: Combined Initialization and Assignment Functions49673 +-Node: Conversion Functions50974 +-Node: Basic Arithmetic Functions60035 +-Node: Comparison Functions69200 +-Node: Special Functions72687 +-Node: Input and Output Functions86672 +-Node: Formatted Output Functions88644 +-Node: Integer Related Functions98431 +-Node: Rounding Related Functions105051 +-Node: Miscellaneous Functions108888 +-Node: Exception Related Functions117568 +-Node: Compatibility with MPF124386 +-Node: Custom Interface127127 +-Node: Internals131526 +-Node: API Compatibility133066 +-Node: Type and Macro Changes134995 +-Node: Added Functions137844 +-Node: Changed Functions141132 +-Node: Removed Functions145545 +-Node: Other Changes145973 +-Node: Contributors147576 +-Node: References150219 +-Node: GNU Free Documentation License151973 +-Node: Concept Index174562 +-Node: Function and Type Index180659 ++Node: Introduction to MPFR3770 ++Node: Installing MPFR5884 ++Node: Reporting Bugs11327 ++Node: MPFR Basics13357 ++Node: Headers and Libraries13673 ++Node: Nomenclature and Types16832 ++Node: MPFR Variable Conventions18894 ++Node: Rounding Modes20438 ++Ref: ternary value21568 ++Node: Floating-Point Values on Special Numbers23554 ++Node: Exceptions26813 ++Node: Memory Handling29990 ++Node: MPFR Interface31135 ++Node: Initialization Functions33249 ++Node: Assignment Functions40559 ++Node: Combined Initialization and Assignment Functions49914 ++Node: Conversion Functions51215 ++Node: Basic Arithmetic Functions60276 ++Node: Comparison Functions69777 ++Node: Special Functions73264 ++Node: Input and Output Functions87862 ++Node: Formatted Output Functions89834 ++Node: Integer Related Functions99621 ++Node: Rounding Related Functions106241 ++Node: Miscellaneous Functions110078 ++Node: Exception Related Functions118758 ++Node: Compatibility with MPF125576 ++Node: Custom Interface128317 ++Node: Internals132716 ++Node: API Compatibility134260 ++Node: Type and Macro Changes136189 ++Node: Added Functions139038 ++Node: Changed Functions142326 ++Node: Removed Functions146739 ++Node: Other Changes147167 ++Node: Contributors148770 ++Node: References151413 ++Node: GNU Free Documentation License153167 ++Node: Concept Index175760 ++Node: Function and Type Index181857 +  + End Tag Table + +diff -Naurd mpfr-3.1.3-a/src/lngamma.c mpfr-3.1.3-b/src/lngamma.c +--- mpfr-3.1.3-a/src/lngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/lngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -603,16 +603,17 @@ + mpfr_get_prec (y), mpfr_log_prec, y, inex)); + + /* special cases */ +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x) || ++ (MPFR_IS_NEG (x) && mpfr_integer_p (x)))) + { +- if (MPFR_IS_NAN (x) || MPFR_IS_NEG (x)) ++ if (MPFR_IS_NAN (x)) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; + } +- else /* lngamma(+Inf) = lngamma(+0) = +Inf */ ++ else /* lngamma(+/-Inf) = lngamma(nonpositive integer) = +Inf */ + { +- if (MPFR_IS_ZERO (x)) ++ if (!MPFR_IS_INF (x)) + mpfr_set_divby0 (); + MPFR_SET_INF (y); + MPFR_SET_POS (y); +@@ -620,8 +621,8 @@ + } + } + +- /* if x < 0 and -2k-1 <= x <= -2k, then lngamma(x) = NaN */ +- if (MPFR_IS_NEG (x) && (unit_bit (x) == 0 || mpfr_integer_p (x))) ++ /* if -2k-1 < x < -2k <= 0, then lngamma(x) = NaN */ ++ if (MPFR_IS_NEG (x) && unit_bit (x) == 0) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3" ++#define MPFR_VERSION_STRING "3.1.3-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:49:24.042113845 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3"; ++ return "3.1.3-p1"; + } +diff -Naurd mpfr-3.1.3-a/tests/tlngamma.c mpfr-3.1.3-b/tests/tlngamma.c +--- mpfr-3.1.3-a/tests/tlngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tlngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -33,7 +33,7 @@ + special (void) + { + mpfr_t x, y; +- int inex; ++ int i, inex; + + mpfr_init (x); + mpfr_init (y); +@@ -46,25 +46,29 @@ + exit (1); + } + +- mpfr_set_inf (x, -1); ++ mpfr_set_inf (x, 1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(-Inf)\n"); ++ printf ("Error for lngamma(+Inf)\n"); + exit (1); + } + +- mpfr_set_inf (x, 1); ++ mpfr_set_inf (x, -1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(+Inf)\n"); ++ printf ("Error for lngamma(-Inf)\n"); + exit (1); + } + + mpfr_set_ui (x, 0, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(+0)\n"); + exit (1); +@@ -72,32 +76,58 @@ + + mpfr_set_ui (x, 0, MPFR_RNDN); + mpfr_neg (x, x, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(-0)\n"); + exit (1); + } + + mpfr_set_ui (x, 1, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(1)\n"); + exit (1); + } + +- mpfr_set_si (x, -1, MPFR_RNDN); +- mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ for (i = 1; i <= 5; i++) + { +- printf ("Error for lngamma(-1)\n"); +- exit (1); ++ int c; ++ ++ mpfr_set_si (x, -i, MPFR_RNDN); ++ mpfr_clear_flags (); ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) ++ { ++ printf ("Error for lngamma(-%d)\n", i); ++ exit (1); ++ } ++ if (i & 1) ++ { ++ mpfr_nextabove (x); ++ c = '+'; ++ } ++ else ++ { ++ mpfr_nextbelow (x); ++ c = '-'; ++ } ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_nan_p (y)) ++ { ++ printf ("Error for lngamma(-%d%cepsilon)\n", i, c); ++ exit (1); ++ } + } + + mpfr_set_ui (x, 2, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(2)\n"); + exit (1); +@@ -127,7 +157,7 @@ + mpfr_set_str (x, CHECK_X2, 10, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str (x, CHECK_Y2, 10, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp (y, x)) ++ if (mpfr_cmp0 (y, x)) + { + printf ("mpfr_lngamma("CHECK_X2") is wrong:\n" + "expected "); +@@ -143,7 +173,7 @@ + mpfr_lngamma (y, x, MPFR_RNDU); + mpfr_set_prec (x, 175); + mpfr_set_str_binary (x, "0.1010001100011101101011001101110010100001000001000001110011000001101100001111001001000101011011100100010101011110100111110101010100010011010010000101010111001100011000101111E7"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (1)\n"); + exit (1); +@@ -155,7 +185,7 @@ + mpfr_lngamma (x, y, MPFR_RNDZ); + mpfr_set_prec (y, 21); + mpfr_set_str_binary (y, "0.111000101000001100101E9"); +- if (MPFR_IS_NAN (x) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (120)\n"); + printf ("Expected "); mpfr_print_binary (y); puts (""); +@@ -169,7 +199,7 @@ + inex = mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 206); + mpfr_set_str_binary (x, "0.10000111011000000011100010101001100110001110000111100011000100100110110010001011011110101001111011110110000001010100111011010000000011100110110101100111000111010011110010000100010111101010001101000110101001E13"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (768)\n"); + exit (1); +@@ -185,7 +215,7 @@ + mpfr_set_str_binary (x, "0.1100E-66"); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str_binary (x, "0.1100E6"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(0.1100E-66)\n"); + exit (1); +@@ -199,7 +229,7 @@ + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 32); + mpfr_set_str_binary (x, "-0.10001000111011111011000010100010E207"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(-2^199+0.5)\n"); + printf ("Got "); +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:50:08.046573308 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:50:08.126574142 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-overflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:50:08.126574142 +0000 +@@ -1 +1 @@ +-3.1.3-p1 ++3.1.3-p2 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -49,7 +49,7 @@ + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +- else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || ++ else if (MPFR_UNLIKELY(n <= 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || + exp > __gmpfr_emax + n)) ) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 +@@ -32,7 +32,7 @@ + rnd_mode), + ("y[%Pu]=%.*Rg inexact=%d", mpfr_get_prec(y), mpfr_log_prec, y, inexact)); + +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (n == 0 || MPFR_IS_SINGULAR (x))) + return mpfr_set (y, x, rnd_mode); + else + { +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p1" ++#define MPFR_VERSION_STRING "3.1.3-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -39,7 +39,7 @@ + { + mpfr_exp_t exp = MPFR_GET_EXP (x); + MPFR_SETRAW (inexact, y, x, exp, rnd_mode); +- if (MPFR_UNLIKELY( n > 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || ++ if (MPFR_UNLIKELY(n >= 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || + exp > __gmpfr_emax - n))) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emin > MPFR_EMAX_MAX + n || +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:50:08.126574142 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p1"; ++ return "3.1.3-p2"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 +@@ -242,6 +242,76 @@ + large (MPFR_EMAX_MAX); + } + ++/* Cases where the function overflows on n = 0 when rounding is like ++ away from zero. */ ++static void ++overflow0 (mpfr_exp_t emax) ++{ ++ mpfr_exp_t old_emax; ++ mpfr_t x, y1, y2; ++ int neg, r, op; ++ static char *sop[4] = { "mul_2ui", "mul_2si", "div_2ui", "div_2si" }; ++ ++ old_emax = mpfr_get_emax (); ++ set_emax (emax); ++ ++ mpfr_init2 (x, 8); ++ mpfr_inits2 (6, y1, y2, (mpfr_ptr) 0); ++ ++ mpfr_set_inf (x, 1); ++ mpfr_nextbelow (x); ++ ++ for (neg = 0; neg <= 1; neg++) ++ { ++ RND_LOOP (r) ++ { ++ int inex1, inex2; ++ unsigned int flags1, flags2; ++ ++ /* Even if there isn't an overflow (rounding ~ toward zero), ++ the result is the same as the one of an overflow. */ ++ inex1 = mpfr_overflow (y1, (mpfr_rnd_t) r, neg ? -1 : 1); ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (mpfr_inf_p (y1)) ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ for (op = 0; op < 4; op++) ++ { ++ mpfr_clear_flags (); ++ inex2 = ++ op == 0 ? mpfr_mul_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 1 ? mpfr_mul_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 2 ? mpfr_div_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 3 ? mpfr_div_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ (MPFR_ASSERTN (0), 0); ++ flags2 = __gmpfr_flags; ++ if (!(mpfr_equal_p (y1, y2) && ++ SAME_SIGN (inex1, inex2) && ++ flags1 == flags2)) ++ { ++ printf ("Error in overflow0 for %s, mpfr_%s, emax = %" ++ MPFR_EXP_FSPEC "d,\nx = ", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r), sop[op], ++ (mpfr_eexp_t) emax); ++ mpfr_dump (x); ++ printf ("Expected "); ++ mpfr_dump (y1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (y2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } ++ mpfr_neg (x, x, MPFR_RNDN); ++ } ++ ++ mpfr_clears (x, y1, y2, (mpfr_ptr) 0); ++ set_emax (old_emax); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -334,6 +404,11 @@ + underflow0 (); + large0 (); + ++ if (mpfr_get_emax () != MPFR_EMAX_MAX) ++ overflow0 (mpfr_get_emax ()); ++ overflow0 (MPFR_EMAX_MAX); ++ overflow0 (-1); ++ + tests_end_mpfr (); + return 0; + } +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-17 08:54:48.592799981 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-17 08:54:48.616811495 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-underflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-17 08:54:48.616811495 +0000 +@@ -1 +1 @@ +-3.1.3-p2 ++3.1.3-p3 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -45,7 +45,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX - (n - 1) || + exp < __gmpfr_emin + (n - 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-17 08:54:48.608807656 +0000 +@@ -44,7 +44,9 @@ + if (MPFR_UNLIKELY (n >= diffexp)) /* exp - n <= emin - 1 */ + { + if (rnd_mode == MPFR_RNDN && +- (n > diffexp || (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ (n > diffexp || ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN (y)); + } +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-17 08:54:48.616811495 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p2" ++#define MPFR_VERSION_STRING "3.1.3-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -48,7 +48,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX + (n + 1) || + exp < __gmpfr_emin - (n + 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-17 08:54:48.616811495 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p2"; ++ return "3.1.3-p3"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-17 08:54:48.608807656 +0000 +@@ -50,77 +50,82 @@ + { + mpfr_t x, y, z1, z2; + mpfr_exp_t emin; +- int i, k; ++ int i, k, s; + int prec; + int rnd; + int div; + int inex1, inex2; + unsigned int flags1, flags2; + +- /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) +- * with emin = e, x = 1 + i/16, i in { -1, 0, 1 }, and k = 1 to 4, +- * by comparing the result with the one of a simple division. ++ /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) with ++ * emin = e, x = s * (1 + i/16), i in { -1, 0, 1 }, s in { -1, 1 }, and ++ * k = 1 to 4, by comparing the result with the one of a simple division. + */ + emin = mpfr_get_emin (); + set_emin (e); + mpfr_inits2 (8, x, y, (mpfr_ptr) 0); + for (i = 15; i <= 17; i++) +- { +- inex1 = mpfr_set_ui_2exp (x, i, -4, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- for (prec = 6; prec >= 3; prec -= 3) +- { +- mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); +- RND_LOOP (rnd) +- for (k = 1; k <= 4; k++) +- { +- /* The following one is assumed to be correct. */ +- inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- mpfr_clear_flags (); +- /* Do not use mpfr_div_ui to avoid the optimization +- by mpfr_div_2si. */ +- inex1 = mpfr_div (z1, y, z1, (mpfr_rnd_t) rnd); +- flags1 = __gmpfr_flags; +- +- for (div = 0; div <= 2; div++) ++ for (s = 1; s >= -1; s -= 2) ++ { ++ inex1 = mpfr_set_si_2exp (x, s * i, -4, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ for (prec = 6; prec >= 3; prec -= 3) ++ { ++ mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); ++ RND_LOOP (rnd) ++ for (k = 1; k <= 4; k++) + { ++ /* The following one is assumed to be correct. */ ++ inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); + mpfr_clear_flags (); +- inex2 = div == 0 ? +- mpfr_mul_2si (z2, x, e - k, (mpfr_rnd_t) rnd) : div == 1 ? +- mpfr_div_2si (z2, x, k - e, (mpfr_rnd_t) rnd) : +- mpfr_div_2ui (z2, x, k - e, (mpfr_rnd_t) rnd); +- flags2 = __gmpfr_flags; +- if (flags1 == flags2 && SAME_SIGN (inex1, inex2) && +- mpfr_equal_p (z1, z2)) +- continue; +- printf ("Error in underflow("); +- if (e == MPFR_EMIN_MIN) +- printf ("MPFR_EMIN_MIN"); +- else if (e == emin) +- printf ("default emin"); +- else if (e >= LONG_MIN) +- printf ("%ld", (long) e); +- else +- printf ("= LONG_MIN) ++ printf ("%ld", (long) e); ++ else ++ printf ("d1 or (np[n-1]=d1 and np[n-2]>=d0) here, ++ since we truncate the divisor at each step, but since {np,n} < D ++ originally, the largest possible partial quotient is B-1. */ ++ if (MPFR_UNLIKELY(np[n-1] > d1 || (np[n-1] == d1 && np[n-2] >= d0))) + q2 = ~ (mp_limb_t) 0; + else + udiv_qr_3by2 (q2, q1, q0, np[n - 1], np[n - 2], np[n - 3], +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-17 08:58:21.118986898 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-10-29 13:47:46.763900609 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p4"; ++ return "3.1.3-p5"; + } +diff -Naurd mpfr-3.1.3-a/tests/tdiv.c mpfr-3.1.3-b/tests/tdiv.c +--- mpfr-3.1.3-a/tests/tdiv.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tdiv.c 2015-10-29 13:47:46.751900855 +0000 +@@ -1099,6 +1099,69 @@ + mpfr_set_emax (old_emax); + } + ++/* Bug in mpfr_divhigh_n_basecase when all limbs of q (except the most ++ significant one) are B-1 where B=2^GMP_NUMB_BITS. Since we truncate ++ the divisor at each step, it might happen at some point that ++ (np[n-1],np[n-2]) > (d1,d0), and not only the equality. ++ Reported by Ricky Farr ++ ++ To get a failure, a MPFR_DIVHIGH_TAB entry below the MPFR_DIV_THRESHOLD ++ limit must have a value 0. With most mparam.h files, this cannot occur. */ ++static void ++test_20151023 (void) ++{ ++ mpfr_prec_t p; ++ mpfr_t n, d, q, q0; ++ int inex, i; ++ ++ for (p = GMP_NUMB_BITS; p <= 2000; p++) ++ { ++ mpfr_init2 (n, 2*p); ++ mpfr_init2 (d, p); ++ mpfr_init2 (q, p); ++ mpfr_init2 (q0, GMP_NUMB_BITS); ++ ++ /* generate a random divisor of p bits */ ++ mpfr_urandomb (d, RANDS); ++ /* generate a random quotient of GMP_NUMB_BITS bits */ ++ mpfr_urandomb (q0, RANDS); ++ /* zero-pad the quotient to p bits */ ++ inex = mpfr_prec_round (q0, p, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ ++ for (i = 0; i < 3; i++) ++ { ++ /* i=0: try with the original quotient xxx000...000 ++ i=1: try with the original quotient minus one ulp ++ i=2: try with the original quotient plus one ulp */ ++ if (i == 1) ++ mpfr_nextbelow (q0); ++ else if (i == 2) ++ { ++ mpfr_nextabove (q0); ++ mpfr_nextabove (q0); ++ } ++ ++ inex = mpfr_mul (n, d, q0, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_nextabove (n); ++ mpfr_div (q, n, d, MPFR_RNDN); ++ MPFR_ASSERTN(mpfr_cmp (q, q0) == 0); ++ ++ inex = mpfr_mul (n, d, q0, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_nextbelow (n); ++ mpfr_div (q, n, d, MPFR_RNDN); ++ MPFR_ASSERTN(mpfr_cmp (q, q0) == 0); ++ } ++ ++ mpfr_clear (n); ++ mpfr_clear (d); ++ mpfr_clear (q); ++ mpfr_clear (q0); ++ } ++} ++ + #define TEST_FUNCTION test_div + #define TWO_ARGS + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) +@@ -1219,6 +1282,7 @@ + consistency (); + test_20070603 (); + test_20070628 (); ++ test_20151023 (); + test_generic (2, 800, 50); + test_extreme (); + diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160601.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160601.patch new file mode 100644 index 0000000000000000000000000000000000000000..042e73d766f811adcdc00bf989dd329ecfa42185 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160601.patch @@ -0,0 +1,358 @@ +downloaded from https://gforge.inria.fr/scm/viewvc.php/mpfr/misc/www/mpfr-3.1.4/allpatches?revision=10393&view=co +on June 3rd 2016 (last change: 2016-06-01) +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-04-13 21:22:23.720604013 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-04-13 21:22:23.744603677 +0000 +@@ -0,0 +1 @@ ++unix-check +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-04-13 21:22:23.744603677 +0000 +@@ -1 +1 @@ +-3.1.4 ++3.1.4-p1 +diff -Naurd mpfr-3.1.4-a/src/mpfr-impl.h mpfr-3.1.4-b/src/mpfr-impl.h +--- mpfr-3.1.4-a/src/mpfr-impl.h 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/mpfr-impl.h 2016-04-13 21:22:23.736603789 +0000 +@@ -252,19 +252,6 @@ + # define MPFR_WIN_THREAD_SAFE_DLL 1 + #endif + +-/* Detect some possible inconsistencies under Unix. */ +-#if defined(__unix__) +-# if defined(_WIN32) +-# error "Both __unix__ and _WIN32 are defined" +-# endif +-# if __GMP_LIBGMP_DLL +-# error "__unix__ is defined and __GMP_LIBGMP_DLL is true" +-# endif +-# if defined(MPFR_WIN_THREAD_SAFE_DLL) +-# error "Both __unix__ and MPFR_WIN_THREAD_SAFE_DLL are defined" +-# endif +-#endif +- + #if defined(__MPFR_WITHIN_MPFR) || !defined(MPFR_WIN_THREAD_SAFE_DLL) + extern MPFR_THREAD_ATTR unsigned int __gmpfr_flags; + extern MPFR_THREAD_ATTR mpfr_exp_t __gmpfr_emin; +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4" ++#define MPFR_VERSION_STRING "3.1.4-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-04-13 21:22:23.744603677 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4"; ++ return "3.1.4-p1"; + } +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-05-22 19:59:43.838399677 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-05-22 19:59:43.866399168 +0000 +@@ -0,0 +1 @@ ++add-sub-ui-flags +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-05-22 19:59:43.866399168 +0000 +@@ -1 +1 @@ +-3.1.4-p1 ++3.1.4-p2 +diff -Naurd mpfr-3.1.4-a/src/add_ui.c mpfr-3.1.4-b/src/add_ui.c +--- mpfr-3.1.4-a/src/add_ui.c 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/add_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -49,6 +49,7 @@ + MPFR_SAVE_EXPO_MARK (expo); + MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); + inex = mpfr_add(y, x, uu, rnd_mode); ++ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); + MPFR_SAVE_EXPO_FREE (expo); + return mpfr_check_range(y, inex, rnd_mode); + } +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p1" ++#define MPFR_VERSION_STRING "3.1.4-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/sub_ui.c mpfr-3.1.4-b/src/sub_ui.c +--- mpfr-3.1.4-a/src/sub_ui.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/sub_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -52,6 +52,7 @@ + MPFR_SAVE_EXPO_MARK (expo); + MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); + inex = mpfr_sub (y, x, uu, rnd_mode); ++ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); + MPFR_SAVE_EXPO_FREE (expo); + return mpfr_check_range (y, inex, rnd_mode); + } +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-05-22 19:59:43.866399168 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p1"; ++ return "3.1.4-p2"; + } +diff -Naurd mpfr-3.1.4-a/tests/tadd_ui.c mpfr-3.1.4-b/tests/tadd_ui.c +--- mpfr-3.1.4-a/tests/tadd_ui.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tadd_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -69,7 +69,9 @@ + + /* nan + 2394875 == nan */ + mpfr_set_nan (x); ++ mpfr_clear_nanflag (); + mpfr_add_ui (y, x, 2394875L, MPFR_RNDN); ++ MPFR_ASSERTN (mpfr_nanflag_p ()); + MPFR_ASSERTN (mpfr_nan_p (y)); + + /* +inf + 2394875 == +inf */ +diff -Naurd mpfr-3.1.4-a/tests/tsub_ui.c mpfr-3.1.4-b/tests/tsub_ui.c +--- mpfr-3.1.4-a/tests/tsub_ui.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsub_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -96,7 +96,9 @@ + + /* nan - 1 == nan */ + mpfr_set_nan (x); ++ mpfr_clear_nanflag (); + mpfr_sub_ui (y, x, 1L, MPFR_RNDN); ++ MPFR_ASSERTN (mpfr_nanflag_p ()); + MPFR_ASSERTN (mpfr_nan_p (y)); + + /* +inf - 1 == +inf */ +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-06-01 13:00:30.748711490 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-06-01 13:00:30.772711162 +0000 +@@ -0,0 +1 @@ ++sub1-overflow +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-05-22 19:59:43.866399168 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-06-01 13:00:30.772711162 +0000 +@@ -1 +1 @@ +-3.1.4-p2 ++3.1.4-p3 +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-06-01 13:00:30.772711162 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p2" ++#define MPFR_VERSION_STRING "3.1.4-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/sub1.c mpfr-3.1.4-b/src/sub1.c +--- mpfr-3.1.4-a/src/sub1.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/sub1.c 2016-06-01 13:00:30.760711326 +0000 +@@ -96,16 +96,15 @@ + /* A = S*ABS(B) +/- ulp(a) */ + MPFR_SET_EXP (a, MPFR_GET_EXP (b)); + MPFR_RNDRAW_EVEN (inexact, a, MPFR_MANT (b), MPFR_PREC (b), +- rnd_mode, MPFR_SIGN (a), +- if (MPFR_UNLIKELY ( ++MPFR_EXP (a) > __gmpfr_emax)) +- inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a))); +- /* inexact = mpfr_set4 (a, b, rnd_mode, MPFR_SIGN (a)); */ ++ rnd_mode, MPFR_SIGN (a), ++ MPFR_EXP (a)); + if (inexact == 0) + { + /* a = b (Exact) + But we know it isn't (Since we have to remove `c') + So if we round to Zero, we have to remove one ulp. + Otherwise the result is correctly rounded. */ ++ /* An overflow is not possible. */ ++ MPFR_ASSERTD (MPFR_EXP (a) <= __gmpfr_emax); + if (MPFR_IS_LIKE_RNDZ (rnd_mode, MPFR_IS_NEG (a))) + { + mpfr_nexttozero (a); +@@ -136,9 +135,14 @@ + i.e. inexact= MPFR_EVEN_INEX */ + if (MPFR_UNLIKELY (inexact == MPFR_EVEN_INEX*MPFR_INT_SIGN (a))) + { +- mpfr_nexttozero (a); ++ if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) ++ mpfr_setmax (a, __gmpfr_emax); ++ else ++ mpfr_nexttozero (a); + inexact = -MPFR_INT_SIGN (a); + } ++ else if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) ++ inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a)); + MPFR_RET (inexact); + } + } +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-05-22 19:59:43.866399168 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-06-01 13:00:30.772711162 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p2"; ++ return "3.1.4-p3"; + } +diff -Naurd mpfr-3.1.4-a/tests/tsub.c mpfr-3.1.4-b/tests/tsub.c +--- mpfr-3.1.4-a/tests/tsub.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsub.c 2016-06-01 13:00:30.760711326 +0000 +@@ -630,6 +630,135 @@ + } + } + ++static void ++check_max_almosteven (void) ++{ ++ mpfr_exp_t old_emin, old_emax; ++ mpfr_exp_t emin[2] = { MPFR_EMIN_MIN, -1000 }; ++ mpfr_exp_t emax[2] = { MPFR_EMAX_MAX, 1000 }; ++ int i; ++ ++ old_emin = mpfr_get_emin (); ++ old_emax = mpfr_get_emax (); ++ ++ for (i = 0; i < 2; i++) ++ { ++ mpfr_t a1, a2, b, c; ++ mpfr_prec_t p; ++ int neg, j, rnd; ++ ++ set_emin (emin[i]); ++ set_emax (emax[i]); ++ ++ p = MPFR_PREC_MIN + randlimb () % 70; ++ mpfr_init2 (a1, p); ++ mpfr_init2 (a2, p); ++ mpfr_init2 (b, p+1); ++ mpfr_init2 (c, MPFR_PREC_MIN); ++ ++ mpfr_setmax (b, 0); ++ mpfr_set_ui (c, 1, MPFR_RNDN); ++ ++ for (neg = 0; neg < 2; neg++) ++ { ++ for (j = 1; j >= 0; j--) ++ { ++ mpfr_set_exp (b, __gmpfr_emax - j); ++ RND_LOOP (rnd) ++ { ++ unsigned int flags1, flags2; ++ int inex1, inex2; ++ ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (rnd == MPFR_RNDN || MPFR_IS_LIKE_RNDZ (rnd, neg)) ++ { ++ inex1 = neg ? 1 : -1; ++ mpfr_setmax (a1, __gmpfr_emax - j); ++ } ++ else ++ { ++ inex1 = neg ? -1 : 1; ++ if (j == 0) ++ { ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ mpfr_set_inf (a1, 1); ++ } ++ else ++ { ++ mpfr_setmin (a1, __gmpfr_emax); ++ } ++ } ++ MPFR_SET_SIGN (a1, neg ? -1 : 1); ++ ++ mpfr_clear_flags (); ++ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); ++ flags2 = __gmpfr_flags; ++ ++ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && ++ mpfr_equal_p (a1, a2))) ++ { ++ printf ("Error 1 in check_max_almosteven for %s," ++ " i = %d, j = %d, neg = %d\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), ++ i, j, neg); ++ printf (" b = "); ++ mpfr_dump (b); ++ printf ("Expected "); ++ mpfr_dump (a1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (a2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ ++ if (i == 0) ++ break; ++ ++ mpfr_clear_flags (); ++ set_emin (MPFR_EMIN_MIN); ++ set_emax (MPFR_EMAX_MAX); ++ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); ++ set_emin (emin[i]); ++ set_emax (emax[i]); ++ inex2 = mpfr_check_range (a2, inex2, (mpfr_rnd_t) rnd); ++ flags2 = __gmpfr_flags; ++ ++ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && ++ mpfr_equal_p (a1, a2))) ++ { ++ printf ("Error 2 in check_max_almosteven for %s," ++ " i = %d, j = %d, neg = %d\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), ++ i, j, neg); ++ printf (" b = "); ++ mpfr_dump (b); ++ printf ("Expected "); ++ mpfr_dump (a1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (a2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } /* j */ ++ ++ mpfr_neg (b, b, MPFR_RNDN); ++ mpfr_neg (c, c, MPFR_RNDN); ++ } /* neg */ ++ ++ mpfr_clears (a1, a2, b, c, (mpfr_ptr) 0); ++ } /* i */ ++ ++ set_emin (old_emin); ++ set_emax (old_emax); ++} ++ + #define TEST_FUNCTION test_sub + #define TWO_ARGS + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) +@@ -647,6 +776,7 @@ + check_rounding (); + check_diverse (); + check_inexact (); ++ check_max_almosteven (); + bug_ddefour (); + for (p=2; p<200; p++) + for (i=0; i<50; i++) diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..89fe1cefe22f7ce9275561d9ac87da8492fc8316 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +homepage = 'https://projects.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('dbus-glib', '0.106'), + ('GLib', '2.47.5'), + ('GObject-Introspection', '1.47.1'), + ('libxml2', '2.9.3'), + ('GTK+', '2.24.28'), + ('intltool', '0.51.0', '-Perl-5.22.1'), +] + +configopts = '--disable-orbit ' + +sanity_check_paths = { + 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + + ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + + ['lib/libgconf-2.%s' % x for x in['a', 'so']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..001e2879dae3dcad958e9a50d9a60741832b69c8 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.1' + +homepage = 'http://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': '2015a'} +toolchainopts = {'opt': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('KEALib', '1.4.4'), + ('netCDF', '4.3.3.1'), + ('HDF5', '1.8.16'), + ('expat', '2.1.0'), + ('libxml2', '2.9.3'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7a28658458c1dc446fa8d949035081bd6b79e820 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('Python', '2.7.11'), +] + +configopts = '--with-python' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..f98a09c22edd0cd9ed9035e004ea87c2645846af --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('expat', '2.1.0'), + ('Python', '2.7.11'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7f2305c130c023f4e65aff6df07629a2eaeab032 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('expat', '2.1.0'), + ('Python', '2.7.11'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..726a6db2a2c33cca8e4949130306dcd390972ece --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', mesa_ver), + ('libGLU', '9.0.0', versionsuffix), + ('freeglut', '3.0.0', versionsuffix), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f83060a449130ff06fdd0db762c2c6ec65dc132f --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('freeglut', '3.0.0'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f9a18be1e4b2fdbbaee3f0d5cc5b6ca129fcee5 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', mesa_ver), + ('libGLU', '9.0.0', versionsuffix), + ('freeglut', '3.0.0', versionsuffix), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d5751eec2af50e198a9d59fbc626bff4d7f35a9e --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.58' + +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': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.1.0')] + +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/g/GLib/GLib-2.47.5-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..06841954c43c2e6a143fefa7a95dca8cab3a5ed8 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/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/g/GLib/GLib-2.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..73ce1be6d6188f150635c1a057c5e6487afda0aa --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.48.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/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/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..918c5aec064dd5b33c8bc696eaecc1e206361584 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.48.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/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/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..84e054bf9ccf013654498c831bab82886f14a657 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2016-05-01' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] + +# with these deps you can use standard compressed files +# to support files in gobby format take a look at README for extra dependencies +# http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# you can change the MAX_READLENGTH for GSNAP with something like this. +# details in the README http://research-pub.gene.com/gmap/src/README +#configopts = 'MAX_READLENGTH=250' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..6658db36ac96658b371159a7b25a752a7ec9ecc1 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb @@ -0,0 +1,25 @@ +# contributed by Luca Marsella (CSCS) +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'lowopt': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +preconfigopts = 'export CFLAGS="$CFLAGS -mcmodel=large" && ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2016.03.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..0f388ec38b6ef8a140107cecb538c8b7f8966eda --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2016.03.eb @@ -0,0 +1,25 @@ +# contributed by Luca Marsella (CSCS) and gppezzi +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'CrayGNU', 'version': '2016.03'} +toolchainopts = {'lowopt': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +preconfigopts = 'export CFLAGS="$CFLAGS -mcmodel=large" && ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..7a5dd73b3c907cda68756c926a74b5f2b1267b63 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215', '', True), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..70b7019537c666cd2c6b4400d8be07e4d8bf5266 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb index 7ae4e4f769fedf8c793c884e8311c3c622ded917..1f246a9bfc2eb62d382ca3eb928a045d92ac2488 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb @@ -18,9 +18,11 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.8'), ('GLib', '2.40.0'), - ('Bison', '3.0.2'), ] +builddependencies = [ + ('Bison', '3.0.2'), +] sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb index 0461a34f5fa98e605430578afc3e2d3e52c120b6..835de46b5ba7b7765bf54d8586d2f605ea4fe992 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb @@ -18,6 +18,9 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.44.1'), +] + +builddependencies = [ ('Bison', '3.0.4', '', ('GCC', '4.9.2')), ] diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ef2d0a1446a1f6dd8439d667317b98d5d3ed6cdc --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.47.1' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +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': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.11'), + ('GLib', '2.47.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb index 7bff36264810cc72f1a959ca49015dc90cc7c723..b1d634cd352ac482fd26e054e4060917e6948809 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb @@ -18,9 +18,21 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.47.1'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), ('Bison', '3.0.4'), + ('cairo', '1.14.4'), ] +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb index eaa343080de350899c80dbdc9c5bf1f93099cb2f..7606731e757adbf0bf3a899ff2b67572169c2cd7 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -20,15 +20,17 @@ pyver = '2.7.11' dependencies = [ ('Python', pyver), ('GLib', '2.47.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), ('flex', '2.6.0'), ('Bison', '3.0.4'), ('cairo', '1.14.6'), - ('libffi', '3.2.1'), ] -builddependencies = [('Autotools', '20150215')] - -preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3d59c6fe7c70a2bda1d72d3452fe547620f12559 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.48.0' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +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': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('Python', '2.7.11'), + ('GLib', glibver), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6', '-GLib-%s' % glibver), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb new file mode 100644 index 0000000000000000000000000000000000000000..e699b7dd9b16de6880d2666bd00d63a0ce3dcd9c --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# 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_2012-93.html +# +# Version 5.1.2 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.2' +versionsuffix = '-hybrid' + +homepage = 'http://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.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.4.1'), + ('libxml2', '2.9.3') +] + +dependencies = [('Boost', '1.60.0')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb new file mode 100644 index 0000000000000000000000000000000000000000..1d0b356a9e2a620c6339cd94c4bc81e843aaf3ae --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# 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_2012-93.html +# +# Version 5.1.2 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.2' +versionsuffix = '-hybrid' + +homepage = 'http://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.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.5.2'), + ('libxml2', '2.9.3') +] + +dependencies = [('Boost', '1.60.0')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb new file mode 100644 index 0000000000000000000000000000000000000000..cd7029cdae85e7c037243b23290e387c3014fcee --- /dev/null +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'GROMOS++' +version = '1.0.2211' +versionsuffix = '-openmp' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': True, 'usempi': False} + +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", + "lib/gromosplugin.a", "lib/libgromos.a"], + 'dirs': ["include", "share/gromos++"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..2b1345c99b330dbed8db36a322dcc946664c9f9a --- /dev/null +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'GROMOS++' +version = '1.0.2211' +versionsuffix = '-serial' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': False} + +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' + +sanity_check_paths = { + 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", + "lib/gromosplugin.a", "lib/libgromos.a"], + 'dirs': ["include", "share/gromos++"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..723ea8a3096e1f1890d78852589126f8dc03e877 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +homepage = 'http://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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://ftpmirror.gnu.org/gsl/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f4a28c0d8f92dacd5f35197ffc598945074e5e37 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = "2.1" + +homepage = 'http://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 = {'version': '2016a', 'name': 'foss'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f2d1e756a585ad08874fbaab8b05643ae219879d --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '0.10.36' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '0.10.36')] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ccd3a73617c8807c50da30435911ec35ba6f42d2 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '0.10.36' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.47.5'), + ('GObject-Introspection', '1.47.1'), + ('zlib', '1.2.8'), +] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['reamer', 'base', + 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'], +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6dfeab052692f1b9ec109d174a03a6da1d8b54d0 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.30' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.20.0'), + ('Gdk-Pixbuf', '2.35.1'), + ('Pango', '1.40.1'), + ('GObject-Introspection', '1.48.0'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..69e22e6cabb7feafcdee8657bd8470a6173db972 --- /dev/null +++ b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'GTOOL' +version = '0.7.5' + +homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' +description = """ GTOOL is a program for transforming sets of genotype data for use with +the programs SNPTEST and IMPUTE. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] +sources = ['gtool_v%(version)s_x86_64.tgz'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["gtool", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cca1bedcdd3e7eae2d7df633486cea4b58ed4757 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb @@ -0,0 +1,25 @@ +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': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.48.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa9873619a6b6d66233253362f7ac0425b48d037 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb @@ -0,0 +1,25 @@ +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': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.48.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec51681b28d81893f02320d227c2709e028fc251 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.35.1' + +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': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb index 468e4e32f471c29166b7c10b44110996d3ddbde1..4bde20b26061ad1e977d088bbfaf1d24f5fd1c96 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '3.2.2')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb index f30dcb1a76ada8386470ee7c3ce829bcdef09fc3..60a8b5c5407b98d0757df863e598fcb6572eaf63 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '3.4.3')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb index 300557f7e0dc8f56feddd1af5f9ad742244d0c20..9f9a3a4002cda0ba837dd004bb71173968ecc8d1 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '3.4.3')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb index 1e0d6874fa7a2bd69689995362c6d36c259d640b..2a6c5adf45e21bdaba55bf85f597c2a853a18afb 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb index b7af10a8488f92a7ac75b6754a3f72c55855d90e..2059df7ff07d5bd20fa71a581dd95e6001bdbd1d 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb index 59a0ae794e5047217f700e55b63a2da7699afabf..a91fcca1a09fb2455a4ffa93547f0223929744ee 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb index 3f34b45154796ac9bf226ecb5c370a1950786fe2..b5d179591ae2874eaa2318b55a6abf2298a75c8f 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb index ec559378298f63be5e0ccc20dde61140947ea78a..73e7a955586fb1eceb9bc78830fb227406bcaa53 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb index 5a4e622db868fad18144f63ed37b82f00458cac8..fa0df53df2078cf49721591f4f91a7685e6984b2 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb index b790b2a3f8cc7ed3325fe488c0ceb459e50382ba..cfa9e5761c52495ebde37a74dc7bbe21a736176b 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '3.4.3')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb index e8b5782036b6729d8a3c6e58707fcbc3e1ebcf78..f342971a264a92a5b75c6caa528c37a1774b1a69 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '3.1.3')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb index 554b9825d7df496a231e8e60385c5459d355f22f..ca80a8a174baf00fb7c990a4ce2b888bd8e23d7e 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb @@ -21,6 +21,6 @@ builddependencies = [ ] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa06ee75b25c99b265923e79bc398a209a33065c --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.19' + +homepage = 'http://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': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +sources = ["ghostpdl-%(version)s.tar.bz2"] + +dependencies = [ + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.3'), + ('fontconfig', '2.11.95'), + ('libjpeg-turbo', '1.4.2'), + ('expat', '2.1.1'), + ('GLib', '2.48.0'), + ('cairo', '1.14.6', '-GLib-2.48.0'), + ('LibTIFF', '4.0.6'), +] + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..22ad6d392a1b5c2e03a408932808d26b3a76d844 --- /dev/null +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'Givaro' +version = '4.0.1' + +homepage = 'http://givaro.forge.imag.fr/' +description = "C++ library for arithmetic and algebraic computations" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/givaro/archive'] + +builddependencies = [ + ('Autotools', '20150215'), +] +dependencies = [ + ('GMP', '6.1.0'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = "--with-gmp=$EBROOTGMP --enable-inline" + +sanity_check_paths = { + 'files': ['bin/givaro-config', 'include/givaro-config.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goalf-1.1.0-no-OFED.eb similarity index 91% rename from easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goalf-1.1.0-no-OFED.eb index 6090cb398e1f6908f6f0f7fb38e55229b8658126..3d16aad0af7ca4b2de7dc2e2f4cbcf71f20aaccd 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goalf-1.1.0-no-OFED.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gnutls' +name = 'GnuTLS' version = '3.1.8' homepage = 'http://www.gnutls.org/' @@ -9,12 +9,12 @@ description = "gnutls-3.0.22: GNU Transport Layer Security library" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['ftp://ftp.gnutls.org/pub/gnutls/'] -sources = [SOURCE_TAR_XZ] +sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('GMP', '5.0.5'), ('nettle', '2.6'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = "--with-guile-site-dir=$EBROOTGUILE" diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb similarity index 91% rename from easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb index f7c7021f17c8dbd48a4fa1c34d2d9ff6d9d3de1f..80b639f6e354f9faec6c75790063b782511e621b 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gnutls' +name = 'GnuTLS' version = '3.1.8' homepage = 'http://www.gnutls.org/' @@ -8,12 +8,12 @@ description = "gnutls-3.0.22: GNU Transport Layer Security library" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['ftp://ftp.gnutls.org/pub/gnutls/'] -sources = [SOURCE_TAR_XZ] +sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('GMP', '5.0.5'), ('nettle', '2.6'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = "--with-guile-site-dir=$EBROOTGUILE" diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.3.21-intel-2016a.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.3.21-intel-2016a.eb similarity index 95% rename from easybuild/easyconfigs/g/gnutls/gnutls-3.3.21-intel-2016a.eb rename to easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.3.21-intel-2016a.eb index 62fd6a4ca6ee045b24bfda22d479a3cd6d036908..dcf1712871080bd2bba6fbfbadbc11ccafdb58a6 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.3.21-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.3.21-intel-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gnutls' +name = 'GnuTLS' version = '3.3.21' homepage = 'http://www.gnutls.org/' @@ -14,14 +14,14 @@ description = """GnuTLS is a secure communications library implementing the SSL, toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] -sources = [SOURCE_TAR_XZ] +sources = [SOURCELOWER_TAR_XZ] guilever = '1.8.8' guileshortver = '.'.join(guilever.split('.')[:2]) dependencies = [ ('GMP', '6.1.0'), ('nettle', '3.1.1'), - ('guile', guilever), + ('Guile', guilever), ('libtasn1', '4.7'), ('libidn', '1.32'), ('p11-kit', '0.23.2'), diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.11-foss-2016a.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.11-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b1ec96f981e9b27f2d0f4d01f6b22d1f46953421 --- /dev/null +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.11-foss-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GnuTLS' +version = '3.4.11' + +homepage = 'http://www.gnutls.org/' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +guilever = '1.8.8' +guileshortver = '.'.join(guilever.split('.')[:2]) +dependencies = [ + ('GMP', '6.1.0'), + ('nettle', '3.1.1'), + ('Guile', guilever), + ('libtasn1', '4.7'), + ('libidn', '1.32'), + ('p11-kit', '0.23.2'), +] + +configopts = "--with-guile-site-dir=$EBROOTGUILE --enable-openssl-compatibility " + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['certtool', 'crywrap', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]] + + ['lib/guile/%s/guile-gnutls-v-2.so' % guileshortver], + 'dirs': ['include/gnutls'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.7-GNU-4.9.3-2.25.eb similarity index 95% rename from easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb rename to easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.7-GNU-4.9.3-2.25.eb index d883037773378e2bb3bb4587b6e5cebf29b0cf34..89d42e526683a041728eea0f7bbc6e019323f4c0 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.7-GNU-4.9.3-2.25.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gnutls' +name = 'GnuTLS' version = '3.4.7' homepage = 'http://www.gnutls.org/' @@ -14,14 +14,14 @@ description = """GnuTLS is a secure communications library implementing the SSL, toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] -sources = [SOURCE_TAR_XZ] +sources = [SOURCELOWER_TAR_XZ] guilever = '1.8.8' guileshortver = '.'.join(guilever.split('.')[:2]) dependencies = [ ('GMP', '6.0.0a'), ('nettle', '3.1.1'), - ('guile', guilever), + ('Guile', guilever), ('libtasn1', '4.7'), ('libidn', '1.32'), ('p11-kit', '0.23.2'), diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb index 513feabb7e000a7b4a2b1d5a84bf57b59f9c77c2..b7e2be06e2168e0ce2cc239e0e7d843e22ea99c3 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb @@ -14,4 +14,6 @@ source_urls = [ ] sources = [SOURCE_TAR_GZ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bd06dcc28139d13a22a4af1f5da11a518128cbe2 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.23' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('libtool', '2.4.6'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('bzip2', '1.0.6'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libxml2', '2.9.3'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), +] + +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb index 755ecbe16c842c3116371cb112de2323e47a7f37..de4cfae31e016e49ff0181de1e9411b85f41fd18 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb @@ -7,6 +7,7 @@ homepage = 'http://www.graphicsmagick.org/' description = """GraphicsMagick is the swiss army knife of image processing.""" toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} source_urls = [ SOURCEFORGE_SOURCE, @@ -31,4 +32,6 @@ dependencies = [ ('zlib', '1.2.8'), ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c8fb9489f25fc46b3c77f617c761abee36e6c691 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Greenlet' +version = '0.4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'lib/python%(pyshortver)s/site-packages/greenlet.so'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..26eafeafb1d1dc4c5fcf364148b3ed6cc600df7a --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'Greenlet' +version = '0.4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': ['include/python%(pyshortver)sm/greenlet/greenlet.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GNU-4.9.3-2.25.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-GNU-4.9.3-2.25.eb index 65946ec224e68fda099e06b38735290f6b2ba104..d2f316742ea045e92bd2c82dcf0099cad924686b 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GNU-4.9.3-2.25.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2015b.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2015b.eb index 8e2c6a3db096ee7443693005d5851547afd0c7f3..26c0164e83ae987d194f79a15d782ae99b28706f 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2015b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2016a.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..becfe06582f74693d89187d686bff8631b140879 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.0'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.29'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-goalf-1.1.0-no-OFED.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-goalf-1.1.0-no-OFED.eb index 35f61dcc34e7f05becb8db06d3180ae926594a51..2665630abaed419c1890f4ff7e0952e01f42d43d 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-goalf-1.1.0-no-OFED.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-goolf-1.4.10.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-goolf-1.4.10.eb index 1ff3a6fc786dc4a56adb72b583124c5613f6aabd..d9813aabe25a4b94197034110662ba566f8fcd13 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-goolf-1.4.10.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-ictce-4.0.6.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-ictce-4.0.6.eb index 88054289c0763f8a4426be409b2f3b34ab51a1e3..d9d73c6e916874e3b53ccc55334de088216a72ed 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-ictce-4.0.6.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-ictce-5.3.0.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-ictce-5.3.0.eb index 0ed91b303989983b225ddc1d5c671b51bf1fd813..e72e93b14b8bec4f1aff1d6e34957f4d70b0e362 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-ictce-5.3.0.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015a.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015a.eb index d10a3259ca1441faf4d7906c0ba5534603b4aa5d..4e4bf543c3dc662cebd011924d2303c7e62ee223 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015b.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015b.eb index ecd844f29d41cf698f839d10eb9ab1232ddfb307..cd7c24301f88089bb13387fc148133d6cfca6d52 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2016a.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016a.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2016a.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016a.eb index a7e7520df8fa003f7293267e94b661f649002ec6..a7b2c1f8edec0f0746651bee1c85156212b989c1 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.0.11-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/g/Guile/Guile-2.0.11-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..8c1960a3c8ffd7826305846e42a5b8f1d50d1acb --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-2.0.11-GCC-4.9.3-2.25.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.0.11' + +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': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] +dependencies = [ + ('libunistring', '0.9.3'), + ('libffi', '3.2.1'), + ('gc', '7.4.4'), + ('GMP', '6.1.0'), +] + +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/g/gc/gc-7.4.4-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/g/gc/gc-7.4.4-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..9c888969f86166b68366ff3d1327ad12f0b699d8 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-7.4.4-GCC-4.9.3-2.25.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '7.4.4' + +homepage = 'http://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': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = [ + 'http://hboehm.info/gc/gc_source/', + 'https://github.com/ivmai/libatomic_ops/archive/', +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-7_4_4.tar.gz', +] + +preconfigopts = "ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && " + +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/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..f6f38f5d9fe9e8d9343d9073fd17bfd225ddc705 --- /dev/null +++ b/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'gdist' +version = '1.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/gdist' +description = """The gdist module is a Cython interface to a C++ library (http://code.google.com/p/geodesic/) for + computing geodesic distance which is the length of shortest line between two vertices on a triangulated mesh in three + dimensions, such that the line lies on the surface.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1fdb744032d4d3a52c2a22305425cb19a69b2a27 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.6' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb index b35aee8501687dde10f2affcce9f5eb17d3cde35..690872c686f14da3d5a18923ded8d5ea5130107e 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb @@ -18,6 +18,6 @@ dependencies = [ ('ncurses', '5.9'), ] -configopts = '--without-emacs' +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4580e48c6a96e10cf91935dae20beb9a837e0453 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f86721ed0a6a07d39b8f9363a715522f20a4c2f --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb new file mode 100755 index 0000000000000000000000000000000000000000..bd4f6deeb967128c87d1b801cf8fbfb288c47bf4 --- /dev/null +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "Tarball" + +name = 'git-lfs' +version = '1.1.1' + +homepage = 'https://git-lfs.github.com/' +description = """Git Large File Storage (LFS) replaces large files such as audio samples, videos, + datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server + like GitHub.com or GitHub Enterprise.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/github/git-lfs/releases/download/v%(version)s/'] +sources = ['%(name)s-linux-amd64-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ["git-lfs"], + 'dirs': [""] +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', + } + +# remove exec permission for the provided installation script +postinstallcmds = ["chmod og-x %(installdir)s/install.sh"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index 6a03e95dbafbc41d59d61b0dbcd5508c4488d4e6..1da07f9d5892b42fb844754069956d1ebf372989 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -36,7 +36,7 @@ preconfigopts = 'make configure && ' # Work around git build system bug. If LIBS contains -lpthread, then configure # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--with-perl=${EBPERLROOT} --enable-pthreads='-lpthread'" +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" sanity_check_paths = { 'files': ['bin/git'], diff --git a/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb b/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..37fb210f885480a3875d6bcd8e498bc9251ca400 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.8.0' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +dependencies = [ + ('cURL', '7.47.0'), + ('expat', '2.1.0'), + ('gettext', '0.19.7'), + ('Perl', '5.22.1', '-bare'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb index f9c5e14a8e3b42f6e1a1e44e40b8f869a894ca55..4282ea773f76b22acccf14bac98fc92f9502ec21 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb index 06b846c04cf64bc56723494b711a004e9489978b..037260e4920322ce9d1cc3bc69e0afbfe9659c9c 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb index 42dc60dd5eaa4e48e825ae00ae2c3bdb8257ac76..aebc924b142b888e8eb0453902ea3df8f2fa18ab 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb index 8b99a901c9ba30ae2af29a320cbeac0cedecd3c7..cb35b322234c43a7c6e73ff8cae9fef8a14b93d8 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb index 6ccc91bb752baaf87e6489e59b798f149c6af04e..c92de947ba38414180f79550cc132a0acf88a822 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb index 256687687906470d69bdc3f6a241e0c009023571..1f4bad7112b82813ed0ba1e3d44fc0cf4309f150 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..850097aee1cedf775e7ba47d48f34a9ae066bbc2 --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'glproto' +version = '1.4.17' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb index 46b9bdb3243822b04a8ccc6db21b7da20405b90c..8a7667c002f7e1cc6de3be36825de2e2de99bdcb 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb index 4eb87a66efd1fe6b55f8d992fb6ca1fe848911ec..b28bfab5ef645b2555469ccc63e4542d7c764879 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb index a1f9a0b9d22a071f09d996b820ddeaa372380c92..191cd512edd3fb5e8eb7daead24b9e8b96c9eb9d 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb index c26a1ac08ae2b86516666ce27bd7b80a2aed1908..5dd250fddb83cb74bdcd9c77717b510b4121f241 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7e42e00e676c02b8b559e32f7f5a1f9ccf847ad5 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 = '5.0.3' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.14.6'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('libgd', '2.1.1'), + ('Pango', '1.39.0'), + ('libcerf', '1.4'), + ('Qt', '4.8.7'), +] + +configopts = '--with-qt=qt4 ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..b978fd902aac939edf1cf5c558427ceb444ca4cd --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.04' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.3.0-2.26' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC 5.3.0 and binutils 2.26 + ('OpenMPI', '1.10.2', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.06.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1a2b47b81b261ce442a2cc87cf2c539a5c03d90 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.06.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.06' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.4.0-2.26' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC 5.4.0 and binutils 2.26 + ('OpenMPI', '1.10.3', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0547875020f632eeefda1c796e94284fd75495d3 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb b/easybuild/easyconfigs/g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..d0c568100e5c022ba25a7f71444460ac5c7ccdf6 --- /dev/null +++ b/easybuild/easyconfigs/g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'gputools' +version = '0.28' +commit = 'e5cb024' +versionsuffix = '-%s-R-%%(rver)s' % commit + +homepage = 'https://github.com/nullsatz/gputools/wiki' +description = """This package provides R interfaces to a handful of common functions implemented + using the Nvidia CUDA toolkit. Some of the functions require at least GPU Compute Capability 1.3.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['https://github.com/nullsatz/gputools/archive'] +sources = ['%s.tar.gz' % commit] +checksums = ['daf006aa7892f641b22f545a1bb3cddb'] + +dependencies = [ + ('CUDA', '5.0.35', '-1', True), + ('R', '3.0.2'), +] + +sanity_check_paths = { + 'files': ["gputools/libs/gputools.so"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb b/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..fc1bd333582b8358ca3b4a69fec32c378097e1e4 --- /dev/null +++ b/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'grabix' +version = '0.1.6' + +homepage = 'https://github.com/arq5x/grabix' +description = """a wee tool for random access into BGZF files""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/arq5x/grabix/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +parallel = 1 + +files_to_copy = [(["grabix"], "bin"), "README.md", "tests", "test.sh"] + +sanity_check_paths = { + 'files': ["bin/grabix"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2016a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..674925f1b9997b83f0acef4e2c882b13fcd02e37 --- /dev/null +++ b/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'grace' +version = '5.1.25' + +homepage = 'http://freecode.com/projects/grace' +description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" + +source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +dependencies = [ + ('motif', '2.3.5'), + ('netCDF', '4.4.0'), +] + +runtest = 'tests' + +# we also need to run make links right before or after make install. +installopts = 'links' + +sanity_check_paths = { + 'files': ['bin/xmgrace'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e538b0ca3bf00d6bb07f2f98833ae6014128d26c --- /dev/null +++ b/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'grace' +version = '5.1.25' + +homepage = 'http://freecode.com/projects/grace' +description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" + +source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('motif', '2.3.5'), + ('netCDF', '4.4.0'), +] + +runtest = 'tests' + +# we also need to run make links right before or after make install. +installopts = 'links' + +sanity_check_paths = { + 'files': ['bin/xmgrace'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb index ffd2e3a7a6b38b432a606ae0ca844c3666297fc2..4bcdb9773bc5cc8533adf9e74dafc202c5a8cdd1 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb index 8f6396f5b825af5b944ed1efd5cd7b3d38d88220..7a4d21e07884792b52abbb24072dbcc1b3b89d5c 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb index ee472aa37273fd21f272bb51b379cb99473f1c33..4e298ad677bbc0638c9480f2b113772a2fc6c294 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb index ef2423ee53111d75fd2653ca06cfe8861c3f8a75..4b6a000d122ba0c8f56dfa5689107496a566dbf3 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb index c0f9f1c6d84ab72e71f15f13bb063ed8b4e3fa5c..9445690c859c10978249a3faabe7996bdf3976b3 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb index 384aa93ebf4a83eb860f32ea75f465dc46ba0e19..1f66eb79d751de87e71563d9b875c9ce977ae5af 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb index 048ac9570d3e78b0aeadcc9724ae231d1ea0b0de..8bc580fd829ce5af4240ebe32edf7d07ee27bd93 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb new file mode 100644 index 0000000000000000000000000000000000000000..3020c00623d6bbd1bf5dab519d23790332dd2d34 --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0.1737' +versionsuffix = '-mpi' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': True} + +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-mpi' + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + 'dirs': ['include/md++'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb new file mode 100644 index 0000000000000000000000000000000000000000..8cae45f338cf3debf8b0fb4de4cf883e26c957a3 --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0.1737' +versionsuffix = '-openmp' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': True, 'usempi': False} + +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + 'dirs': ['include/md++'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..075812f642abe8ddb2da3b48cd79018f0ea324d4 --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0.1737' +versionsuffix = '-serial' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': False} + +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + 'dirs': ['include/md++'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..28e5e6ad3626ad60b49496476b9887f442feb4cd --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.11' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] +dependencies = [ + ('Szip', '2.1'), + ('libjpeg-turbo', '1.4.2'), +] + +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..2936e9795e141ba85e0e29bb22751f0d526812c1 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.16' +versionsuffix = '-serial' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..d1c17ce30e587c89343aa470163633f0c3eba61a --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.16' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7ab0f77fbacea4cbe12453b5d29c76f22451a586 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.17' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..46dd3d15ada97e5cf7db37e6ebaada9010c1606b --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.8.9' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab9ee05adb88df725d57f5a0114e5a51c83cffae --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.3-beta' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +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': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +checksums = ['deb29e32e48045b2f970fb999946b411'] + +dependencies = [ + ('NGS', '1.2.3'), + ('ncbi-vdb', '2.5.8-1'), +] + +buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..35be5919017ba96bc272791a9460d913f9a08a8b --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 = '3.1b2' + +homepage = 'http://hmmer.janelia.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': 'foss', 'version': '2016a'} + +sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] +source_urls = ['http://selab.janelia.org/software/hmmer%(version_major)s/%(version)s/'] + +installopts = ' && cd easel && make install' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", + "esl-alimap", "esl-cluster", "esl-mask"]], + 'dirs': [] +} + +runtest = 'check' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..f64bec348b182077ae3001f5fb4b62469e7948e9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '2016.03'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..e65fa73edae405813768602c29b28c43f3f096b5 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2016.04'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..e44a4ac54d1f94d5060c6251d9a82bd7f814b77f --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2016.06'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..ffa453cdb4c22027945f80f38f679b2b266c405d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-5.3'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..f2d54cf6714852cf5f4d1e7ee498b5082a1a612a --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.03-GCC-4.9'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..7eaca67c162c11e2ba28214466a4f616ff575c9b --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.03-GCC-5.3'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..660c68898c6491851ec7de24000f66d3ebecb556 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.03-GCC-5.4'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..9552b4d6538310a00355f603dd608df9a95ed9fc --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'pomkl', 'version': '2016.03'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..4d48990b54201f49d2431bf8708ced105e36212d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'pomkl', 'version': '2016.04'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..40ff5797bac6c3ddecec02981d732eabb49524b7 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.6.1p1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..93d7d3c6dfeabd1ac3bce9afa692144f79f315ab --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.3' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a935ba287085c25e4ae7dccd7a9482a63f466586 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """A C library for reading/writing high-throughput sequencing data. + HTSlib also provides the bgzip, htsfile, and tabix utilities""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/samtools/htslib/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/htsfile", "bin/tabix", "include/htslib/hts.h", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..f75133a502dd54a6de512154f6b94eebdc09cf00 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """A C library for reading/writing high-throughput sequencing data. + HTSlib also provides the bgzip, htsfile, and tabix utilities""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/samtools/htslib/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/htsfile", "bin/tabix", "include/htslib/hts.h", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb new file mode 100644 index 0000000000000000000000000000000000000000..b5884a562e492466a88019e707d10cc3a7e31832 --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb @@ -0,0 +1,30 @@ +name = 'Hadoop' +version = '2.6.0-cdh5.7.0' +versionsuffix = '-native' + +homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' +description = """Hadoop MapReduce by Cloudera""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] + +patches = ['Hadoop-TeraSort-on-local-filesystem.patch'] + +builddependencies = [ + ('Maven', '3.3.9'), + ('protobuf', '2.5.0'), # *must* be this version + ('CMake', '3.5.2'), + ('snappy', '1.1.3', '', ('GCC', '4.9.3-2.25')), +] + +dependencies = [('Java', '1.7.0_80')] + +build_native_libs = True + +extra_native_libs = [('snappy', 'lib/libsnappy.so*')] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..91db4cfacdf229a5e1d9681230ce31f4d690f986 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6'), + ('freetype', '2.6.2'), + ('GObject-Introspection', '1.47.1') +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..23c2924fab3f5bbd4215203264ad6d8d5fa728b2 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.2.7' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('freetype', '2.6.3'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..783b534519d5f33ac68f69b77528765c9a6354b8 --- /dev/null +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'Harminv' +version = '1.4' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/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': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'cstd': 'c99'} + +source_urls = ['http://ab-initio.mit.edu/harminv/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --with-blas=openblas --with-lapack=openblas --enable-shared" + +moduleclass = 'math' \ No newline at end of file diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.11.1-foss-2016a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.11.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5f5821f26c1efd47e4c756ffa1d74681b911e31b --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.11.1-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'Hypre' +version = '2.11.1' + +homepage = "https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html" +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': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://computation.llnl.gov/project/linear_solvers/download/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b6bd52a313b118ebdcee8008a404080568a7dee --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +homepage = 'http://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': '2016a'} +toolchainopts = {'usempi': False} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.16' +hdf5versuffix = '-serial' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s%s' % (hdf5ver, hdf5versuffix) + +prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.11'), + ('HDF5', hdf5ver, hdf5versuffix), +] + +builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..5f53eb490128ef4d60b63583332a1fa9ed4466d8 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.16' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.11'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb new file mode 100644 index 0000000000000000000000000000000000000000..2c68b1bfaa0490e9a9d7c771c7bdbff3cc0286bc --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.0' +versionsuffix = '-cli' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) +dependencies = [ + ('pbs_python', '4.6.0'), + ('vsc-base', '2.5.1'), +] + +use_easy_install = True +zipped_egg = True + +# use 'hod' rather than 'hanythingondemand' in module name +modaltsoftname = 'hod' + +options = {'modulename': 'hod'} + +modextravars = { + # site-specific settings, hence commented out + # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) + #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # specify location on shared 'scratch' filesystem for HOD working directories + #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', +} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..efd171cae5eba0bd00befb3400c9f0bd288bda62 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime +dependencies = [ + ('Python', '2.7.11'), # provides netaddr, netifaces, mpi4py + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.5.1'), +] + +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'hod'} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..5a122dc9232ce0cec021780bca8f0fcf0e780fd4 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://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': 'GCC', 'version': '5.3.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..0bf174a3ffce95efb791fea3cda8e82e943875f5 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..7ea9401fcdd61d14592a9fe53deb3cec15d0a395 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://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': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numactl', '2.0.11', '', ('GCCcore', '4.9.3')), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..e7bd276c18f06f89e8820c62e76ada83eb72efe3 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numactl', '2.0.11', '', ('GCCcore', '5.3.0')), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..aad28dd23b6cb27ba76824d625504cb0a129658b --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..af0616b491d09844d250c58a3543147372e99fad --- /dev/null +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'IGVTools' +version = '2.3.72' + +homepage = 'http://www.broadinstitute.org/software/igv/' +description = """ This package contains command line utilities for preprocessing, + computing feature count density (coverage), sorting, and indexing data files. + See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] +sources = ['%(namelower)s_%(version)s.zip'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["igvtools.jar", "igvtools"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..d2575fc6ec14782d88e24ceae02f0d6f4588ffb6 --- /dev/null +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'IGVTools' +version = '2.3.75' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/software/igv/' +description = """ This package contains command line utilities for preprocessing, + computing feature count density (coverage), sorting, and indexing data files. + See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] +sources = ['%(namelower)s_%(version)s.zip'] + +dependencies = [('Java', '1.7.0_80')] + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["igvtools.jar", "igvtools"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb index 693b2889a64f1047e282af613aeecec47e09b80f..59f875819a2bc60d49f98174c1beb7da97bd545d 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'IPython' version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -13,13 +14,8 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'foss', 'version': '2015a'} -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.11'), ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), ] @@ -52,9 +48,18 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), @@ -73,11 +78,11 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..5a7a6fc6ee332041aa8a21312e0badb06d14e52a --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,94 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb index e3341fcf310c84e80da1b0cb87ab9db71444b77e..4c8be19f1d3b7d404fb6bbeb1a783ac1990b1af5 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'IPython' version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -13,13 +14,8 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015b'} -python = 'Python' -pyver = '2.7.10' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.10'), ('PyZMQ', '15.1.0', '%s-zmq4' % versionsuffix), ] @@ -52,9 +48,18 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), @@ -73,11 +78,11 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..b9c58c257f86837dd3bfb28471094611bacbc532 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,94 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..4ba4b8c0f8c6a8f8bad55ca42a372271c6a3a530 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '4.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://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': 'intel', 'version': '2015a'} + +dependencies = [ + ('Python', '2.7.10'), + ('testpath', '0.2', versionsuffix), +] + +# this is a bundle of Python packages +# override extensions sanity check for IPython, importing a Python module doesn't work there +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('traitlets', '4.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pexpect', '3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('path.py', '7.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + 'modulename': 'path', + }), + ('pickleshare', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('iptest', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..cc3235c7077bb9d8a6b3ad1e645f7a60e5b6c2e8 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,153 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'IPython' +version = '4.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://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': 'goolf', 'version': '1.4.10'} + +dependencies = [ + ('Python', '2.7.5'), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('testpath', '0.3', versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('setuptools', '19.6', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.14.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('jupyter_client', '4.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools_scm', '1.10.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'source_tmpl': 'setuptools_scm-%(version)s.tar.bz2', + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('path.py', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + 'modulename': 'path', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pickleshare', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('pbr', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], + }), + ('notebook', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..4cb75395cca9617a8fbba4802f0eb38f0d1fc485 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,148 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'IPython' +version = '4.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://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': 'goolf', 'version': '1.7.20'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), + ('testpath', '0.3', versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysqlite', '2.8.2', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2016.2.28', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('jupyter_client', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools_scm', '1.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('path.py', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + 'modulename': 'path', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pathlib2', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('pickleshare', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..0626eb2c280f0dda6d8abf3ade6caa06fde5597a --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,148 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'IPython' +version = '4.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), + ('testpath', '0.3', versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysqlite', '2.8.2', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2016.2.28', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.io/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('jupyter_client', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools_scm', '1.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('path.py', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + 'modulename': 'path', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pathlib2', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('pickleshare', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b38a91f39ee72a74dd68ba78fe266d1d76e9dbc --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.16' + +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': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GMP', '6.1.0')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bcbe21baac1e1abf56cfd3d58705c89a472999cb --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '6.9.4-8' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://www.imagemagick.org/download'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('freetype', '2.6.3'), + ('Ghostscript', '9.19'), + ('JasPer', '1.900.1'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXt', '1.1.5'), + ('LittleCMS', '2.7'), +] + +builddependencies = [ + ('pkg-config', '0.29'), +] + +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/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cc86162edac40d38fd3608cb211b4818e2d8799f --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.1-6' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://www.imagemagick.org/download'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('freetype', '2.6.3'), + ('Ghostscript', '9.19'), + ('JasPer', '1.900.1'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXt', '1.1.5'), + ('LittleCMS', '2.7'), +] + +builddependencies = [ + ('pkg-config', '0.29'), +] + +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/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7765318123ddad977e8952e269cfde8122919a33 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.1-9' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://www.imagemagick.org/download'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('freetype', '2.6.3'), + ('Ghostscript', '9.19'), + ('JasPer', '1.900.1'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXt', '1.1.5'), + ('LittleCMS', '2.7'), +] + +builddependencies = [ + ('pkg-config', '0.29'), +] + +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/i/Inspector/Inspector-2013_update6.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb index 6959edee5c90246e162d2b19969f05f84f7e7752..59aa3e741492c6b9b1f44f67b2743d00a5d432eb 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb @@ -6,18 +6,10 @@ description = "Intel Inspector XE 2013 is an easy to use memory error checker an toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['inspector_xe_%s.tar.gz' % version] +sources = ['inspector_xe_%(version)s.tar.gz'] dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - -# hackish sanity check paths -sanity_check_paths = { - 'files': [], - 'dirs': ['.'], -} +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb new file mode 100644 index 0000000000000000000000000000000000000000..264e117584bed2a99da7dda72cb2dd727825e6d7 --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb @@ -0,0 +1,16 @@ +name = 'Inspector' +version = '2013_update7' + +homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial + and parallel applications""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['inspector_xe_%(version)s.tar.gz'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb new file mode 100644 index 0000000000000000000000000000000000000000..9e9351c66392aed56fcc0d630f37d29c3240c138 --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb @@ -0,0 +1,16 @@ +name = 'Inspector' +version = '2016_update3' + +homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial + and parallel applications""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['inspector_xe_%(version)s.tar.gz'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..a0ac2c0885e18b579609756bf050f20b90bc0439 --- /dev/null +++ b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name ='i-PI' +version = '1.0-20160213' +commit = '2a09a6d' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/i-pi/i-pi' +description = """A Python wrapper for (ab initio) (path integrals) molecular dynamics""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/i-pi/i-pi/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('Python', '2.7.11'), +] + +options = {'modulename': 'ipi'} + +sanity_check_paths = { + 'files': ['bin/i-pi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..5d57424030b47e665dedd5365de6e5f002aab098 --- /dev/null +++ b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'i-cisTarget' +version = '20160602' # corresponds to f8be714885560ddabdb1612cf9921a348ffac468 +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget' +description = """An integrative genomics method for the prediction of regulatory features and cis-regulatory modules + in Human, Mouse, and Fly""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + # airspeed requires this specific version of cachetools + ('cachetools', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cachetools/'], + }), + ('airspeed', '0.5.4dev-20150515', { + 'source_urls': ['https://pypi.python.org/packages/source/a/airspeed/'], + }), + ('bx-python', '0.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bx-python/'], + 'modulename': 'bx', + }), + ('Wand', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Wand/'], + 'modulename': 'wand.image', + }), + # i-cisTarget sources are not freely available, contact lcbtools@ls.kuleuven.be + (name, version, { + 'source_tmpl': 'icisTarget-%(version)s.tar.gz', + 'modulename': 'cistargetx', + }), +] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3'), + ('MySQL-python', '1.2.5', versionsuffix + '-MariaDB-10.1.14'), + ('ImageMagick', '6.9.4-8'), + ('STAMP', '1.2'), + ('Cluster-Buster', '20160106'), + ('Kent_tools', '20130806', '-linux.x86_64', True), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ctx-convert', 'ctx-db2r', 'ctx-gt', 'ctx-r2db', 'ctx-rcc']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 4ec5788f7fdff6ec2071dfef95b8dfdce4b6aac8..32978c0fbefda3cf7eba628d0d7627109bce171e 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', 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-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index c6144a5afd71b431b272866a66443c471a2c78e3..e56edba4dbd114128b90d96e06a41e1083cc9fe4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -12,6 +12,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] checksums = ['f57a892fb494db3c80f20a88aa3e901f'] +# 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-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index 2a840e4a5b01583ad4b9547930a707cce737e556..9d56289dfcdb4fe2dbbe093232f3f1d04cd4f600 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', 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-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..5c1c6d97c5481d9ba12f629bd7d636fd54c343f1 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['d6f8529a44231e427219c8e025dec3b2'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', 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-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..4511a57a9e080c021aa9dae539e19165b349e2f0 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['b256c5573d4bba3692c9c4a6ac994d1c'] + +gccver = '4.9.3' +binutilsver = '2.25' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', 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-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..2192bcc50619f64c1cd66b857a5b8172002b118a --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['b256c5573d4bba3692c9c4a6ac994d1c'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', 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-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..9ce84e0f30037300a9c39401a24123eccba08fea --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['b256c5573d4bba3692c9c4a6ac994d1c'] + +gccver = '5.4.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', 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-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..e07e4371a20e3d6d836330d7dfb2f21d088c286c --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.2.181' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..73f4eda01fade1c0d4a9bb6629725bfe8f3a3483 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.3.210' +versionsuffix = '-GCC-4.9.3-2.25' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1f40c75aed8a2894454f626f2b3588b032f4e82 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.3.210' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..944d7a23b2fc72a2d39794af3a64e96db9b69648 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.3.210' +versionsuffix = '-GCC-5.4.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index 930a3dc326c96245d2e4e712421822273ba855bf..d331cd8e4a550d99529d4e4a37f49a48f78c78c8 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', 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-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index b01714a6f586ff92646cf1f5a8f73660fdc578b7..c64470205a7a7123fbab6c4b14f5a796823c83ad 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -12,6 +12,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tg checksums = ['bce7f6a71f7e44f67956197501d00b7c'] +# 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-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index dd3cee42fa29a7920144a99e0b66e7e9c2d78a77..aee6ae915ef9191c408fb4fd85bf073126ccaf67 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', 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-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..5844c8abd9ac08bf0718250d6390280218d0942d --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', 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-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..303793bfad7bc581285dddee4f2c82ef66528300 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] + +gccver = '4.9.3' +binutilsver = '2.25' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', 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-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..b354753609298ae005d9a9487b713c908a940db3 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', 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-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..29953965f2869faaf89aff44b8831e06a5f00840 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] + +gccver = '5.4.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', 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-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..9e93414ff173b03c012148d861570bd55e52ae9c --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -0,0 +1,22 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.02' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '2.181' +compver = '2016.%s' % suff + +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..f4a56beef10f27064abb8825f75baa31a377ae86 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.03' +versionsuffix = '-GCC-4.9.3-2.25' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..8e5a35ceef5afc05d3bde68106758613257a709d --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.03' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..8ee7c61e95bee2febd89f186b1413f2e598ee856 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.03' +versionsuffix = '-GCC-5.4.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..dd473f56b968fdf75202906b98ed67825bd157af --- /dev/null +++ b/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'imake' +version = '1.0.7' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['ftp://artfiles.org/x.org/pub/individual/util/'] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['ccmakedep', 'cleanlinks', 'imake', 'makeg', 'mergelib', + 'mkdirhier', 'mkhtmlindex', 'revpath', 'xmkmf']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..d1edf0b015abf516ebe2cd76890a1b34685b41a4 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.2.181' + +homepage = 'http://software.intel.com/en-us/intel-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': '2016.02-GCC-5.3.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..ac3a95728c618ceefe9b60177420a7d1e02e4ef1 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.2.181' + +homepage = 'http://software.intel.com/en-us/intel-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': 'pompi', 'version': '2016.03'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..0a5bb0e3eeb2c364616979d4fe7db62e52e6dd8a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +homepage = 'http://software.intel.com/en-us/intel-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': '2016.03-GCC-4.9.3-2.25'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..09806746b295042be535ed42ff06b174f1d104ba --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +homepage = 'http://software.intel.com/en-us/intel-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': '2016.03-GCC-5.3.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..490c4fbf4200decba44a6a2a48bc8d55710f15c7 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +homepage = 'http://software.intel.com/en-us/intel-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': '2016.03-GCC-5.4.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab281bf6b12d050ad330da9b31c2d8269442b300 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +homepage = 'http://software.intel.com/en-us/intel-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': 'pompi', 'version': '2016.04'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..eaf9a3b7a7f8919345981dd160591167eb6dc260 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-5.3.0-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..56d81448bff58bb1cdaa85ab6c0c0edc3b9e5f14 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..cc0d58235f6186c6d5a9fe81c45943e0287deaa1 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.3.0-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..837f343b9c4d35575a9c2cd0cbd78e2506ccc035 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb index 3297e8dea09165c14f6698d6219d142ec5e0fe47..ce9480d3aab34d69213d7f402c7e5217d137aad4 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb index 1e1be175b1ca661d8c30acd4896a8a0520ccde15..475b25485eaf4bbd40edba958fd8fc527652883b 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb index 56a7e864e0e45e6c60b8ed68302e7c32bfc1638b..7ae3e0efff6490868088fc5cbe4ffe0ecef7eca1 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb index 75a9c42cf7dbf238bfec04445049cf31312d6732..9931bbca58940676d7653ab7ca738281ac0191fc 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb index 804a25ce18b2749c7c2cecbfd4818fa3998c42bb..19917b0ef7a46ad8164749234fe55ae0bd8c8adb 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb index e307d5deb42a98db29f4a8ab594137d2f41d8642..eb95b2f34ad69b2e4846861a9cd2a0e71a90e61c 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb index 0437a042dbb3891fc9d8440e099ce18063758faa..d652aba38761ae5fd2e0ea36858831b00645a566 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cad6b846e63049c686d5093064bc0147f7078d1f --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb index 1a5db1eefa851137f32ffb3816e9e4af1dfe1c69..b26cb202221b665bd81f703f70d0661012e528d9 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb index 66fc05b6d48e235bd1eb2786b2664004c30d9e28..6a557da522dc83287aa7d83a71196b134fff5541 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb index 21d5d376d510549336698e88bb30a242a93995e9..512fcad71516a14cdca671ed83b918db0baba312 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb index 83bc32fc03af99e8eddbd87fbb25b347c2a2ea8a..00ad73c8ec6e2729f5a1d6d2c3eeeb8ce51c391f 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb index 323816dd0b58c3ada562ced00e0ad65885aeced6..f40968ca7adab37d947e251cb4564c6a8c7df3d1 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..4d1e0dddac5b2974f4488b8ced16d846c81657dc --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.02' +gcc_maj_min = '5.3' +versionsuffix = '-GCC-%s' % gcc_maj_min + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.2.181' +gccver = '%s.0' % gcc_maj_min +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.2.181', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa6be8f54d47abbed78a8663231c9374fa380a85 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.03' +gcc_maj_min = '4.9' +versionsuffix = '-GCC-%s' % gcc_maj_min + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +gccver = '%s.3' % gcc_maj_min +binutilsver = '2.25' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..3de185ca6388eb7dc8032ea2e1e6595a7caf6f9f --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.03' +gcc_maj_min = '5.3' +versionsuffix = '-GCC-%s' % gcc_maj_min + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +gccver = '%s.0' % gcc_maj_min +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..1de4297cceeadc693a73588b680f4c47234c198f --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.03' +gcc_maj_min = '5.4' +versionsuffix = '-GCC-%s' % gcc_maj_min + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +gccver = '%s.0' % gcc_maj_min +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0b8aa4117cd46777e80796d29c1cc0cdff1a90d --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.22.1' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.44', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..0b9db08cffb0e74087cd214b8dbf8979dec7449e --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.22.1' + +homepage = 'http://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': 'intel', 'version': '2016a'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.44', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1474dde18b67235d6ad742edac1b6185daa4e4bd --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.2.0' + +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': 'intel', 'version': '2016a'} + +source_urls = [('http://sourceforge.net/projects/mcmc-jags/files/JAGS/%(version_major)s.x/Source/', 'download')] +sources = [SOURCE_TAR_GZ] + +configopts = ' --with-blas="-lmkl" --with-lapack="-lmkl" ' + +sanity_check_paths = { + 'files': ["bin/jags", "libexec/jags-terminal", "lib/libjags.%s" % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/JAGS', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..754b3694f892120d79964a412bb8b8dd26873111 --- /dev/null +++ b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'JWM' +version = '2.3.5' + +homepage = 'https://joewing.net/projects/jwm/' +description = """JWM is a light-weight window manager for the X11 Window System.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['https://joewing.net/projects/jwm/releases'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libX11', '1.6.3'), + ('libXft', '2.3.2', '-fontconfig-2.11.95'), + ('libXext', '1.3.3'), + ('libXmu', '1.1.2'), + ('libXpm', '3.5.11'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), + ('libXinerama', '1.1.3'), + ('fontconfig', '2.11.95'), + ('cairo', '1.14.6', '-GLib-2.48.0'), + ('libcroco', '0.6.11'), + ('librsvg', '2.40.15'), +] + +sanity_check_paths = { + 'files': ['bin/jwm'], + 'dirs': ['etc', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ea3c5924273ee2707de04ad3305063ae1fc5deb3 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://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': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa48d66cd4810cd690dedd16d86c25e37556fd33 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_77' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8e2a518511e709daf5f8565c76a99578c30538ca --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '1.1.11' + +homepage = 'http://www.cbcb.umd.edu/software/jellyfish/' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cbcb.umd.edu/software/jellyfish/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7bee41cdcd56b03d3650179a1c339f1bcc029bf6 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.1.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " +prebuildopts = "make dist && " + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..dccd9491cd5f755bb20cddb0bc35a468caaa7f67 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.0-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.2.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " +prebuildopts = "make dist && " + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20130806-linux.x86_64.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20130806-linux.x86_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..d103de7895830adcb2c10f2ff62080148725a281 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20130806-linux.x86_64.eb @@ -0,0 +1,28 @@ +easyblock = 'BinariesTarball' + +name = 'Kent_tools' +version = '20130806' +versionsuffix = '-linux.x86_64' + +homepage = 'http://genome.cse.ucsc.edu/' +description = """Kent tools: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/, and pack into tarball with: +# mkdir Kent_tools +# rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ Kent_tools +# tar cfvz Kent_tools-20130806.tar.gz Kent_tools +sources = [SOURCE_TAR_GZ] + +postinstallcmds = [ + "cp -a %(builddir)s/Kent_tools/blat/{blat,gfClient,gfServer} %(installdir)s/bin", + "cp -a %(builddir)s/Kent_tools/blat/FOOTER.txt %(installdir)s/bin/FOOTER_blat.txt", +] + +sanity_check_paths = { + 'files': ['bin/FOOTER', 'bin/blat', 'bin/getRna', 'bin/liftOver', 'bin/mafGene', 'bin/splitFile', 'bin/twoBitToFa'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..4bb09cbfe2ae21d6675f245aff4201cd39948460 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,44 @@ +easyblock = 'PackedBinary' + +name = 'Kraken' +version = '0.10.5-beta' +versionsuffix='-Perl-%(perlver)s' + +homepage = 'http://ccb.jhu.edu/software/kraken/' +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': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://ccb.jhu.edu/software/kraken/dl/'] +sources = [SOURCELOWER_TGZ] + +patches = ['Kraken_%(version)s_makefile.patch'] + +dependencies = [ + ('Perl', '5.22.1'), + ('Jellyfish', '1.1.11'), + ('wget', '1.17.1'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken.sh %(installdir)s' + +sanity_check_paths = { + 'files': ['add_to_library.sh', 'build_kraken_db.sh', 'check_for_jellyfish.sh', 'classify', 'clean_db.sh', + 'cp_into_tempfile.pl', 'db_shrink', 'db_sort', 'download_genomic_library.sh', + 'download_taxonomy.sh', 'kraken', 'kraken-build', 'kraken-filter', 'krakenlib.pm', + 'kraken-mpa-report', 'kraken-report', 'kraken-translate', 'make_seqid_to_taxid_map', + 'read_merger.pl', 'report_gi_numbers.pl', 'set_lcas', 'shrink_db.sh', + 'standard_installation.sh', 'upgrade_db.sh', 'verify_gi_numbers.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch b/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch new file mode 100644 index 0000000000000000000000000000000000000000..4a0bc26aa6fd4d0feffa14a21078a8399e5c5449 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch @@ -0,0 +1,12 @@ +#Pick CXX and CXXFLAGS from EasyBuild via pre-defined variables +#May 11th 2016 by B. Hajgato (Free Uninrrsity Brussels, VUB) +--- kraken-0.10.5-beta/src/Makefile.orig 2015-02-18 12:38:00.000000000 +0100 ++++ kraken-0.10.5-beta/src/Makefile 2016-05-11 13:33:39.370016057 +0200 +@@ -1,5 +1,5 @@ +-CXX = g++ +-CXXFLAGS = -Wall -fopenmp -O3 ++CXX ?= g++ ++CXXFLAGS ?= -Wall -fopenmp -O3 + PROGS = db_sort set_lcas classify make_seqid_to_taxid_map db_shrink + + .PHONY: all install clean diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2287c59cc6394473d2b0b126d907e20a5015712d --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.42.5' + +homepage = 'http://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': '2016a'} + +source_urls = ['https://github.com/pachterlab/kallisto/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.4.3')] +dependencies = [('HDF5', '1.8.16', '-serial')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb index 7482053f6fbc7c8dc9feff3ce3991b03353d2fb2..30967e9fe4abed96f90d52bf179820f781afba2a 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb index e54e5f74c9e153b886de8c7ea6c5337bab14ee22..7e3ad5f572220a5fdc898699caaf985fba9f04b3 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb index 3790a57f153907bf8b8db691991fad9941bf0df0..ee1d8ab5ad55532412bf84cff5f1df1b0a5d59ad 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb index 664996727e1b7fa8466ecd087f0e09c0f1f0b09d..48cbc77814c28b90be3186e1559dd2201f65bae7 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb index 31cb837d0f63198bf32e19f04b5ed2fce9f5bcb6..2393fe61dcce30ef59a0f22fd44c867c55b04cae 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb index 2d16cb0b139c8a45182b87fcc39e93290e476cd1..295d7b8f948bab9c1ec9349516b83652f21b0e7e 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..86f8eb23deab5d8ecf18f05b9112073eb106751a --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb index 050b2bda557dd00f1e93ba730e6af188f9f48449..a2add0de300401cf9e5aae6aae4e4adf5f6ad8c5 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb index 62923f260f75b2e09b1850a3cba8f59e1c2c4838..13dbd2eb082b9a415d0f71aed6e10934c0ae761c 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb index d692faf3931201d1a5d698a4205e08b48976fc71..9a5a48c48021938d165be20e0cfacaaccbd5c00f 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb index 29d6a6987afc6b9f25d2a4204ea8d31df8204b6d..e5d229774cb855a940a5dfddae98e54b8fa30cb7 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1da0d2c9035d2f509ed1ae8512dea8d60d94a80 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.99.5' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] + +dependencies = [('ncurses', '5.9')] + +# 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/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..10dacf3472931bf7fb63aa00f358858c17335bf6 --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'LASTZ' +version = '1.02.00' + +homepage = 'http://www.bx.psu.edu/~rsharris/lastz/' +description = """ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle + sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS + sequencing technologies such as Roche 454. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] + +patches = ['LASTZ-%(version)s_Makefile.patch'] + +skipsteps = ['configure'] + +installopts = 'installDir=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["lastz", "lastz_D"]], + 'dirs': ["bin"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch new file mode 100644 index 0000000000000000000000000000000000000000..39bfb5c65520110c97734c69bfa56d97b984d7d1 --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch @@ -0,0 +1,15 @@ +# Remove use of -Werror because Werror is not used (discussed in http://seqanswers.com/forums/showthread.php?t=20113). +# Using -Werror gives warnings which result in a failure of the installation. +# Author: Fokke Dijkstra - Rijksuniversiteit Groningen (RUG) +--- lastz-distrib-1.02.00/src/Makefile 2010-01-13 18:00:09.000000000 +0100 ++++ lastz-distrib-1.02.00/src/Makefile 2015-02-09 17:22:41.030256461 +0100 +@@ -28,7 +28,7 @@ + # + #--------- + +-definedForAll = -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE ++definedForAll = -Wall -Wextra -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE + + + VERSION_FLAGS= \ + diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fc0af540c128df6179fa4443bdd92f6760b5a482 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.0' + +homepage = "http://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': 'foss', 'version': '2016a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Python', '2.7.11'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7a9543d2601c5863d6636ad210ffd33fc637db33 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.0' + +homepage = "http://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': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.5.1'), + ('Python', '2.7.11'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7aa3b2df4bd6dcc6ecb234794f355d42815bd74 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.6' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..56cf148c48df8b112d85d0dbe91aaca049655e72 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb @@ -0,0 +1,23 @@ +name = 'Libint' +version = '1.1.4' + +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': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0951b2b358a8a861db8e1aab7a8f0f02d723a0e --- /dev/null +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'LinBox' +version = '1.4.0' + +homepage = 'http://linalg.org/' +description = "C++ library for exact, high-performance linear algebra" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/linbox/archive'] + +builddependencies = [ + ('Autotools', '20150215'), +] +dependencies = [ + ('FFLAS-FFPACK', '2.2.0'), + ('Givaro', '4.0.1'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = "--with-givaro=$EBROOTGIVARO --with-fflas-ffpack=$EBROOTFFLASMINFFPACK --enable-openmp" + +sanity_check_paths = { + 'files': ['bin/linbox-config', 'include/linbox/linbox-config.h', 'lib/liblinbox.a'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-intel-2016a.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a11a17f3e07dee031c70b0225963738a3eb96224 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.7' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] + +dependencies = [('libjpeg-turbo', '1.4.2')] + +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/l/Lmod/Lmod-6.4.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-6.4.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..5133bc8fbde48cdccb1d73358aa68bafea468f3f --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-6.4.2.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = "Lmod" +version = "6.4.2" + +homepage = "http://sourceforge.net/projects/lmod/" +description = """Lmod is a Lua based module system. Modules allow for dynamic modification + of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod + for a complete description. Lmod is a new implementation that easily handles the MODULEPATH + Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/TACC/Lmod/archive', + 'http://sourceforge.net/projects/lmod/files/', + 'http://sourceforge.net/projects/lmod/files/Testing' +] + +dependencies = [("Lua", "5.1.4-8")] + +sanity_check_paths = { + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], + 'dirs': [] +} + +moduleclass = "tools" diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..07ee05389366f94e66cbe48f755dae163fcf2587 --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Loki' +version = '0.1.7' + +homepage = 'http://loki-lib.sourceforge.net/' +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and + idioms. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths={ + 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], + 'dirs': ['include/loki'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..353bbfd9402a768028ef1373e2e1cd88827f0cca --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Loki' +version = '0.1.7' + +homepage = 'http://loki-lib.sourceforge.net/' +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and + idioms. """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths={ + 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], + 'dirs': ['include/loki'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb new file mode 100644 index 0000000000000000000000000000000000000000..99b579fe3ebc1b0918a7adfbe0dd820915251477 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = "Lua" +version = "5.1.4-8" + +homepage = "http://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': 'dummy', 'version': 'dummy'} + +sources = ['lua-%s.tar.gz' % version.replace('-', '.')] +source_urls = ['http://sourceforge.net/projects/lmod/files/'] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/lua"], + 'dirs': [] +} + +moduleclass = "lang" diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb index 143cec914499e94920e6bc42271f4fdd68367912..cca49e12bf84748b0d7f6a65a4a6d1f87af2a177 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb @@ -30,7 +30,7 @@ source_urls = [ 'http://ftp.yar.ru/pub/source/lftp/old/', ] -dependencies = [('gnutls', '3.1.8')] +dependencies = [('GnuTLS', '3.1.8')] sanity_check_paths = { 'files': ['bin/lftp'], diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb index e96735ec2cf1d29cb7687c0356336456731fab88..d1eb5179b8511d6649ba1a59e8a7a2acd54a92dd 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb @@ -29,7 +29,7 @@ source_urls = [ 'http://ftp.yar.ru/pub/source/lftp/old/', ] -dependencies = [('gnutls', '3.1.8')] +dependencies = [('GnuTLS', '3.1.8')] sanity_check_paths = { 'files': ['bin/lftp'], diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb index a70f4084e336f1d6476b1dface08574c3dba61c2..f9975e31e2983291b5753b4308132d42608cc57c 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb @@ -30,7 +30,7 @@ source_urls = [ ] dependencies = [ - ('gnutls', '3.4.7'), + ('GnuTLS', '3.4.7'), ('gettext', '0.19.6'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..38c8310594fa7615f7936e6db4e9394c1f2f6be3 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('Mesa', mesa_ver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..087bd589cbe5e211bd341b68d36ac6702444145c --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '11.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe3cfb14d679d516d2baf16d42fb5484d646b37b --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesaver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesaver + +dependencies = [ + ('Mesa', mesaver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb index bb3839e6a656332beb122593752b4cd2aaaf64ef..ff2702cd71881b7dde43aeb1a7b8990a8dcd273d 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.4'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..78420c88a590034de06fce4417ca4bad9af04eba --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libICE' +version = '1.0.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('xtrans', '1.3.5'), +] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb index 407ce4845dc4fff3083f3e082fbf5c26cd488777..b63222e9d8bccccab6121f685160a848907fb9a7 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb index 0fb685525a9ab458f3e046a77cddb9c6b605bd98..1bd7511944cae10a9cae63bd8c43a79759d91fa2 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb index d28d3a6e76598182c9fe359a02891d3a95faa57f..2f28c257c5ee52f7d17ed4162e99aeae158775d1 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb index 0038b410475db16b6328d9f2f9a843091352091a..bd5ecc8bcd8f1d04a11ffc308d7a8573d32fe62d 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f7a781e6b096180de6243a4dfb320f6f226b137 --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,23 @@ +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('libGLU', '9.0.0', versionsuffix), +] + +builddependencies = [('Qt', '4.8.7', '-GLib-2.48.0')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7bcbf378aab6b483017fccaf56fe76839e80933b --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb @@ -0,0 +1,20 @@ +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libGLU', '9.0.0'), +] + +builddependencies = [('Qt', '4.8.7')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..3e6a70b031cfcc844633f3d1fd24e241e13b7933 --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,23 @@ +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('libGLU', '9.0.0', versionsuffix), +] + +builddependencies = [('Qt', '4.8.7', '-GLib-2.48.0')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb index a15bba69ef0ac314ec20b4812bcab675c87addf0..30a7625681691bd6ab3533acb8c4bf792103c2d2 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.8'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..289966eec9e12f3ff0c65cbc9c1c96f9d35878e0 --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libSM' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Session Management library, which allows for applications to both manage sessions, + and make use of session managers to save and restore their state for later use.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libICE', '1.0.9'), +] +builddependencies = [ + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb index 580ce7f28a1dc19dbbf6c92fba8c3b7cd163bc6e..a8d0c1fc5507025fcb002a8f4e74f6c20d7a55ca 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb index 2a2391d84707047a1c92746781d8beb9550b813f..c3a28914e6b1c3b46eebb46b211b2506c21ec0ae 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb index 641ea444768c8466cb450155f6ba31748e645a4c..503006a89b3aa433b3af2bf8aaa17791a3e7105b 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb index b34ef0db3325dbe5bd1ef75cfabd5d6e96472b8d..1bab5701feb9f0dd86b8630edad1b63106a22873 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb index 3522b7de999bcd34f1608722b5ebd4d85ca5cd52..3a034255d64a7b39a43e87c2b1212102acaae51a 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X11 client-side library""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] pythonversion = '-Python-2.7.8' builddependencies = [ diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7bbdcf2dc4fb174924175df615f4b5c21a6f131f --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9f49697147bae9290a9a921ea3c702f77639b874 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('pkg-config', '0.29'), + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb index 2e88286d07dd5193b4a6c78cba93a27eb278570c..934e207665c7f6f71fbdd4162db4783b19c40130 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb index f1bc2bfb36875150420155b91c7a9d1722f124cd..bd0254a3352dc7a87d065bbb9e85f42500fd18de 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb index 22bf8016cf0fdc86c152fe18f46913fd5eee4b88..afa4166c18f76f1bea52d47b9935e641a3e3f976 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.26'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb index 408dc4aede5be980d0830bd718f95963e3351909..1accebb77fe4d857550ecfaac4d70bbb82ddcb27 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb index 9304d0fc7923a5a9e3a090ac67aed9a4dfd402c5..dafc84e4632ae5b3cec558a2b80043f972c873a6 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb index 243dbd6f22b4c08fdf9b93aec56d036ffc025ea3..8003dc09d5d3cd0b349f966978efd6969b40fcfe 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1fc949ad4e5cd2e60767ee593359b56e2cb6de9d --- /dev/null +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXcursor' +version = '1.1.14' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Cursor management library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXfixes', '5.0.1'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['include/X11/Xcursor/Xcursor.h', 'lib/libXcursor.%s' % SHLIB_EXT, 'lib/libXcursor.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..19c75463d3f65c4878f29968c1535732cd8292ca --- /dev/null +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdamage' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Damage extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xdamage.h', 'lib/libXdamage.%s' % SHLIB_EXT, 'lib/libXdamage.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb index 735a0391abffd08d8c9c8d6a79dd8bcaea45739d..efb7a8e46c3fc806dfb3e504c1df354dc2889d9e 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.26'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..09bc32a4bba3ae5d7f9bea473fc2c4be2f39f331 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('pkg-config', '0.29'), + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb index 9233da540e70d56efd4f9d04c138dba19857dc4e..395760652d78ee240234c25ab2d2f1228415029e 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb index cc513f2315aedf275183f042cf6dd839d6626ad8..599620e265d8e9c31e34abb9e53844feb4fcf9f5 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb index 79416debddbfd359a5066c65424137059358e1f9..0912eb03113c9f6e18fad7914685309cdc4c3020 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb index 93de3908f000986abdaeb6fc0ad9ccfd0341ebfb..1639916a6f8d952f18c5791e007a117ce3046100 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb index 24fc239d5ebde295fab3546a4a1a758b9600c629..6ec7ecf45d88d64d24fa159f1350cf2a3c7f0cef 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb index 1eeae06c66d2b5b79961527fc7b1668ffcd3b04a..b642948a1ba44534488bae2bf2fea97ecc0b282a 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libX11', '1.6.1'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0a0acbe42bf70074256a9de37d354bb918784788 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb index 9ce9ef676fe9465303638102fd43833d395d947b..388076a4983eadc943f7bfe5e05f8aca4713c82e 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb index f5d31320ddbee49261ed4016dcf4f41c24f5c000..e0c74eaaa7fe52d58ddcc63d5ec72e239ed1fc3b 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb index fea0b330b99710ce3e39220e175ae7aaf70974ac..59f66ccd07df0f164d8f711b45730815ebda667e 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb index c076690abe4da871c64288d82729c17c1924848b..3b9f118decc98974da5179a39d364465ae79b403 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb index 23544e2ee33727185a21dda798561a31e8754b36..7c257d0a2f52971e5e7f6f3501da39c745a78f2c 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb index 93ffb79a95543fc3edab3697f6d404b61a979720..3751e0a221fbd5c750d78b75a5ba6b865e81e08c 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 3e89327b588652cdf88285d9f631460b8e3b4eb4..2d93058e5e8b822d4af7a1fb10549da9bd12706b 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -10,11 +10,12 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa11951f76a4627bd897f4b8978f517b9a556a97 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..63d5bbf4440b3e813fb24e839ddb9f45fb026c7a --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +freetype_ver = '2.6.3' +versionsuffix = '-freetype-%s' % freetype_ver + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', freetype_ver), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b62ce08a63a7ce8cd23bc4e1681f04abfe2ccc1a --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', '2.6.2'), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..45a31bc1bd1db238ed8ffef5a33588a265e99c55 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +freetype_ver = '2.6.3' +versionsuffix = '-freetype-%s' % freetype_ver + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', freetype_ver), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1a968a5adaeef52cd3170d1f441505b873c67ae9 --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXrender', '0.9.9'), + ('freetype', '2.6.2'), + ('fontconfig', '2.11.94'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb new file mode 100644 index 0000000000000000000000000000000000000000..3c4a37832119f5d6995418c9db25f52736f50007 --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' +versionsuffix = '-fontconfig-2.11.95' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXrender', '0.9.9'), + ('freetype', '2.6.3'), + ('fontconfig', '2.11.95'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb index 6943d3e084c3390e2243d96887d7cf344f1a29c5..68589245d1f3450dd0cbc0777d51fa734e804d1d 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb index eaa232fe89b5623e244200c86516ddb54de93610..cd973d2ea0b74d22c5fbe732b0e1985eb5596838 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' versionsuffix = '-Python-2.7.11' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb index 0ed8e42a2078618241a5c260eead5a7814d8ef01..60cd626d31f6380b26c3d664c8cde29a1c284192 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c94df236e015e156d9b1a069c959cf1e4eb42496 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXi' +version = '1.7.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('inputproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb index 265985f5e5de76edaf2cca81ea7bd08f1697dcf4..5e9d4cb87a9181d5ba3d50c5a01659c2484d6181 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.6' diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0a2e3d206ef13162384e489b00dbf8340a2fdf6 --- /dev/null +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXinerama' +version = '1.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Xinerama multiple monitor library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('xineramaproto', '1.2.1'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXinerama.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c219eeb168131241503dc9c13206753ea390174e --- /dev/null +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXmu' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. + libXmuu is a lighter-weight version that does not depend on libXt or libXext""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libXt', '1.1.5'), + ('libXpm', '3.5.11'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%%(name)s.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..996267718150ad403086217078104e145b75c32e --- /dev/null +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXp' +version = '1.0.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('printproto', '1.0.5'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXp.a', 'libXp.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1cc567cb363b01f220b0bdaf4e1aac8e8a0c0469 --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libXpm' +version = '3.5.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [('gettext', '0.19.6')] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6614e79e7fc4785f278a783d5d1771dcdf785a2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXrandr' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Resize, Rotate and Reflection extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('randrproto', '1.5.0'), + ('renderproto', '0.11'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrandr.%s' % SHLIB_EXT, 'lib/libXrandr.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1e63340752407e5ab7b4abfa4fe7878a4c47fa69 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28') +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb index 6f7913580175e47fb1fdc3415c4a5831f52773a5..4646632358335e1bb325e533531dedfdc591ae1f 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libSM', '1.2.1'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e37e36b1f5b4cfc120c6b3f86aa181a8d4cbef97 --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'libXt' +version = '1.1.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are + based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('kbproto', '1.0.7'), +] + +dependencies = [ + ('libSM', '1.2.2'), + ('libICE', '1.0.9'), + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', + 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', + 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', + 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', + 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..873ae3da80b4e0b797043e11aeb81eae0251f2ae --- /dev/null +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXxf86vm' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 XFree86 video mode extension library""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xf86vidmodeproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xf86vmode.h']+ + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f3471b4f66aa55aca5038c82d48649ed813b807 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libcerf' +version = '1.4' + +homepage = 'http://gnuplot.sourceforge.net/' +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': 'foss', 'version': '2016a'} + +sources = [SOURCE_TGZ] +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..dd509f93684e4b29cb5cbc12f087c61cf9733cac --- /dev/null +++ b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libcroco' +version = '0.6.11' + +homepage = 'https://github.com/GNOME/libcroco' +description = """Libcroco is a standalone css2 parsing and manipulation library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/libcroco/%(version_major_minor)s/'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), + ('GLib', '2.48.0'), +] + +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/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb index c9f79a726b7928e6d3c0a30a3f8cc7f4f0db21fc..b65c18c3e27b8b1caed6effffb6270fc3ae5a5e1 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('guile', '1.8.8')] +dependencies = [('Guile', '1.8.8')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb index e765208e8d31bbf53fbccb161fc7747da2f3cfd9..d1965504ac23730d66fbe94f4a213caa135a2d28 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb @@ -11,7 +11,7 @@ toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('guile', '1.8.8')] +dependencies = [('Guile', '1.8.8')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb index cd7968e31d0574a922d3df1f00df9327aff3148e..9c89029e06d1ce9cb35d089b2ea5b632365b1ba0 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('guile', '1.8.8')] +dependencies = [('Guile', '1.8.8')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb index d73a51293468555a9e2bae5c79ad4e1f56fba2ad..e2eae48a9cc16c38c04aecbc1397d92a4f419116 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('guile', '1.8.8')] +dependencies = [('Guile', '1.8.8')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb index 0de2f0bd938d65de14493ce42034937df366cd65..86ba253737cf9997f183843783f6512144cc5aea 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('guile', '1.8.8')] +dependencies = [('Guile', '1.8.8')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..93d87d95336cce4c98418ec9cca5883577a6389c --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.67' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..68f8a6be8998abb2cf0e67dd219866f517bf7919 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.68' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e64ac66c51a1d7428c076fdf5a7a55df0e6a3f41 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.68' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb index cc9e86a7d03a48197779f067635ad063ca4d8da0..8c554c3e242e8b69228275318ae25b933c0d4e92 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb @@ -15,7 +15,7 @@ source_urls = ['http://www.prevanders.net'] dependencies = [('libelf', '0.8.13')] with_configure = True -preconfigopts = 'CFLAGS="-fPIC $CFLAGS" ' +preconfigopts = 'env CFLAGS="-fPIC $CFLAGS" ' configopts = "--enable-shared " # This is dirty but libdwarf cannot find it's own library in the build process... diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..7d27b9549934ec63b9678ab135fa332eca2363ab --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.9.2.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'libdwarf' +version = '20150310' + +homepage = 'http://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.prevanders.net'] + +dependencies = [('libelf', '0.8.13')] + +with_configure = True +preconfigopts = 'env CFLAGS="-fPIC $CFLAGS" ' +configopts = "--enable-shared " + +# This is dirty but libdwarf cannot find it's own library in the build process... +prebuildopts = ' LD_LIBRARY_PATH="../libdwarf:$LD_LIBRARY_PATH" ' + +files_to_copy = [ + (["dwarfdump/dwarfdump"], "bin"), + (["libdwarf/libdwarf.a", "libdwarf/libdwarf.%s" % SHLIB_EXT], "lib"), + (["libdwarf/libdwarf.h", "libdwarf/dwarf.h"], "include"), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["bin", "lib", "include"] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..370d7d47bc7608ef05f4d296439ea52ec39a713c --- /dev/null +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'libelf' +version = '0.8.13' + +homepage = 'http://www.mr511.de/software/english.html' +description = """libelf is a free ELF object file access library""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.mr511.de/software/'] + +modextrapaths = {'CPATH': 'include/libelf'} + +sanity_check_paths = { + 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.9.2.eb index 9babe1877c9ef230910b0577610b4573492a5ad7..2157a2a132af00833a075d759ef780405060d206 100644 --- a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.9.2.eb @@ -11,8 +11,10 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.mr511.de/software/'] +modextrapaths = {'CPATH': 'include/libelf'} + sanity_check_paths = { - 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf.h'], + 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], 'dirs': ['lib/pkgconfig'] } diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..2de9d3663c6cbc00a42adadc0789cb496578f69b --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.0.22' + +homepage = 'http://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': '4.9.3'} + +source_urls = [ + 'https://github.com/downloads/%(name)s/%(name)s/', + 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', +] +sources = ['%(name)s-%(version)s-stable.tar.gz'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..7a3944e39b3e9278e33a0ae98f87997d341e9f58 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://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': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c7c638b6fa058bde0d773dc12d165c00b3d208b2 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b21fd6654ef5273b817c42258a2d78b40bbf78a6 --- /dev/null +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfontenc' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/xlibs/' +description = """X11 font encoding library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/fonts/fontenc.h', 'lib/libfontenc.%s' % SHLIB_EXT, 'lib/libfontenc.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b645a0059566931c64a35dbcae8b6b7a7564f97b --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.1.1' + +homepage = 'http://libgd.bitbucket.org/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/libgd/gd-libgd/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fontconfig', '2.11.94'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1b5b27e46314bb614b18bfed50044e1690acde6 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , 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 = 'libgtextutils' +version = '0.7' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/libgtextutils/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..be095e8cc212757aa1b6dc5aaf35227874ce8da2 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.32' + +homepage = 'http://www.gnu.org/software/libidn' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1f7d100e0771d507e49b0fe723e48d16f0f2447 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.2' + +homepage = 'http://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': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +nasmver = '2.12.01' +versionsuffix = '-NASM-%s' % nasmver + +dependencies = [ + ('NASM', nasmver), +] + +configopts = "--with-jpeg8" +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/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb index 2fd935d0b5e5b5100d7893e711c282d54c805e23..e1b1e8de360914306a697eadf9804345c047e38e 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), ('byacc', '20150711'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb index 5c07ab422c00b5f43f6641ccebbd687d59137667..61dae0d3d6a1dc4a92617148a4dbc5a5caab654a 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), ('byacc', '20150711'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e8c49e497ec884bcf9dbbe639e39271adb489485 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('byacc', '20160324'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb index f753b8b744e405d9f1dfc615b7409ac450b2b0a3..ef19cb94f186948096a74f0fdbba330b2aa23fc0 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), ('byacc', '20120526'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb index f514350317d8a3396e0a98ab0739848978f39ad9..5c4d14cc828662b693c8a158021412fd5109c9aa 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), ('byacc', '20120526'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb index a8ede070974aaaff7fcf2d7b399dd3bca92d9d46..c50391d5e21c3fb972e168c26d976bbf9a6ae3ac 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), ('byacc', '20120526'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb index 9c911d9a3d98b8f8b0518c2dd0550aca8cc9d609..69e1e6bcedf93b9529f1bfcc3226700299c84c18 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), ('byacc', '20120526'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb index 6ac9b7d5c3de3333b3efa4a1e6726f967d608b83..01c9c7b5d722b432caebcbf661f7cea578632820 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb index a021127537b826548d71320914b00d825ffb4e44..3c63b8747026f31463e89e7ebdccfa88fa8403e5 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb index 11090d4b7a795f4bbba096076fd4be56bb88f3b0..437954d342ed05ae7676c59467ef56059030ecc1 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb index f66aff6454aa0fdea7f45ee0d7dc803b40153dad..f0291301fc3cee91301038c0a2e8c8aa5e21554d 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb index f03e2b9b6023073fe14bd15b50427f193fb428bb..e43c36e89ce9dac706dc33af28e5b842f657df8f 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb index 33c34a406a067a1c3fff444753e8f1c30e35f248..834a292992b6924848156c8e604b2ee28dbd66aa 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb index 7e3d115240e3b7d820bb882469644c1c147046e1..c3e51b68546d76a1dec9c53b3a6706e565d0cfe3 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb index ce77f3502c1b3bfd484cc33b8b316d852459faab..8f259d339afe094a2d29a189e1a67108c19f7912 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb index e28f16cff6c3aedfb3731be4ae131774dafbe438..5f22d77a36b0bd54932e7b09e6d37ec94ab33505 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c39482e40cf6f7a4a9da00a233f83b8497dc6de9 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.4' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('Autotools', '20150215'), + ('xorg-macros', '1.19.0'), +] + +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb index 2a5e9c8d05e635d50f0be873bf2197031d7f2d89..ea05edccedb37f6684b81ce4d5d747cad15b573e 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb index 4281029487a9cdf3fd79dc289fecba45bcd26153..1af83efe6669d154e184893ea443ed883e59367b 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb index 2ac72299c577f48e9860b484aa069709f9638e9f..c0a23d9702e9d266c112a6df21943bc50ac9877c 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..1b97f391040ef77b162ca16a3b6a8e6af6460dfc --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +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' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fcb767cfdbf67a88c1f959932d14d30be69c7b11 --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb index 17ca0fce10780c03c992cf8f78ff36459e4eab0e..084f6453704ab55c45cad9b9c0662f2d695f8c34 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb index 8d2ea29b4ccb46917e2fb6b1aba8bb3791c309ae..f0751a5aa27e8d291e7609b0c3f3f393d9becc9c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb index aea7099ee49367d5d3ac4f4284a74fd2900710a0..0ae01c0783960e8bea817e7c1bfa8f808bdc1c55 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb index 7216c9ca1c0b1062947134f1b0e5a45aae88e03a..39cc8963117309d04a09291179038c097c099e1d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb index 6589e3ba7ce41e899af911bb9266a0da1f03b130..9a9c4dd1a0957579f22127b048218cc88d6b3a0f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb index a36ac06d7496201adeb72f7268a69c7caa5aaa53..245f1b2b64442219efd1ac036378239ed7684715 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb index 44256963645070ebc9397f8f754f7a7c06e64003..8e8d97c9af7c05b9f42b610f4b9df0b07a90d70b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb index 8892dfc907e2ffe7fec8ea376d8bc81dd23d936a..0e2ab07ab0fddaa4cd6c368ce92d019734097e27 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb index 7778abffff5dda0354515b41f0432ed3a473929e..c6a66c33d9c60f73f9ac283f11f2360365b94468 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb index 157a15b6bbc87d4d5911bffeccfcdcbcca0a8598..f765c408885c159af688d500780c53e1b8fe1bc0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb index 6a9bcf9cdd20df999f2d5d4e5eb7d9757f482b44..f13cdef9581dd4137af0d4de86ef17ee6fd99de3 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb index c5324cbad17bf175b5edf389d2d1137c3b7cd8d2..f5f1c5bd47560f2210f06bef15ae0e8be6be751a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb index b07b7634b9378a6e3cc51067addf0af43f2682f2..5c9d193cce6420adf0f583c17e6959e5d07f9fa4 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..be707f2f9def765fb3b3eaa50dadf0498be34a17 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.2' + +homepage = 'http://cnswww.cns.cwru.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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-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/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb index 853816b19b74252c39cd4f68750b6a32c459a7d2..596222a189a166f7a9a7ecf79f2a10f33a0b288b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb index 26cadb84b9a2e811c060b66e5287914f7b23480c..2ed024170ca02b6f8a715505d6922a6a51fb3469 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb index 055d457da0daf5dcb7f56dcfe9ea760607859dbd..fd8d7fabf043e3e7e37b687e151d6dd92f35379f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb index 6f9a153abf6d4091831d18e02db1b0a2cc1ed77b..35b967c78dbe0f0e79740a763dbb2ee3278e9d72 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb index a4bce470a581a429d2db91ccbd4dfb427d16ecc2..54fd902c426f311cfd0b1e8a7084e079c23d973d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb index 8003f03676c67211eddf93fa2cfb6f4fa325002c..12e011a8ed784f28fc302e0897afc9a56185dde2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb index 15a227218e589f36cad4c80cfe1033487c5775a9..18ebd1a1e7d1e4cb5a3b49a4e6381189f0744d9c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb index 9236fd84d0e29a2f4e2c0d827be11f8afe2eed1e..cdb4bf6f5a9e6c274c70cd6b5bdc84eb724439f8 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb index 7435fb5029668831e02b53a1b22fe8729a85e617..0f7e91280563b57bbe7c81774641b47d6e033d12 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb index a669b4f5be98d4f4d08ca6e5f4b73cc1d3cf987e..27560c2cd2d8fb11c3d964940d828abc2d24152e 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb index a120dd43072133e15932f1ecc39c22507677fd92..7ca975dc767da4f95511cf46c0642323ce6ee4b3 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb index 883868add2ebdf3d75d60ed4f7706e6621d9e3e0..1710b5c8bc4dce739def12e8db8ced5fa616e208 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb index d828f262a5d4c38cce659691f3b3f3ef2abe2fa2..a4fb8619cbc8911dff1da7a7048eedddd9ab2804 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..c434630db4d4707fa07e9a6982c63946512afdff --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.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': 'CrayGNU', 'version': '2016.03'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-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/l/libreadline/libreadline-6.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb index 252a86c5272777c1e73cb40a1b2157a44f522ec0..55d005e4b82e316d63398755953eb6f1d33547be 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb @@ -14,10 +14,12 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb index afd0f9f313dd4937045b4ab3c5509f01bca1ba7b..a9127a3eded4ba73e041c3063ecc2e8885485d0f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c4b37fadc3908d427e672bbd287f88474ffbf34 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.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': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-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/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb index 46e89b5a9631cb5358043e3ac5817d97f33b546b..4b526bf82795c488fb72e10dba24aa19c29da7e7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb @@ -15,11 +15,13 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + builddependencies = [('binutils', '2.25')] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb index 05d84769350f732f669f87267245163622ce84c2..5c7bdc2d3d9f0c3e358ab2119f1c67a466e85d1c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-bugfix.patch b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-bugfix.patch new file mode 100644 index 0000000000000000000000000000000000000000..a1ead913f9a56816a7213df0484d21a77d62935e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-bugfix.patch @@ -0,0 +1,13 @@ +fix segfault problem in libreadline, cfr. http://ftp.gnu.org/gnu/readline/readline-6.3-patches/readline63-002 +--- readline-6.3.orig/readline.c 2013-10-28 19:58:06.000000000 +0100 ++++ readline-6.3/readline.c 2016-05-20 14:09:43.322571000 +0200 +@@ -744,7 +744,8 @@ + r = _rl_subseq_result (r, cxt->oldmap, cxt->okey, (cxt->flags & KSEQ_SUBSEQ)); + + RL_CHECK_SIGNALS (); +- if (r == 0) /* success! */ ++ /* We only treat values < 0 specially to simulate recursion. */ ++ if (r >= 0 || (r == -1 && (cxt->flags & KSEQ_SUBSEQ) == 0)) /* success! or failure! */ + { + _rl_keyseq_chain_dispose (); + RL_UNSETSTATE (RL_STATE_MULTIKEY); diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb index 362df4f9bdb1c527421254122e94a0d4d0d33f98..5b3cca129dae2919339f9c3e605b48b9537ede20 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 763ccd948895bc5c2f4a8bf79edce3ed7bcbc06a..eb7231e26e0b010ac7a782c500d205a81b9fd8f5 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb index d3b76459b6d44c14213c55fcfe4732b0a9f6881d..3e5da522ae08001e46d457df2edadb4bfa1dc42f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb index 66ecad79ff5cb8aab4c9881ac3b3b40065bbe447..0424a3562b79e2911e5f62e6de2e573a8359fa25 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb index 037141ab778ea9d9405bc2774f34d54c103c75f3..13e43d52186c097e1f51d2718c7dea3cb1caca61 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb index fb2145ca857437d4442fcb075c14d247c0a96c58..3c05861407be3f8717d567ae053fe7adcbba5e64 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb index 8845b7c009d1113640f85777f69d7906534f8b77..7deb83a3a595ec71d5e2bd6165bf33c9bf7c913f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb index 793dcaf0af9d518ec1a17da92d992c39914f9853..6335970ba229e880aca18f41591d2b0f5ba988bc 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb index e594babc962286447e5cf8a60625ed8d96ad63e6..f188f82da8808f26406920f0c0857b07eb3ee2f8 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..cf388a86378c943c403716f67d608b7221b72fb8 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.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': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-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/l/libreadline/libreadline-6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb index ec5413615c6946b0b1f010599aaa86f039b41fbb..b6ff84302c10fb76ee92dd1531a997644054adb7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb index 35af50be83bdce6ffaf60f2c5bea696c9622cd54..f9c95dc4d2552c5d383799a7d9137aebdb4cd548 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb @@ -17,10 +17,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb index 2db2e8532677fee8a12e72fd49e4541825180391..3993c02643e7651d7726c785b68e48644291d036 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb @@ -17,10 +17,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb index c9c675d48425bc1729e581c730a89ce19f78a154..3b71140ccafcce3d406df8fbceb91043210c5fac 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb index 46eef59b197a2643bcfa3c8e4b06bb4703163b2e..335348483618c0b238d76d77f581ce09c1503147 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb index 583b41298f853b2d02f64efe757f7033b71c9f1a..ad201df4f50284ac8267838c90508fe0ab284ff8 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb index 3e67c2044917732df64cd7683b7c69cb103687ce..39a9f63bc4137f7aba764d5c86f804748c0a135d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb index 2c8752c40012c517201fbbcb8e10906ff544e252..73390b32ef62c4c6190dd7d1ccb520447c3c9789 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb index de76493eec8f84523ea05be91cf16de0d76741fe..75d210520b8d00a50348c56c367a7c496dcb4fea 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..514b88fcb78f6dda1ac183fa79c3fb1c66dd1a4f --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.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': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-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/l/libreadline/libreadline-6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb index 0762f90f29f7d4705159aa0ac8590730bf7013da..8df95a95b6caa160f5ba4c47b043202082ca099b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] +patches = ['libreadline-%(version)s-bugfix.patch'] + dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..42fc4d50b129ac573a84968fea26cb78411d12f0 --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.40.15' + +homepage = 'https://wiki.gnome.org/action/show/Projects/LibRsvg' +description = """librsvg is a library to render SVG files using cairo.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s'] + +dependencies = [ + ('Gdk-Pixbuf', '2.35.1'), + ('libcroco', '0.6.11'), + ('Pango', '1.40.1'), + ('cairo', '1.14.6', '-GLib-2.48.0'), +] + +# this loader wants to install in the directory of Gdk-Pixbuf itself, so disable +configopts = '--disable-pixbuf-loader' + +sanity_check_paths = { + 'files': ['bin/rsvg-convert', 'lib/librsvg-%%(version_major)s.%s' % SHLIB_EXT, 'lib/librsvg-2.a'], + 'dirs': ['include/librsvg-2.0', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8cd02bafe0871bc8ef3e8fb29827b8e4b653310f --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.6' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +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/l/libsodium/libsodium-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ef8bb83cbf81737589c38ce4fe540833524df9b4 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.8' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..398c61d22c22b9175f69a7574e06c4d6fda7bdb0 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-goolf-1.7.20.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.8' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0a37b2e3929fc0cb7e19b2517741394c5ea66be3 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.7' + +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': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +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/l/libtool/libtool-2.4.6-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..1b3599b1eda6d5d1e9dc394962e7738aad2d1620 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.16')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..857c0faabb3e2a5666bc4d8a64258ce4309a9d52 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://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': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..6d7bea7d3d375e9962e77f668d4a3ac104470d8d --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://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': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..052063704a27337eaa7379021de783dd94b3eb79 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..6bc89f03e758c89c71eb1d8fd7b6cd8ae5096000 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = "libunwind" +version = "1.1" + +homepage = 'http://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': 'GCC', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +sanity_check_paths = { + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb index 74be1e3d78a12d5a0d1553607b2466396e5bd102..15053fb3db8820e958deb64c2aef7d2458505c06 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb @@ -15,6 +15,16 @@ toolchain = {'version': '2015a', 'name': 'foss'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ac65492ae4f28425f21352e8c628fb01b109200c --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.1' + +homepage = 'http://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': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..cdac53c708aadffc4870fd14cb0c232f6406663e --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,31 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.1' + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of this project 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.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] + +sanity_check_paths = { + 'files': ['include/libunwind.h', ('lib/libunwind.a', 'lib64/libunwind.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index 957e854ad961127a11789b5cd1809e2aaa8ec378..6d87f1040086312119a937e3edad8d178b8775d0 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -15,6 +15,16 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index 505985144323a2ad807cfdb71f4fcee5a8c8af4f..6e07f1886553648b16d9cb5f92405a5892ee4b57 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -15,6 +15,16 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f8d72a6348448066ad51e5093f386222e0a0904 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd83352b3068984fde6c1590772f4d38bec2a18c --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '3.0.0' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa27444b38602619c535a125c015a34a5f30e451 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('pkg-config', '0.29'), + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5f450a09888a55b8da1306ac37a3d9bfffec94a6 --- /dev/null +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxkbcommon' +version = '0.6.1' + +homepage = 'http://xkbcommon.org/' +description = """xkbcommon is a library to handle keyboard descriptions, + including loading them from disk, parsing them and handling their state. + It's mainly meant for client toolkits, window systems, + and other system applications.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xkbcommon.org/download/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libxcb', '1.11.1'), + ('XKeyboardConfig', '2.17'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': ['lib/libxkbcommon%s.so' % x for x in ['', '-x11']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8611f0332bd3f25d136cb0b0941c0bccfb71e6be --- /dev/null +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxkbcommon' +version = '0.6.1' + +homepage = 'http://xkbcommon.org/' +description = """xkbcommon is a library to handle keyboard descriptions, + including loading them from disk, parsing them and handling their state. + It's mainly meant for client toolkits, window systems, + and other system applications.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xkbcommon.org/download/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libxcb', '1.11.1'), + ('XKeyboardConfig', '2.17'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': ['lib/libxkbcommon%s.so' % x for x in ['', '-x11']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..ae7f22f7a4879db23c81cc74d16da7ac406148c4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,24 @@ +name = 'libxml2' +version = '2.9.1' +versionsuffix = '-Python-%(pyver)s' + +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': 'goolf', 'version': '1.4.10'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.5'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..173e4c18707e8f04582d1c7d4b6b22d3fdfb4006 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +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': 'GCC', 'version': '4.8.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..54c5dad803dc36681877716fb5eed01f228cc478 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba6d0a4c3f26989449ef72ed359a4fb73933c8a8 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +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': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..59e0331739e491981981c5cba731ee5ee494be69 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [ + ('zlib', '1.2.8'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..0df5cbd9574ae3f33a2dfe201fbf9d97571fbeb2 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +name = 'libxml2' +version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b593148b42230fc6428d4c30621d68aed43bade --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +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': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b3d064b443f0aebb54c7c9dc35b8ecd6142bcdb5 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +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': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-intel-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..75e9ce2ed7138a3f5688368e37f35b0dd4e21f9d --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.29' + +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': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e6719ce26146c6b9818377a365d0f9981d9f10be --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.4' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/hfp/libxsmm/archive/'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..cda484e29cbf51c2939315442e9482a9ce287f97 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '4.1.0' + +homepage = 'http://code.google.com/p/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': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] + +patches = ['likwid-%(version)s-config-mk.patch'] + +builddependencies = [('binutils', '2.25', '', ('GCCcore', '4.9.3'))] + +skipsteps = ['configure'] +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' +installopts = 'PREFIX=%(installdir)s' + +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], + 'dirs': ["man/man1"] +} + +maxparallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch new file mode 100644 index 0000000000000000000000000000000000000000..735ec88bea55b87984a87c828da367ab76308592 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch @@ -0,0 +1,43 @@ +# Patches the build system +# Ward Poelmans +diff -ur likwid-likwid-4.1.0.orig/config.mk likwid-likwid-4.1.0/config.mk +--- likwid-likwid-4.1.0.orig/config.mk 2016-05-19 13:16:28.000000000 +0200 ++++ likwid-likwid-4.1.0/config.mk 2016-05-19 13:46:33.345284562 +0200 +@@ -9,7 +9,7 @@ + COLOR = BLUE#NO SPACE + + # Path were to install likwid +-PREFIX = /usr/local#NO SPACE ++#PREFIX = /usr/local#NO SPACE + + ################################################################# + # Common users do not need to change values below this comment! # +@@ -33,7 +33,7 @@ + # chown installed tools to this user/group + # if you change anything here, make sure that the user/group can access + # the MSR devices and (on Intel) the PCI devices. +-INSTALL_CHOWN = -g root -o root ++INSTALL_CHOWN = + + # For the daemon based secure msr/pci access configure + # the absolute path to the msr daemon executable. +@@ -44,7 +44,7 @@ + # Build the accessDaemon. Have a look in the WIKI for details. + BUILDDAEMON = true#NO SPACE + #Build the setFrequencies tool +-BUILDFREQ = true#NO SPACE ++BUILDFREQ = false#NO SPACE + + # Set the default mode for MSR access. + # This can usually be overriden on the commandline. +@@ -71,8 +71,8 @@ + # a proper config file at CFG_FILE_PATH) + MAX_NUM_THREADS = 263 + MAX_NUM_NODES = 64 +-CFG_FILE_PATH = /etc/likwid.cfg +-TOPO_FILE_PATH = /etc/likwid_topo.cfg ++CFG_FILE_PATH = $(PREFIX)/etc/likwid.cfg ++TOPO_FILE_PATH = $(PREFIX)/etc/likwid_topo.cfg + + # Versioning Information + VERSION = 4 diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.6.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/lxml/lxml-3.6.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..6408a5d655ceec766980f3bedb4380630befe74f --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-3.6.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '3.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('Python', '2.7.11'), + ('libxml2', '2.9.3'), + ('libxslt', '1.1.29'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb index 31c851b3d9f0ed91d11ee4c0cd8f96ca59ecc106..8398e40d0665ca4cb92593c45b2d9755f0ab75a4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.06'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb index 30107113469f251b2f192e3dbcf563b143095aff..b84761b60206ddb7270a05110e8911573dff7510 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb index b62284872a3046da08afe97e8232ba453bc4cbc0..b4bb4c955de91f15c5df15b89d700e7f478985b8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb index c2e9e524263cf8b1ad1c47ff8bf3122339382036..5df1dda5a3a107ec921112511cac14152963ffbc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb index 90c7eb901795056f3886b41b97c523aebb22d6c9..f406268a87d92714529bd138dc1bc61b06b4e56e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb index a79d153988e395f5ecf8028734d4ae26f9a94afe..560606e07ad3dd4ea3ca3539d3d9ad54d2b81db4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb index 372d1c346d6ba6bfc2c7f0d3024dbb9dad988c21..00b1eb05a83cdc8d243782bd6c3d2a161cfce06a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb index 0fa72c61c98b4f6fb3b8fed618866eeed23b0c70..a939e01023030f76edf9fecb7f56645dec2f7402 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb index 89984f9bafa395c2faeedb88f29ee71e079670c0..64c98aad337a5a17e87cac3f43c2d6d53179804d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb index 52fc84e052cf9619db2407ef2e4b9dee38e6c6db..745063ebad907909453d1dbb099e4b281055023e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb index e856a3fd434a4481589f2c44fdc0d2860aaf8433..a95ac9f601f6972c311353e9c0e715fd747174cb 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..5551b81d856ade255716f92fadf4c88d12171249 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://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': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb index c1c8a529489457a26d7f9aa9f43edb6ce2edf59e..02f06d5cfecef51fae9e7c29c4c0af3ff45ad090 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..434b6f02ff3f4b9dad73a58e0c12d4f92a307b03 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://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': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..114b490972e5c12a1a94a3850b8c331c2a6236d8 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://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': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb index e2764250bf50989e531d962b75283e395d30600f..134d181212255831296c9a1adb305b9e41f99628 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb index ad83091b2bf417349aeb8cbf74bc223951fd67fd..25f9aacaceb2cbc08c6c99d7f4f2fab8032a3278 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb index e83b261924d4a2783a0f5e6aa1151bd2864ee363..5ca90d16a7bee62a427909a9a79c3c4933481ce4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb index 94ec58056bd19a15fe6fe924516739ca49f4cb6e..4abe05a74fd0d16c61ffb7ba6dd6672c936745aa 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb index 411820a76bb3e8fef73e6da7d5917889be8273ee..f58173164e6ea7ee31df0b14fd8d96326a31d73a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb index b66775c7a65ed48fb4d386435270650e7355355a..6a7048dcf1a81e7ed9e3195bdc1bc4e74b11b506 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb index 0d030e3264daafe90d23c28443ae3d9bf0ec2a2b..ce563e7def08932c4809c482a06c4c3c99f3ddaa 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb index 42808d7b77877d0028d644a87f5bfb67f6609168..aa806c1087065210003cfcabf47d2bbb61b64de5 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb index 3b4187acd1295cd2cee41412784368927dbb1cc2..304b160de546e23ba7198d1f926052cce3edb377 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb index e8d95f1f54580e10eab238b13fea40fe38ba2828..46c1b375cb08699f4194031bbfb38da5fa5cd760 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb index 68b3d851f696c48726bad1c53ab6fd40c7d07cea..0289e6c40e65fe26562286578cc747158621bf4c 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '7.1.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb index d6a8a6e705f5ef75ad38737c691e658c401b43ee..857e1b9ffca6ede724bcf7a8a8948c18fcd55f9d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb index f842bdc90ab31d328074da745a9f0b6503455219..a805266216045a722e5ca7f7d064c3e65cc97863 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb index 292da57c7e93ecf3914f8ace0f702ef7ef7f3426..6746b4b3a40b5725a49d1bb400af40a19392e934 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..899804b18fe298245f2dca804f36be571f10c59b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://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': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb index 519be6b6b35287fd2d2c870271b33bcaa569412e..4472772492e50783de3c1929f5c2c6f003611f06 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb index 37a6837b2bc890908c3f4911dc0cd1414a61f0c2..104ad6a3bde2127f348767ec3b8b17b37dbb88fa 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel-para', 'version': '2014.12'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 3f396ce26b1f9699142abde0d13df234d7552e9a..2bc8d9c022922f54733c35a70f59eb90fd7c9537 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..111f00bfda2bb536a7698d334934f1139f0e62a1 --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus' +version = '7.0.67' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a + methodology for management of complex scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['stable_release-%s.zip' % version.replace('.','-')] + +dependencies = [ + ('Java', '1.7.0_79', '', True), + ('Python', '2.7.11'), + ('HDF5', '1.8.16'), + ('libxml2', '2.9.3', '-Python-%(pyver)s'), + ('zlib', '1.2.8') +] + +configopts = '--with-jdk=$JAVA_HOME' + +preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' + +parallel = 1 + +modextravars = { + 'MDSPLUS_DIR': '%(installdir)s', + 'MDS_PATH': '%(installdir)s/tdi', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..25d836f8e532a1dac488f9d0b177f214576e948d --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus' +version = '7.0.67' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a methodology + for management of complex scientific data.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['stable_release-%s.zip' % version.replace('.','-')] + +dependencies = [ + ('Java', '1.7.0_79', '', True), + ('Python', '2.7.9'), + ('HDF5', '1.8.9'), + ('libxml2', '2.9.2'), + ('zlib', '1.2.8') +] + +configopts = '--with-jdk=$JAVA_HOME' + +preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' + +parallel = 1 + +modextravars = { + 'MDSPLUS_DIR': '%(installdir)s', + 'MDS_PATH': '%(installdir)s/tdi', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb new file mode 100644 index 0000000000000000000000000000000000000000..a9aa0626e9309a58ac687a19702e46288556a343 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb @@ -0,0 +1,24 @@ +name = 'METIS' +version = '5.1.0' +# default 32-bit IDTYPEWIDTH, no patch used +versionsuffix = '-32bitIDX' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.5.2')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MM-align/MM-align-20130815-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MM-align/MM-align-20130815-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..6c78bbddafbee7052f01c57e9a95343e47c6aaea --- /dev/null +++ b/easybuild/easyconfigs/m/MM-align/MM-align-20130815-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CmdCp' + +name = 'MM-align' +version = '20130815' + +homepage = 'http://zhanglab.ccmb.med.umich.edu/MM-align/' +description = """ MM-align is an algorithm for structurally aligning + multiple-chain protein-protein complexes. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://zhanglab.ccmb.med.umich.edu/MM-align/'] +sources = ['MMalign.f'] + +checksums = [('md5', '1456e12b1697ea3758d2ac361ae1a7d8')] + +skipsteps = ['source'] + +cmds_map = [('MMalign.f', '$F77 -static -O3 -ffast-math -lm -o MMalign %(source)s')] + +files_to_copy = [(['MMalign'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/MMalign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b23296323609c153956821f81aff57083cd5946 --- /dev/null +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'MOSAIK' +version = '2.2.28' +git_commit_id = '24cf06' #first six digits of the commit id we will download from github +versionsuffix = '-20140425-%s' % git_commit_id + +homepage = 'https://code.google.com/p/mosaik-aligner/' +description = """ MOSAIK is a reference-guided aligner for next-generation + sequencing technologies """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] +sources = ['%s.tar.gz' % (git_commit_id)] + +dependencies = [('zlib', '1.2.8')] + +parallel = 1 + +start_dir = "src" + +buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' + +files_to_copy = ["bin", "../README", "demo"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb new file mode 100644 index 0000000000000000000000000000000000000000..77047640bff14a422b775c5a282966e3c32103a4 --- /dev/null +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'MOSAIK' +version = '2.2.28' +git_commit_id = '24cf06' #first six digits of the commit id we will download from github +versionsuffix = '-20140425-%s' % git_commit_id + +homepage = 'https://code.google.com/p/mosaik-aligner/' +description = """ MOSAIK is a reference-guided aligner for next-generation + sequencing technologies """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] +sources = ['%s.tar.gz' % (git_commit_id)] + +dependencies = [('zlib', '1.2.8')] + +parallel = 1 + +start_dir = "src" + +buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' + +files_to_copy = ["bin", "../README", "demo"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe347368b1440fa0cd71a7f99134a86e539fb4f9 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.0')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6101f2969d4a2b97ab504a476373cdadca35ecfe --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.0')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb new file mode 100644 index 0000000000000000000000000000000000000000..9830a06815e154406bd90ac3dfe295383ef4b698 --- /dev/null +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "PackedBinary" + +name = 'MRIcron' +version = '20150601' + +homepage = 'http://www.mccauslandcenter.sc.edu/mricro/mricron/' +description = """ MRIcron allows viewing of medical images. It +includes tools to complement SPM and FSL. Native format is NIFTI +but includes a conversion program (see dcm2nii) for converting DICOM images. +Features layers, ROIs, and volume rendering. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Automatic Download doesn't work for this software as you need to accept their license, +# so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ +# and place it in a folder where Easybuild can see it. +# Also rename the zip file to lx-20150601.zip +sources = ['lx-%(version)s.zip'] + +checksums = ['a2d8b1c053384220953f6b670d0fd4df'] + +sanity_check_paths = { + 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], + 'dirs': ["example", "lut", "templates"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..19d636f959317146711f3ac599d74087828e2bf9 --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +name = 'MRtrix' +version = '0.3.14' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = ['MRtrix-%(version)s_intel-fixes.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + ('Mesa', '11.2.1'), + ('Qt', '4.8.7'), + ('Eigen', '3.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch new file mode 100644 index 0000000000000000000000000000000000000000..bbc46048dbaf432715372084f132234c7a99a581 --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch @@ -0,0 +1,41 @@ +fix compilation with Intel compilers, cfr. https://github.com/MRtrix3/mrtrix3/pull/622 +author: Kenneth Hoste (HPC-UGent) +diff --git a/src/dwi/tractography/seeding/base.h b/src/dwi/tractography/seeding/base.h +--- a/src/dwi/tractography/seeding/base.h ++++ b/src/dwi/tractography/seeding/base.h +@@ -62,7 +62,7 @@ namespace MR + uint32_t get_count (ImageType& data) + { + std::atomic count (0); +- ThreadedLoop (data).run ([&] (decltype(data)& v) { if (v.value()) count.fetch_add (1, std::memory_order_relaxed); }, data); ++ ThreadedLoop (data).run ([&] (ImageType& v) { if (v.value()) count.fetch_add (1, std::memory_order_relaxed); }, data); + return count; + } + + +diff --git a/lib/adapter/base.h b/lib/adapter/base.h +--- a/lib/adapter/base.h ++++ b/lib/adapter/base.h +@@ -25,7 +25,7 @@ namespace MR + namespace Adapter + { + +- template