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 a3e8287af779d16f6c0066e1899df60f66e863d6..2b32873f47d07c495a09f592041bdacdbe96f10c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,160 @@ 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 5,093 easyconfig files, for 799 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) +------------------------ + +feature + bugfix release +- added example easyconfig files for 63 new software packages: + ATSAS (#616, #2587), astropy (#2724, #2727), attr (#2706), BamUtil (#2654), BBMap (#2322), BH (#2508), + CheMPS2 (#2445), CosmoloPy (#2723, #2727), csvkit (#2639), Firefox (#2648), FreeXL (#2422), GL2PS (#2667), + Glade (#2631), htop (#2538), IGV (#2019), IGVTools (#2019), ImageMagick (#2438), jModelTest (#2529), + KEALib (#2420), libcerf (#2656), libgcrypt (#2201), libglade (#2631), libgpg-error (#2201), libspatialite (#2431), + LittleCMS (#2438), MAST (#2542), MLC (#2577), MPJ-Express (#2529), mutil (#2201), neon (#758), NextClip (#2544), + npstat (#2686, #2703), Octopus (#2643), QuickFF (#2721), p4vasp (#2328), PCMSolver (#2445), PFFT (#2643), + PHYLIP (#2694), pkgconfig (#2475, #2476), Platypus (#2618), pplacer (#1056), PRINSEQ (#2437, #2444, #2585), + PyFFmpeg (#2501, #2519), PyGObject (#2443), PyGTK (#2443), PyOpenGL (#2628), pyringe (#2533), qrupdate (#2675), + rgeos (#2635), rpmrebuild (#2402), shift (#2201), SNAPE-pooled (#2688), SNPhylo (#2701), sratoolkit (#2715), + STAR-Fusion (#2463), statsmodels (#2719), StringTie (#2527), synchronicity (#2508), testpath (#2461), + USEARCH (#2537), VarScan (#2464), vsc-install (#2165), Whoosh (#2725), xprop (#2645) +- added new easyconfigs for existing toolchains: + intel/2016.02-GCC-4.9 (#2620), gmpolf/2016a & gmvolf/2016a (#2589) +- stable Cray-specific easyconfigs + - delete deprecated Cray toolchains and easyconfig files (#2400) + - don't hardcode PrgEnv version, remove craype and fftw components in Cray toolchains (#2554) + - remove -XC versionsuffix for stable definitions for Cray* toolchains (#2714) + - support for various software packages with CrayGNU and CrayIntel toolchains: CP2K, GROMACS, WRF +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including BWA 0.7.13, CMake 3.4.3, GATE 7.2, GROMACS 5.1.2, Mesa 11.1.2, netCDF 4.4.0, Perl 5.22.1, Python 3.5.1, + R 3.2.3, R-bundle-Bioconductor 3.2, scipy 0.17.0, SuiteSparse 4.5.1 +- various other enhancements, including: + - copy contrib dir in Velvet easyconfigs so scripts are also available (#2456) + - redefine matplotlib 1.5.1 easyconfig as a bundle, also include cycler extension (dep for matplotlib) (#2470) + - add bitstring extension to Python 2.7.11 easyconfigs (#2471) + - enable building of MetaVelvet in Velvet 1.2.10 easyconfigs (#2473) + - add custom sanity check for libjpeg-turbo (#2480) + - add Velvet easyconfigs that include BioPerl dependency, so VelvetOptimizer can use it (#2495, #2729, #2733) + - add source URL in RAxML 7.2.6 easyconfigs (#2536) + - update MPICH easyconfigs to use new MPICH easyblock (#2589) + - free libX11 & co from unneeded Python dependency/versionsuffix (#2549, #2563, #2605, #2664) + - add '--enable-utf --enable-unicode-properties' configure options in PCRE easyconfigs (#2561) + - required for latest R versions + - add HCsnip, metagenomeSeq in Bioconductor 3.1 bundles (#2553, #2578) + - add additional extensions in R 3.2.x easyconfigs that are required for extra Bioconductor extensions (#2547, #2556) + - update psmpi easyconfig files to use the new psmpi easyblock (#2619) + - add easyconfig for Python 2.7.11 on top of X11-enabled Tk (#2614, #2621) + - add virtualenv as extension in Python 2.7.11 easyconfigs (#2660) +- various bug fixes, including: + - fix software name for GTK+ (was 'gtk+'), PyCairo (was 'pycairo') and Gdk-Pixbuf (was 'gdk-pixbuf') (#2468) + - don't hardcode CC/CXX in OpenMPI easyconfigs (#2472) + - remove Google Code source URL for mpi4py (#2474) + - rename ffmpeg to FFmpeg (#2425, #2481) + - use available easyblock for flex (#2486) + - fix determining list of easyconfigs in unit test suite, don't assume locations are correct (#2530) + - fix specifying DB dependency in DB_File easyconfigs (#2539) + - remove hard-coded -xSSE4.2 for numpy/scipy with Intel compilers (#2546) + - fix license headers: Hercules foundation is now FWO (#2550) + - add --with-zlib configure argument in libxml easyconfigs (#2555) + - don't hardcode optarch=True in xextproto/xtrans easyconfigs (#2601) + - change toolchain version to '' in easyconfigs that use dummy toolchain and include dependencies (#2612) + - GLib doesn't require libxml2 with Python bindings (#2632) + - add patch file to imkl 10.2.6.038 32-bit easyconfig to fix installer not being able to deal with '--' in build path (#2634) + - add missing 'pkgconfig' dependency for h5py (#2476, #2650) + - correct software name in FastQC easyconfigs (was 'fastqc'), use 'dummy' toolchain for all FastQC version (#2657, #2666) + - add missing libxml2 dependencies in GLib easyconfigs (#2658) + - fix Xerces-C++ download location (#2668) + - enable XML::Bare extension in all Perl easyconfigs (#2672) + - update dead link for SuiteSparse (#2679) + - remove custom exts_filter in easyconfigs used PythonPackage easyblock (#2683, #2685) + - add M4 as build dep for binutils & flex (#2681) + - add missing dependencies in Python 3.5.x easyconfigs: SQLite, Tk, GMP (#2704) + - fix (OS) deps, add checksums, remove parameter definition with default values in MVAPICH2 easyconfigs (#2707) +- style cleanup in various easyconfigs (#2378, #2387, #2395, #2396, #2488-#2493, #2496-#2500, #2502-#2504, #2602) + - working towards automated style review of pull requests v2.6.0 (January 26th 2016) -------------------------- diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb index b75c3fcda900325dd19d64698f6d0770efe3ed68..094f64851263b26e234b3e09ce596b69f1f96f8c 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb @@ -5,7 +5,7 @@ versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TGZ] diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb index 5f10d53c0034ca3c2f1026b4499590a57efd43a2..f899ce8f01ef0aa926aa3c5c19d2286a14c7a788 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb @@ -5,7 +5,7 @@ versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TGZ] diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb index db92841b05d4e98a86aab0e790c7a5897ab0bb25..2063066a889925d36cd7747413d2c49899664c6e 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb @@ -5,7 +5,7 @@ versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TGZ] 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/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb index 6395f17b38d2e35896d2b5a8e14737237cebecd2..107e9cc6684965f85360d881df630e15f52783cb 100755 --- a/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb @@ -6,7 +6,7 @@ version = '2009.01a.pc64_linux.intelmpi' homepage = 'http://www.scm.com/' description = "ADF is a premium-quality quantum chemistry software package based on Density Functional Theory (DFT)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s%(version)s.bin.tgz'] diff --git a/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb b/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb new file mode 100644 index 0000000000000000000000000000000000000000..5fe5e14c146083d6f013deb7017b3af4199b8707 --- /dev/null +++ b/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'ADF' +version = '2016.101' + +homepage = 'http://www.scm.com/ADF/' +description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and + predict chemical structure and reactivity with density functional theory (DFT).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['adf%(version)s.pc64_linux.intelmpi.tgz'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +modextravars = { + 'ADFHOME': '%(installdir)s', + 'ADFBIN': '%(installdir)s/bin', + 'ADFRESOURCES': '%(installdir)s/atomicdata', +} + +modloadmsg = "These environment variables need to be defined before using ADF:\n" +modloadmsg += " * $SCMLICENSE: path to ADF license file\n" +modloadmsg += " * $SCM_TMPDIR: path to user scratch directory" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20160329-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20160329-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..f69d4cd5999f79d6d6ceed458cffcef06b53a087 --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20160329-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,64 @@ +easyblock = 'ConfigureMake' + +name = 'AFNI' +version = '20160329' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://afni.nimh.nih.gov/' +description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - + a technique for mapping human brain activity.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True, 'pic': True} + +# download afni_src.tgz manually from http://afni.nimh.nih.gov/pub/dist/tgz/, and rename to include datestamp +# detailed release notes are available at http://afni.nimh.nih.gov/pub/dist/doc/misc/history/afni_hist_level1_all.html +# but last update doesn't match datestamp of most recent afni_src.tgz? +sources = ['afni_src-%(version)s.tgz'] +checksums = ['f6a1fd2893ad9963ffd4356ccdc1ae4b'] + +patches = ['AFNI-20150717_omp-pragma-statement-fix.patch'] + +dependencies = [ + ('tcsh', '6.19.00'), + ('Python', '2.7.11'), + ('libXp', '1.0.3'), + ('libXt', '1.1.5'), + ('libXpm', '3.5.11'), + ('libXmu', '1.1.2'), + ('motif', '2.3.5'), + ('R', '3.2.3'), + ('PyQt', '4.11.4', versionsuffix), + ('expat', '2.1.0'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('GSL', '2.1'), + ('GLib', '2.47.5'), # must match version used in Qt (via PyQt) + ('zlib', '1.2.8'), +] + +skipsteps = ['configure', 'install'] + +prebuildopts = "cp Makefile.linux_openmp_64 Makefile && " +buildopts = 'totality LGIFTI="$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/APR-util/APR-util-1.5.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..1a3a23018b80cc6918a37497a96d992598a6a6bd --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..bbe4a3f6c2ecebaa3cadb649796b52c5a8635d09 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +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-gimkl-2.11.5.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..2a267fa96b70ff6e4f070f62ea7b114413ec7957 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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/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-1.14-intel-2016a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1f5954bb7ade685fa9111fe9acfd58598880f2d --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14-intel-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 +# 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 = "1.14" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'intel', 'version': '2016a'} + +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-gimkl-2.11.5.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..d521a6ebe2125dba2f34f4e77704c05963a1776b --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-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-gimkl-2.11.5.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f48668b1263dd0725601fc735b676b8af02ea77 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-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/a/ant/ant-1.9.6-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb new file mode 100644 index 0000000000000000000000000000000000000000..3ee7c5b406ade6929d3a8426c37ec64041e5e8df --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb @@ -0,0 +1,23 @@ +name = 'ant' +version = '1.9.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.7.0_79')] + +builddependencies = [('JUnit', '4.11', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..bab7a31bcf175a43f04661ffc218578bbef517fa --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'astropy' +version = '1.0.6' + +homepage = 'http://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('setuptools', '18.4', versionsuffix), + ('numpy', '1.7.1', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..8a4e822bba9cf2bd5cefb2de1690f001c3fe6b13 --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.4.47' + +homepage = 'http://savannah.nongnu.org/projects/attr' +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCC', 'version': '4.6.3'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = ['attr-%(version)s.src.tar.gz'] + +installopts = 'install-dev install-lib' + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'include/attr/attributes.h', 'include/attr/error_context.h', + 'include/attr/libattr.h', 'include/attr/xattr.h', 'lib/libattr.a', 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb index 1e64be716a5971ad42365867025bb6968c03a66c..2ee4f6221607759d9e9abc625910ca00fc599073 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb @@ -28,7 +28,7 @@ installopts = ' prefix=%(installdir)s' postinstallcmds = [ 'mkdir -p %(installdir)s/lib/plugins', - 'cp plugins/*.so %(installdir)s/lib/plugins/.', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb index 2143e1fd78e17f4e04c52ebd3aa5ce51e1dc9abc..f9319eca14c9ad0a98ecc06c96987eb6eeca51fd 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb @@ -28,7 +28,7 @@ installopts = ' prefix=%(installdir)s' postinstallcmds = [ 'mkdir -p %(installdir)s/lib/plugins', - 'cp plugins/*.so %(installdir)s/lib/plugins/.', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', ] sanity_check_paths = { 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-intel-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bd1b04228ad5d8688b0adb35bfa1817fcad47f32 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-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': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('HTSlib', '1.3'), + ('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/BCFtools/BCFtools-1.3_extHTSlib_Makefile.patch b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3_extHTSlib_Makefile.patch new file mode 100644 index 0000000000000000000000000000000000000000..e8a56d6411b04d5b18f13b7e5c7eed5f4a1f455b --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3_extHTSlib_Makefile.patch @@ -0,0 +1,38 @@ +patch Makefile to pick up HTSlib, GSL and zlib provided thorugh EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- bcftools-1.3/Makefile.orig 2015-12-15 22:58:35.000000000 +0100 ++++ bcftools-1.3/Makefile 2016-03-02 15:22:03.656821071 +0100 +@@ -29,11 +29,10 @@ + all: $(PROG) $(TEST_PROG) + + # Adjust $(HTSDIR) to point to your top-level htslib directory +-HTSDIR = htslib-1.3 +-include $(HTSDIR)/htslib.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip +-TABIX = $(HTSDIR)/tabix ++HTSDIR = $(EBROOTHTSLIB)/include ++HTSLIB = $(EBROOTHTSLIB)/lib/libhts.a ++BGZIP = $(EBROOTHTSLIB)/bin/bgzip ++TABIX = $(EBROOTHTSLIB)/bin/tabix + + CC = gcc + CPPFLAGS = +@@ -57,7 +56,7 @@ + ifdef USE_GPL + EXTRA_CPPFLAGS += -DUSE_GPL + OBJS += polysomy.o peakfit.o +- GSL_LIBS = -lgsl -lcblas ++ GSL_LIBS = -L${EBROOTGSL}/lib -lgsl -lcblas + endif + + prefix = /usr/local +@@ -181,7 +180,7 @@ + $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS) + + bcftools: $(HTSLIB) $(OBJS) +- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) ++ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -L${EBROOTZLIB}/lib -lz -lm -ldl $(GSL_LIBS) $(LIBS) + + doc/bcftools.1: doc/bcftools.txt + cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..50f76cdae7065ab6b201133efa8e0b9d005bf7d3 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.25.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$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-0.7.13-foss-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..419aba7bab7fe6cfef40db2c9093e3efc6243b61 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-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 >= 0.7.13 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.13' + +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/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..9cbb01f19159fdaa5eb5f8bfa09132d8eab17325 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +## +# 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 , Daniel Navarro +# 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 +## + +name = 'BWA' +version = '0.7.13' + +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f4774cbbbe1440cbc59188a6b06783e2e7ae4e0c --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-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 >= 0.7.13 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.13' + +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': 'intel', '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/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/BamUtil/BamUtil-1.0.13-foss-2015b.eb b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..66b054ccebd90db9a6298310d0657db059fc5486 --- /dev/null +++ b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute +# +# This is the version with the bundled libStatGen library + +name = 'BamUtil' +version = '1.0.13' + +easyblock = 'MakeCp' + +homepage = 'http://genome.sph.umich.edu/wiki/BamUtil' +description = """BamUtil is a repository that contains several programs + that perform operations on SAM/BAM files. All of these programs + are built into a single executable, bam.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['%(name)sLibStatGen.%(version)s.tgz'] +source_urls = ['http://genome.sph.umich.edu/w/images/7/70/'] + +files_to_copy = ["bamUtil/bin", "libStatGen"] + +sanity_check_paths = { + 'files': ["bin/bam"], + 'dirs': ["libStatGen"], +} + +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-2.1.3.eb b/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb index 16f5b548acef3a6efbcb5eb6ebcbd9b3549d33f9..f28387fbee35d9206b62e42bdee6455bf7d64b3d 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb @@ -16,7 +16,7 @@ description = """ BEAST is a cross-platform program for Bayesian MCMC analysis o tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://github.com/CompEvol/beast2/releases/download/v%(version)s/'] sources = ['BEAST.v%(version)s.tgz'] 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-3.0.2-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb similarity index 90% rename from easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb index 77bb4a043c6890614f7d515fffc37c0f3e507e9d..1e373e5c59b17a5df1a6cf3e8a608fb4e057c136 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb @@ -7,7 +7,7 @@ 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': 'CrayGNU', 'version': '2015.06-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb similarity index 90% rename from easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb index cfb18be138f7c0e6fec969bd32021b12d6ac2311..fbde1c1bed1c5e6027cb8574ca149df57e9e1f74 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb @@ -7,7 +7,7 @@ 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': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..570b1b1c8b45862447f62194a567f52fbbd8c8aa --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.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': 'GCC', 'version': '4.9.3-2.25'} + +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/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-1.59.0-intel-2015b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..61f63ebb4eaa04a08df4f9c246bd223dc36680b7 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.59.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +configopts = '--without-libraries=python' +toolchain = {'name': 'intel', 'version': '2015b'} +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/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/bbFTP/bbFTP-3.2.1-intel-2016a.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3c955962eb55405780233452ab3b8d87e4cafd45 --- /dev/null +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-intel-2016a.eb @@ -0,0 +1,42 @@ +## +# 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 = 'bbFTP' +version = '3.2.1' + +homepage = 'http://doc.in2p3.fr/bbftp/' +description = """bbFTP is a file transfer software. It implements its own transfer protocol, + which is optimized for large files (larger than 2GB) and secure as it does not read the + password in a file and encrypts the connection information. bbFTP main features are: + * Encoded username and password at connection * SSH and Certificate authentication modules + * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression + * Automatic retry * Customizable time-outs * Transfer simulation + * AFS authentication integration * RFIO interface""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# fi. http://doc.in2p3.fr/bbftp/dist/bbftp-client-3.2.0.tar.gz +sources = ['%s-client-%s.tar.gz' % (name.lower(), version)] +source_urls = [homepage + 'dist'] + +start_dir = 'bbftpc' + +buildopts = "CC=$CC" + +dependencies = [('zlib', '1.2.8')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/bbftp'], + 'dirs': [] +} + +moduleclass = 'tools' 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 5fcc8fc6b3b23886cbde2b48fc3bfb7a3b31c3fa..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' @@ -12,30 +10,13 @@ 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 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="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 3a95cee4b62c2bf044d66a8974170ed3d5213ea0..e08cd975ad8390ca71b24ccc2327ca7ce761515b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -12,28 +10,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] builddependencies = [ + ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$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-2015.06-XC.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb similarity index 89% rename from easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb index 5b74aeb4ae2d557bb178051891e9aa903ccf0aff..afe1e361bf4127b59425c0273948a8211c6778ce 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb @@ -6,7 +6,7 @@ description = """bzip2 is a freely available, patent free, high-quality data com 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': '2015.06-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'pic': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb similarity index 89% rename from easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb index 5666a2e9f5905e0d1cb60e954dad508ab0c47f5b..4907113147dc01b0a57e137af8825ce4557ebddb 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb @@ -6,7 +6,7 @@ description = """bzip2 is a freely available, patent free, high-quality data com 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': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} sources = [SOURCE_TAR_GZ] 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/CFITSIO/CFITSIO-3.38-intel-2016a.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6291c9714715cbfd328e7d5940c8f7bc6b4c9f82 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.38' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +srcversion = '%s0' % version.replace('.', '') +source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +sources = ['%%(namelower)s%s.tar.gz' % srcversion] + +sanity_check_paths = { + 'files': ["lib/libcfitsio.a"], + 'dirs': ["include"], +} + +moduleclass = 'lib' 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=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.5.2'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ceed3e9cd305e107b3ff5a31206219f6d28e4773 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'CLHEP' +version = '2.1.1.0' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +# CLHEP compiles with icc instead of icpc +configopts = 'CXX="$CC" CXXFLAGS="$CXXFLAGS -gcc"' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0e16a666125df270174fd917192a1f551fca6c1a --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.1.3.1' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '3.4.3')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb index 9408c50361728c93b17344d0b374918fddb26230..cf96d8d47a288ebe2c0339165a7d11f68d426027 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb @@ -18,4 +18,6 @@ builddependencies = [('CMake', '3.2.2')] separate_build_dir = True +configopts = '-DCMAKE_BUILD_TYPE=Release' + moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fb7adb464b245f386c33f41c551759bf824f881d --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.2.0.8' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '3.4.3')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c5534a7378e0c2b74a89f75e7d5294722f71850 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.3.1.1' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '3.4.3')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +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-3.1.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb index d2b515088f737c17fe88added3a4bab2d7bed6ca..873f4f2f7250a39e9c4910ad6506ab8298621f7b 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb @@ -7,7 +7,7 @@ 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': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb similarity index 90% rename from easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb index d4b9c663529b41bc34a4a86ca6707bb3812c127e..3de7ff42c388ec88c7ac76f3febbad3d8057de72 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb @@ -7,7 +7,7 @@ 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': 'CrayGNU', 'version': '2015.06-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb similarity index 90% rename from easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb index 1a73916b52324dba8eda1b73de3525986a6880c5..1f3739c57eef627eca29bc23a26b6360fa05eaed 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb @@ -7,7 +7,7 @@ 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': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7c87dffeabbf68044fd0dfa85c8c7544973851cf --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +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': 'CrayIntel', 'version': '2015.11'} + +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-3.3.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb index 3107e6dbdffd82b11b418d575929710f4dbb7086..fea9079c88e4e488007f7683e4120d27351c9824 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb @@ -7,7 +7,7 @@ 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': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] 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-gimkl-2.11.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..f5527c16d6f57b6b93f03667371009553e590f1e --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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', '1.0.1p'), +] + +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-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb new file mode 100644 index 0000000000000000000000000000000000000000..7188e62917bfc8f1ab2a30c9afc3b1981d470ca1 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -0,0 +1,37 @@ +name = 'CP2K' +version = '2.4.0' +versionsuffix = '-ipi' + +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': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/cp2k/files/'] + +sources = [SOURCELOWER_TAR_BZ2] + +patches = [ + 'CP2K-%(version)s_ipi.patch', + 'CP2K-%(version)s-fix_compile_date_lastsvn.patch', + 'do_regtest_nocompile.patch' +] + +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5') +] + +dependencies = [('Libint', '1.1.4')] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# about 100 tests fail +ignore_regtest_fails=True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..5c6f21e19503adef60c533a883c482a7b2736655 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +name = 'CP2K' +version = '2.4.0' + +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': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/cp2k/files/'] + +sources = [SOURCELOWER_TAR_BZ2] + +patches = [ + 'CP2K-%(version)s-fix_compile_date_lastsvn.patch', + 'do_regtest_nocompile.patch' +] + +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5') +] + +dependencies = [('Libint', '1.1.4')] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# about 100 tests fail +ignore_regtest_fails=True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch new file mode 100644 index 0000000000000000000000000000000000000000..3c7cc4aaec8804e6b76410c4dfe0a20c84b6bc35 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch @@ -0,0 +1,512 @@ +#This patch makes CP2K source code compatible with i-pi +#It was created by the CP2K team and can be found in the following link: +#https://github.com/i-pi/i-pi/tree/master/patches +diff -rupN cp2k-2.4.0_ref/makefiles/Makefile cp2k-2.4.0/makefiles/Makefile +--- cp2k-2.4.0_ref/makefiles/Makefile 2013-08-15 10:46:04.535899216 +0100 ++++ cp2k-2.4.0/makefiles/Makefile 2013-08-15 10:53:45.827911028 +0100 +@@ -354,7 +354,7 @@ else + LIB_OBJECTS = + endif + +-$(LIB_CP2K_ARCHIVE): $(OBJECTS) ++$(LIB_CP2K_ARCHIVE): $(OBJECTS) sockets.o + $(AR) $(LIB_CP2K_ARCHIVE) $? + ifneq ($(RANLIB),) + $(RANLIB) $(LIB_CP2K_ARCHIVE) +diff -rupN cp2k-2.4.0_ref/src/cp2k_runs.F cp2k-2.4.0/src/cp2k_runs.F +--- cp2k-2.4.0_ref/src/cp2k_runs.F 2013-08-15 10:46:04.091899205 +0100 ++++ cp2k-2.4.0/src/cp2k_runs.F 2013-08-15 10:56:31.715915275 +0100 +@@ -73,10 +73,10 @@ MODULE cp2k_runs + USE input_constants, ONLY: & + bsse_run, cell_opt_run, debug_run, do_atom, do_band, do_cp2k, do_ep, & + do_farming, do_fist, do_mixed, do_opt_basis, do_optimize_input, & +- do_qmmm, do_qs, do_tamc, do_test, ehrenfest, electronic_spectra_run, & +- energy_force_run, energy_run, geo_opt_run, linear_response_run, & +- mol_dyn_run, mon_car_run, none_run, pint_run, real_time_propagation, & +- vib_anal ++ do_qmmm, do_qs, do_tamc, do_test, driver_run, ehrenfest, & ++ electronic_spectra_run, energy_force_run, energy_run, geo_opt_run, & ++ linear_response_run, mol_dyn_run, mon_car_run, none_run, pint_run, & ++ real_time_propagation, vib_anal + USE input_cp2k, ONLY: create_cp2k_input_reading,& + create_cp2k_root_section,& + create_global_section,& +@@ -117,6 +117,7 @@ MODULE cp2k_runs + USE timings, ONLY: timeset,& + timestop + USE vibrational_analysis, ONLY: vb_anal ++ USE driver, ONLY: run_driver + #include "cp_common_uses.h" + + IMPLICIT NONE +@@ -362,6 +363,8 @@ CONTAINS + error=suberror) + CASE (mol_dyn_run) + CALL qs_mol_dyn ( force_env, globenv, error=suberror ) ++ CASE (driver_run) ++ CALL run_driver ( force_env, globenv, error=suberror ) + CASE (geo_opt_run) + CALL cp_geo_opt(force_env,globenv,error=suberror) + CASE (cell_opt_run) +diff -rupN cp2k-2.4.0_ref/src/driver.F cp2k-2.4.0/src/driver.F +--- cp2k-2.4.0_ref/src/driver.F 1970-01-01 01:00:00.000000000 +0100 ++++ cp2k-2.4.0/src/driver.F 2013-08-15 15:43:44.895650242 +0100 +@@ -0,0 +1,216 @@ ++! ***************************************************************************** ++!> \brief Driver mode - To communicate with i-PI Python wrapper ++!> \par History ++!> none ++!> \author Michele Ceriotti 03.2012 ++! ***************************************************************************** ++MODULE driver ++ ++ USE force_env_methods, ONLY: force_env_calc_energy_force ++ USE force_env_types, ONLY: force_env_get,& ++ force_env_type, & ++ force_env_set_cell ++ USE kinds, ONLY: default_path_length,& ++ dp ++ USE input_section_types, ONLY: section_vals_get_subs_vals,& ++ section_vals_type,& ++ section_vals_val_get ++ ++ USE cell_types, ONLY: cell_clone,& ++ cell_create,& ++ cell_release,& ++ cell_type,& ++ compare_cells,& ++ init_cell,& ++ real_to_scaled,& ++ scaled_to_real ++ USE global_types, ONLY: global_environment_type ++ USE f77_interface, ONLY: default_para_env ++ USE cp_external_control, ONLY: external_control ++ USE message_passing, ONLY: mp_bcast, mp_sync ++ USE cp_subsys_types, ONLY: cp_subsys_release,& ++ cp_subsys_type ++ USE iso_c_binding ++ USE virial_types, ONLY: virial_type ++#include "cp_common_uses.h"t ++ ++ IMPLICIT NONE ++ ++ interface ++ subroutine usleep(useconds) bind(C) ++ ! integer(c_int) function usleep(useconds) bind(C) ++ use iso_c_binding ++ implicit none ++ integer(c_int32_t), value :: useconds ++ ! end function ++ end subroutine ++ end interface ++ ++ CONTAINS ++ SUBROUTINE run_driver ( force_env, globenv, error ) ++ TYPE(force_env_type), POINTER :: force_env ++ TYPE(global_environment_type), POINTER :: globenv ++ TYPE(cp_error_type), INTENT(inout) :: error ++ ++ TYPE(section_vals_type), POINTER :: drv_section, motion_section ++ TYPE(virial_type), POINTER :: virial ++ ++ CHARACTER(len=default_path_length) :: drv_hostname, c_hostname ++ INTEGER :: drv_port ++ LOGICAL :: drv_unix ++ ++ !MIK DRIVER ++ ! server address parsing ++ CHARACTER*1024 :: serveraddr, host ++ INTEGER socket, port, inet, nread, readbuffer, slock, swait, uwait ++ ! buffers and temporaries for communication ++ INTEGER, PARAMETER :: MSGLEN=12 ++ LOGICAL :: isinit=.true., hasdata=.false., ionode=.false. ++ CHARACTER*12 :: header ++ CHARACTER*1024 :: parbuffer ++ INTEGER nat ++ REAL *8 :: cellh(3,3), cellih(3,3), vir(3,3), pot ++ REAL*8, ALLOCATABLE :: combuf(:) ++ REAL*8 :: sigma(3,3) ++ ! access cp2k structures ++ TYPE(cp_subsys_type), POINTER :: subsys ++ integer ip, ii, idir ++ TYPE(cell_type), POINTER :: cpcell ++ logical should_stop ++ ionode=(default_para_env%source==default_para_env%mepos) ++ ++ ! reads driver parameters from input ++ motion_section => section_vals_get_subs_vals(force_env%root_section,"MOTION",error=error) ++ drv_section => section_vals_get_subs_vals(motion_section,"DRIVER",error=error) ++ ++ CALL section_vals_val_get(drv_section,"HOST",c_val=drv_hostname,error=error) ++ CALL section_vals_val_get(drv_section,"PORT",i_val=drv_port,error=error) ++ CALL section_vals_val_get(drv_section,"UNIX",l_val=drv_unix,error=error) ++ ++ ++ ! opens the socket ++ socket=0 ++ inet=1 ++ if (ionode) then ++ write(*,*) "@ i-PI DRIVER BEING LOADED" ++ write(*,*) "@ INPUT DATA: ", TRIM(drv_hostname), drv_port, drv_unix ++ c_hostname=TRIM(drv_hostname)//achar(0) ++ CALL open_socket(socket, .not. drv_unix, drv_port, c_hostname) ++ endif ++ ++ !now we have a socket, so we can initialize the CP2K environments. ++ NULLIFY(cpcell) ++ call cell_create(cpcell,error=error) ++ uwait=10000 ! number of MICROseconds to be waited in filesystem lock ++ driver_loop: DO ++ ! do communication on master node only... ++ header = "" ++ ++ ! this syncs the processes, possibly (see sockets.c) without calling MPI_Barrier, ++ ! which is nice as MPI_barrier eats up a lot of CPU for nothing ++ inet=slock(default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ ++ if (ionode) nread=readbuffer(socket, header, MSGLEN) ++ if (ionode) write(0,*) "returned from readbuffer" ++ ++ inet=swait(uwait, default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ ++ call mp_bcast(nread,default_para_env%source, default_para_env%group) ++ if (nread .eq. 0) then ++ if (ionode) write(*,*) " @ DRIVER MODE: Could not read from socket, exiting now." ++ exit ++ endif ++ ++ call mp_bcast(header,default_para_env%source, default_para_env%group) ++ ++ if (ionode) write(*,*) " @ DRIVER MODE: Message from server: ", trim(header) ++ if (trim(header) == "STATUS") then ++ ++ inet=slock(default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ if (ionode) then ! does not need init (well, maybe it should, just to check atom numbers and the like... ) ++ if (hasdata) then ++ call writebuffer(socket,"HAVEDATA ",MSGLEN) ++ else ++ call writebuffer(socket,"READY ",MSGLEN) ++ endif ++ endif ++ inet=swait(uwait,default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ else if (trim(header) == "POSDATA") then ++ if (ionode) then ++ nread=readbuffer(socket, cellh, 9*8) ++ nread=readbuffer(socket, cellih, 9*8) ++ nread=readbuffer(socket, nat, 4) ++ cellh=transpose(cellh) ++ cellih=transpose(cellih) ++ endif ++ call mp_bcast(cellh,default_para_env%source, default_para_env%group) ++ call mp_bcast(cellih,default_para_env%source, default_para_env%group) ++ call mp_bcast(nat,default_para_env%source, default_para_env%group) ++ if (.not.allocated(combuf)) allocate(combuf(3*nat)) ++ if (ionode) nread=readbuffer(socket, combuf, nat*3*8) ++ call mp_bcast(combuf,default_para_env%source, default_para_env%group) ++ ++ CALL force_env_get(force_env,subsys=subsys,error=error) ++ if (nat/=subsys%particles%n_els) WRITE(*,*) " @DRIVER MODE: Uh-oh! Particle number mismatch between i-pi and cp2k input!" ++ ii=0 ++ DO ip=1,subsys%particles%n_els ++ DO idir=1,3 ++ ii=ii+1 ++ subsys%particles%els(ip)%r(idir)=combuf(ii) ++ END DO ++ END DO ++ CALL init_cell(cpcell, hmat=cellh) ++ CALL force_env_set_cell(force_env,cell=cpcell,error=error) ++ ++ CALL force_env_calc_energy_force(force_env,calc_force=.TRUE. ,error=error) ++ ++ if (ionode) write(*,*) " @ DRIVER MODE: Received positions " ++ ++ combuf=0 ++ ii=0 ++ DO ip=1,subsys%particles%n_els ++ DO idir=1,3 ++ ii=ii+1 ++ combuf(ii)=subsys%particles%els(ip)%f(idir) ++ END DO ++ END DO ++ CALL force_env_get(force_env, potential_energy=pot, error=error) ++ CALL force_env_get(force_env,cell=cpcell, virial=virial, error=error) ++ vir = transpose(virial%pv_virial) ++ ++ CALL external_control(should_stop,"DPI",globenv=globenv,error=error) ++ IF (should_stop) EXIT ++ ++ hasdata=.true. ++ else if (trim(header)=="GETFORCE") then ++ if (ionode) write(*,*) " @ DRIVER MODE: Returning v,forces,stress " ++ if (ionode) then ++ call writebuffer(socket,"FORCEREADY ",MSGLEN) ++ call writebuffer(socket,pot,8) ++ call writebuffer(socket,nat,4) ++ call writebuffer(socket,combuf,3*nat*8) ++ call writebuffer(socket,vir,9*8) ++ ++ ! i-pi can also receive an arbitrary string, that will be printed out to the "extra" ++ ! trajectory file. this is useful if you want to return additional information, e.g. ++ ! atomic charges, wannier centres, etc. one must return the number of characters, then ++ ! the string. here we just send back zero characters. ++ nat=0 ++ call writebuffer(socket,nat,4) ! writes out zero for the length of the "extra" field (not implemented yet!) ++ endif ++ hasdata=.false. ++ else ++ if (ionode) write(*,*) " @DRIVER MODE: Socket disconnected, time to exit. " ++ exit ++ endif ++ ENDDO driver_loop ++ ++ END SUBROUTINE run_driver ++ ++END MODULE driver ++ ++ +diff -rupN cp2k-2.4.0_ref/src/input_constants.F cp2k-2.4.0/src/input_constants.F +--- cp2k-2.4.0_ref/src/input_constants.F 2013-08-15 10:46:04.107899205 +0100 ++++ cp2k-2.4.0/src/input_constants.F 2013-08-15 10:53:45.839911028 +0100 +@@ -135,7 +135,8 @@ MODULE input_constants + cell_opt_run=14,& + real_time_propagation=15,& + ehrenfest=16, & +- do_tamc=17 ++ do_tamc=17, & ++ driver_run=18 + + ! Run Types of Atom Code + INTEGER, PARAMETER, PUBLIC :: atom_no_run=1,& +diff -rupN cp2k-2.4.0_ref/src/input_cp2k.F cp2k-2.4.0/src/input_cp2k.F +--- cp2k-2.4.0_ref/src/input_cp2k.F 2013-08-15 10:46:04.131899206 +0100 ++++ cp2k-2.4.0/src/input_cp2k.F 2013-08-15 10:53:45.843911028 +0100 +@@ -422,13 +422,13 @@ CONTAINS + "BAND", "CELL_OPT", "WFN_OPT", "WAVEFUNCTION_OPTIMIZATION",& + "MOLECULAR_DYNAMICS", "GEOMETRY_OPTIMIZATION", "MONTECARLO",& + "ELECTRONIC_SPECTRA", "LINEAR_RESPONSE", "NORMAL_MODES","RT_PROPAGATION",& +- "EHRENFEST_DYN","TAMC" ),& ++ "EHRENFEST_DYN","TAMC","DRIVER" ),& + enum_i_vals=(/ none_run, energy_run, energy_force_run, mol_dyn_run,& + geo_opt_run, mon_car_run, electronic_spectra_run, debug_run,& + bsse_run, linear_response_run, pint_run, vib_anal,do_band,& + cell_opt_run, energy_run, energy_run, mol_dyn_run, geo_opt_run,& + mon_car_run, electronic_spectra_run, linear_response_run,& +- vib_anal,real_time_propagation,ehrenfest,do_tamc/),& ++ vib_anal,real_time_propagation,ehrenfest,do_tamc,driver_run/),& + enum_desc=s2a("Perform no tasks", "Computes energy","Computes energy and forces",& + "Molecular Dynamics","Geometry Optimization","Monte Carlo", "Computes absorption Spectra",& + "Performs a Debug analysis","Basis set superposition error","Linear Response",& +@@ -437,7 +437,7 @@ CONTAINS + "Alias for MC","Alias for SPECTRA","Alias for LR","Alias for VIBRATIONAL_ANALYSIS",& + "Real Time propagation run (fixed ionic positions)",& + "Ehrenfest dynamics (using real time propagation of the wavefunction)",& +- "TAMC"),& ++ "TAMC","i-PI driver mode"),& + supported_feature=.TRUE.,error=error) + CALL section_add_keyword(section,keyword,error=error) + CALL keyword_release(keyword,error=error) +diff -rupN cp2k-2.4.0_ref/src/input_cp2k_motion.F cp2k-2.4.0/src/input_cp2k_motion.F +--- cp2k-2.4.0_ref/src/input_cp2k_motion.F 2013-08-15 10:46:04.095899205 +0100 ++++ cp2k-2.4.0/src/input_cp2k_motion.F 2013-08-15 10:53:45.843911028 +0100 +@@ -103,6 +103,10 @@ CONTAINS + CALL section_add_subsection(section,subsection,error=error) + CALL section_release(subsection,error=error) + ++ CALL create_driver_section(subsection,error=error) ++ CALL section_add_subsection(section,subsection,error=error) ++ CALL section_release(subsection,error=error) ++ + CALL create_fe_section(subsection,error=error) + CALL section_add_subsection(section, subsection, error=error) + CALL section_release(subsection,error=error) +@@ -1713,6 +1717,59 @@ CONTAINS + END SUBROUTINE create_md_section + + ! ***************************************************************************** ++!> \param section will contain the driver section ++!> \param error variable to control error logging, stopping,... ++!> see module cp_error_handling ++!> \author mceriotti ++! ***************************************************************************** ++ SUBROUTINE create_driver_section(section,error) ++ TYPE(section_type), POINTER :: section ++ TYPE(cp_error_type), INTENT(inout) :: error ++ ++ CHARACTER(len=*), PARAMETER :: routineN = 'create_driver_section', & ++ routineP = moduleN//':'//routineN ++ ++ LOGICAL :: failure ++ TYPE(keyword_type), POINTER :: keyword ++ ++ failure=.FALSE. ++ ++ CPPrecondition(.NOT.ASSOCIATED(section),cp_failure_level,routineP,error,failure) ++ IF (.NOT. failure) THEN ++ CALL section_create(section,name="DRIVER",& ++ description="This section defines the parameters needed to run in i-PI driver mode.",& ++ n_keywords=3, n_subsections=0, repeats=.FALSE., required=.TRUE.,& ++ error=error) ++ ++ NULLIFY(keyword) ++ CALL keyword_create(keyword, name="unix",& ++ description="Use a UNIX socket rather than an INET socket.",& ++ usage="unix LOGICAL",& ++ default_l_val=.FALSE., lone_keyword_l_val=.TRUE., error=error) ++ CALL section_add_keyword(section,keyword,error=error) ++ CALL keyword_release(keyword,error=error) ++ ++ CALL keyword_create(keyword, name="port",& ++ description="Port number for the i-PI server.",& ++ usage="port ",& ++ default_i_val=12345, error=error) ++ CALL section_add_keyword(section,keyword,error=error) ++ CALL keyword_release(keyword,error=error) ++ ++ ++ CALL keyword_create(keyword, name="host",& ++ description="Host name for the i-PI server.",& ++ usage="host ",& ++ default_c_val="localhost", error=error) ++ CALL section_add_keyword(section,keyword,error=error) ++ CALL keyword_release(keyword,error=error) ++ ++ END IF ++ ++ END SUBROUTINE create_driver_section ++ ++ ++! ***************************************************************************** + !> \brief Defines AVERAGES section + !> \param error variable to control error logging, stopping,... + !> see module cp_error_handling +diff -rupN cp2k-2.4.0_ref/src/OBJECTDEFS cp2k-2.4.0/src/OBJECTDEFS +--- cp2k-2.4.0_ref/src/OBJECTDEFS 2013-08-15 10:46:04.091899205 +0100 ++++ cp2k-2.4.0/src/OBJECTDEFS 2013-08-15 10:53:45.843911028 +0100 +@@ -180,6 +180,7 @@ OBJECTS_GENERIC =\ + dm_ls_scf.o\ + dm_ls_scf_qs.o\ + dm_ls_scf_types.o\ ++ driver.o\ + efield_utils.o\ + eigenvalueproblems.o\ + eip_environment.o\ +diff -rupN cp2k-2.4.0_ref/src/sockets.c cp2k-2.4.0/src/sockets.c +--- cp2k-2.4.0_ref/src/sockets.c 1970-01-01 01:00:00.000000000 +0100 ++++ cp2k-2.4.0/src/sockets.c 2013-08-15 15:27:36.971625458 +0100 +@@ -0,0 +1,112 @@ ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++ ++ ++//#define FS_WAIT 1 // uncomment to use a file system lock rather than mpi_barrier. ++ ++void error(const char *msg) ++{ perror(msg); } ++ ++void open_socket_(int *psockfd, int* inet, int* port, char* host) // the darn fortran passes an extra argument for the string length. here I just ignore it ++{ ++ int sockfd, portno, n; ++ struct hostent *server; ++ ++ fprintf(stderr, "Connection requested %s, %d, %d\n", host, *port, *inet); ++ struct sockaddr * psock; int ssock; ++ if (*inet!=0) ++ { ++ struct sockaddr_in serv_addr; psock=(struct sockaddr *)&serv_addr; ssock=sizeof(serv_addr); ++ sockfd = socket(AF_INET, SOCK_STREAM, 0); ++ if (sockfd < 0) error("ERROR opening socket"); ++ ++ server = gethostbyname(host); ++ if (server == NULL) ++ { ++ fprintf(stderr, "ERROR, no such host %s \n", host); ++ exit(-1); ++ } ++ ++ bzero((char *) &serv_addr, sizeof(serv_addr)); ++ serv_addr.sin_family = AF_INET; ++ bcopy((char *)server->h_addr, (char *)&serv_addr.sin_addr.s_addr, server->h_length); ++ serv_addr.sin_port = htons(*port); ++ } ++ else ++ { ++ struct sockaddr_un serv_addr; psock=(struct sockaddr *)&serv_addr; ssock=sizeof(serv_addr); ++ sockfd = socket(AF_UNIX, SOCK_STREAM, 0); ++ bzero((char *) &serv_addr, sizeof(serv_addr)); ++ serv_addr.sun_family = AF_UNIX; ++ strcpy(serv_addr.sun_path, "/tmp/ipi_"); ++ strcpy(serv_addr.sun_path+9, host); ++ } ++ ++ if (connect(sockfd, psock, ssock) < 0) error("ERROR connecting"); ++ ++ *psockfd=sockfd; ++} ++ ++void writebuffer_(int *psockfd, char *data, int* plen) ++{ ++ int n; ++ int sockfd=*psockfd; ++ int len=*plen; ++ ++ n = write(sockfd,data,len); ++ if (n < 0) error("ERROR writing to socket\n"); ++} ++ ++ ++int readbuffer_(int *psockfd, char *data, int* plen) ++{ ++ int n, nr; ++ int sockfd=*psockfd; ++ int len=*plen; ++ ++ n = nr = read(sockfd,data,len); ++ ++ while (nr>0 && n +# 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/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..61bd20053b095072e8c087852f46bc57fc9dd576 --- /dev/null +++ b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'CosmoloPy' +version = '0.1.104' + +homepage = 'https://github.com/roban/CosmoloPy' +description = """A cosmology package for Python. CosmoloPy is +built on and designed for use with NumPy and SciPy.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('numpy', '1.7.1', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb rename to easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb index bf917722672ccce2d9d135cbbe4bd0c7ca0ed634..da34dc3b8219327b8e50bd85241a17e77536ea18 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayCCE' -version = '2015.06-XC' +version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb rename to easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb index dbf091ccf30cb7baa1015258480481e8be89e006..f6426373ddcc90f5e56cbe4f54b96281e6077027 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayCCE' -version = '2015.11-XC' +version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb index 0612076d5abe2a38fe4bced37ef267d5cf334783..af4314daa96ad4769572d4c650e079e4c0ea6376 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayGNU' -version = '2015.06-XC' +version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1506' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb index 370978db7611ef668f766e23d7f9fdb961616ea3..fdcd8836c8ee452ab296f853ba4b9bb03ebc67b0 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayGNU' -version = '2015.11-XC' +version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" 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/CrayIntel/CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb rename to easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb index c80854490aa4b41523d97e422ecf4d51031d9dc5..5d9b4c1609a475d9a83c2cc22afbee598fac2989 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayIntel' -version = '2015.06-XC' +version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb rename to easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb index cc105734db6613e99bab01a569413e9e853d629a..8632b007b7c86813e763b8107d93b7ae1f07f5b1 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayIntel' -version = '2015.11-XC' +version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: November 2015).\n""" 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${EBROOTEIGEN}/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.47.0-foss-2016a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa67e92bf933c5a56ed4f6b1eea5b71b3f40cfff --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.47.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1s')] +# configopts = "--with-ssl=$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/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=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f21ebdf8a9af01c7497f72b8ea8abfbb3afce2ba --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.47.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1s')] +# configopts = "--with-ssl=$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 0a62de36aa1beeb743bb0efd624510970f9ace5f..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 @@ -24,6 +24,17 @@ dependencies = [ ('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 diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb index 928b078aac4b112449fc8c1ceaa5be6863568b3d..d2027312f5b2b01d8454d75ed22887c6272eb205 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb @@ -9,7 +9,7 @@ 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': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/enasequence/%(name)s/archive/'] 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/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..87ecf8bccdff717affc25ab71c65fc1ef1a19f76 --- /dev/null +++ b/easybuild/easyconfigs/c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'csvkit' +version = '0.9.1' + +homepage = 'https://github.com/wireservice/csvkit' +description = """csvkit is a suite of command-line tools for converting to and working with CSV, + the king of tabular file formats.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +postinstallcmds = ["chmod -R +r %(installdir)s/lib/"] + +sanity_check_paths = { + 'files': ['bin/in2csv', 'bin/sql2csv', 'bin/csvclean', 'bin/csvcut', 'bin/csvgrep', 'bin/csvjoin', + 'bin/csvsort', 'bin/csvstack', 'bin/csvformat', 'bin/csvjson', 'bin/csvlook', 'bin/csvpy', + 'bin/csvsql', 'bin/csvstat'], + 'dirs': [], +} + +sanity_check_commands = [('csvlook', '-h')] + +moduleclass = 'tools' 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/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/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 new file mode 100644 index 0000000000000000000000000000000000000000..45e774b0e381a8b6a5bc693fc87371bf23ecc3fd --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb @@ -0,0 +1,21 @@ +name = 'Doxygen' +version = '1.8.11' + +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': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.3'), + ('flex', '2.6.0'), + ('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 new file mode 100644 index 0000000000000000000000000000000000000000..a63ff80fea99963b24142537f73563091eb9397b --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb @@ -0,0 +1,21 @@ +name = 'Doxygen' +version = '1.8.11' + +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': '2016a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.3'), + ('flex', '2.6.0'), + ('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/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0e4a07c55e65a3f32f1761ceccddee3a2b152da9 --- /dev/null +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ETSF_IO' +version = '1.0.4' + +homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' +description = """A library of F90 routines to read/write the ETSF file +format has been written. It is called ETSF_IO and available under LGPL. """ + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://www.etsf.eu/system/files'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-netcdf-prefix=$EBROOTNETCDF " +configopts += "--with-netcdf-libs='-L$EBROOTNETCDF/lib -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdf -lnetcdff' " +configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include '" + +dependencies = [ + ('netCDF', '4.3.3.1'), + ('netCDF-Fortran', '4.4.2'), +] + +sanity_check_paths = { + 'files': ["bin/etsf_io"], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..1ca29896e871f529687b320b23a2b1ae17faaf00 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.7.0' + +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/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# 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-2.8.0.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-2.2.0-foss-2015b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a9d4b53984092800ab6df5bd6779171ee2a6c86 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb @@ -0,0 +1,33 @@ +# 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: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.2.0' + +homepage = 'http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('GLib', '2.34.3')] + +# 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/Exonerate/Exonerate-2.4.0-foss-2015b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..524d427c0e606daea1e67f2e151f1b13ed62fc64 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.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': '2015b'} + +source_urls = ['https://github.com/nathanweeks/exonerate/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GLib', '2.46.2')] + +# 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/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/eudev/eudev-3.1.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..2d6463fa7e116f6863bbe1f0add91feb996129a9 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-2.1.0-foss-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c31495cceea6b2b08f08bde7dd2935682e1e7b5a --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +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_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' 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-6.0.1-no-OFED.eb b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb index a1ceee68c98071778a0c81c5d2d38ef79623aedc..f79371e678dfa0efe7f9d9895c3f0036d249f5c2 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb @@ -9,7 +9,7 @@ description = """ Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download .sh from https://bintray.com/nist-fire-research/releases/FDS-SMV/6.0.1/view/files to create tarball sources = ['FDS_6.0.1-SMV_6.1.5_linux64.tar.gz'] 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-gmpich-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmpich-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..71efac9c7e2c35c760db4da6d1d30b5e3bc7ff83 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmpich-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': 'gmpich', 'version': '2016a'} +toolchainopts = {'optarch': True, '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-gmvapich2-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..757b5eba9134faf0e45889bd7252f23398e6a6a2 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-2016a.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': 'gmvapich2', 'version': '2016a'} +toolchainopts = {'optarch': True, '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-2016.04.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-intel-2015b-PFFT-20150905.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb new file mode 100644 index 0000000000000000000000000000000000000000..d127590485df29af5932806de6a21ba89a5d71e8 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' +versionsuffix = '-PFFT-20150905' + +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': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +patches = ['%(name)s_%(version)s%(versionsuffix)s.patch'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# the patch changed a Makefile.am, so we need to call autoreconf +preconfigopts = "autoreconf --verbose --symlink --force && " + +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/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/FFTW/FFTW_3.3.4-PFFT-20150905.patch b/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-PFFT-20150905.patch new file mode 100644 index 0000000000000000000000000000000000000000..a5895cfc2c561a8f535e40f7cfda60ff97c10435 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-PFFT-20150905.patch @@ -0,0 +1,875 @@ +#https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en#scripts +#This patch is needed by PFFT +#https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en#pfft +#Within these scripts we apply the following patches that have been submitted to FFTW but are not yet included in FFTW-3.3.4: +#We add two more global transposition algorithms to the planner. +#We patch file mpi/transpose-pairwise.c in order to fix a double free bug. +#The patch file is fleshed out from install_fftw-3.3.4_gcc.sh +#at https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software/install_fftw-3.3.4_gcc.sh +diff -rupN fftw-3.3.4/mpi/conf.c fftw-3.3.4-patched/mpi/conf.c +--- fftw-3.3.4/mpi/conf.c 2014-03-04 19:41:03.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/conf.c 2015-09-05 05:53:19.085516467 +0200 +@@ -29,6 +29,8 @@ static const solvtab s = + SOLVTAB(XM(transpose_pairwise_register)), + SOLVTAB(XM(transpose_alltoall_register)), + SOLVTAB(XM(transpose_recurse_register)), ++ SOLVTAB(XM(transpose_pairwise_transposed_register)), ++ SOLVTAB(XM(transpose_alltoall_transposed_register)), + SOLVTAB(XM(dft_rank_geq2_register)), + SOLVTAB(XM(dft_rank_geq2_transposed_register)), + SOLVTAB(XM(dft_serial_register)), +diff -rupN fftw-3.3.4/mpi/Makefile.am fftw-3.3.4-patched/mpi/Makefile.am +--- fftw-3.3.4/mpi/Makefile.am 2013-03-18 13:10:45.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/Makefile.am 2015-09-05 05:53:19.084516437 +0200 +@@ -16,6 +16,7 @@ BUILT_SOURCES = fftw3-mpi.f03.in fftw3-m + CLEANFILES = fftw3-mpi.f03 fftw3l-mpi.f03 + + TRANSPOSE_SRC = transpose-alltoall.c transpose-pairwise.c transpose-recurse.c transpose-problem.c transpose-solve.c mpi-transpose.h ++TRANSPOSE_SRC += transpose-alltoall-transposed.c transpose-pairwise-transposed.c + DFT_SRC = dft-serial.c dft-rank-geq2.c dft-rank-geq2-transposed.c dft-rank1.c dft-rank1-bigvec.c dft-problem.c dft-solve.c mpi-dft.h + RDFT_SRC = rdft-serial.c rdft-rank-geq2.c rdft-rank-geq2-transposed.c rdft-rank1-bigvec.c rdft-problem.c rdft-solve.c mpi-rdft.h + RDFT2_SRC = rdft2-serial.c rdft2-rank-geq2.c rdft2-rank-geq2-transposed.c rdft2-problem.c rdft2-solve.c mpi-rdft2.h +diff -rupN fftw-3.3.4/mpi/mpi-transpose.h fftw-3.3.4-patched/mpi/mpi-transpose.h +--- fftw-3.3.4/mpi/mpi-transpose.h 2014-03-04 19:41:03.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/mpi-transpose.h 2015-09-05 05:53:19.085516467 +0200 +@@ -59,3 +59,5 @@ int XM(mkplans_posttranspose)(const prob + void XM(transpose_pairwise_register)(planner *p); + void XM(transpose_alltoall_register)(planner *p); + void XM(transpose_recurse_register)(planner *p); ++void XM(transpose_pairwise_transposed_register)(planner *p); ++void XM(transpose_alltoall_transposed_register)(planner *p); +diff -rupN fftw-3.3.4/mpi/transpose-alltoall-transposed.c fftw-3.3.4-patched/mpi/transpose-alltoall-transposed.c +--- fftw-3.3.4/mpi/transpose-alltoall-transposed.c 1970-01-01 01:00:00.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/transpose-alltoall-transposed.c 2015-09-05 05:53:19.085516467 +0200 +@@ -0,0 +1,280 @@ ++/* ++ * Copyright (c) 2003, 2007-11 Matteo Frigo ++ * Copyright (c) 2003, 2007-11 Massachusetts Institute of Technology ++ * Copyright (c) 2012 Michael Pippig ++ * ++ * This program is free software; you can redistribute it and/or modify ++ * it under the terms of the GNU General Public License as published by ++ * the Free Software Foundation; either version 2 of the License, or ++ * (at your option) any later version. ++ * ++ * This program is distributed in the hope that it will be useful, ++ * but WITHOUT ANY WARRANTY; without even the implied warranty of ++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++ * GNU General Public License for more details. ++ * ++ * You should have received a copy of the GNU General Public License ++ * along with this program; if not, write to the Free Software ++ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA ++ * ++ */ ++ ++/* plans for distributed out-of-place transpose using MPI_Alltoall, ++ and which destroy the input array (also if TRANSPOSED_IN is used) */ ++ ++#include "mpi-transpose.h" ++#include ++ ++typedef struct { ++ solver super; ++ int copy_transposed_out; /* whether to copy the output for TRANSPOSED_OUT, ++ which makes the first transpose out-of-place ++ but costs an extra copy and requires us ++ to destroy the input */ ++} S; ++ ++typedef struct { ++ plan_mpi_transpose super; ++ ++ plan *cld1, *cld2, *cld2rest, *cld3; ++ ++ MPI_Comm comm; ++ int *send_block_sizes, *send_block_offsets; ++ int *recv_block_sizes, *recv_block_offsets; ++ ++ INT rest_Ioff, rest_Ooff; ++ ++ int equal_blocks; ++} P; ++ ++/* transpose locally to get contiguous chunks ++ this may take two transposes if the block sizes are unequal ++ (3 subplans, two of which operate on disjoint data) */ ++static void apply_pretranspose( ++ const P *ego, R *I, R *O ++ ) ++{ ++ plan_rdft *cld2, *cld2rest, *cld3; ++ ++ cld3 = (plan_rdft *) ego->cld3; ++ if (cld3) ++ cld3->apply(ego->cld3, O, O); ++ /* else TRANSPOSED_IN is true and user wants I transposed */ ++ ++ cld2 = (plan_rdft *) ego->cld2; ++ cld2->apply(ego->cld2, I, O); ++ cld2rest = (plan_rdft *) ego->cld2rest; ++ if (cld2rest) { ++ cld2rest->apply(ego->cld2rest, ++ I + ego->rest_Ioff, O + ego->rest_Ooff); ++ } ++} ++ ++static void apply(const plan *ego_, R *I, R *O) ++{ ++ const P *ego = (const P *) ego_; ++ plan_rdft *cld1 = (plan_rdft *) ego->cld1; ++ ++ if (cld1) { ++ /* transpose locally to get contiguous chunks */ ++ apply_pretranspose(ego, I, O); ++ ++ /* transpose chunks globally */ ++ if (ego->equal_blocks) ++ MPI_Alltoall(O, ego->send_block_sizes[0], FFTW_MPI_TYPE, ++ I, ego->recv_block_sizes[0], FFTW_MPI_TYPE, ++ ego->comm); ++ else ++ MPI_Alltoallv(O, ego->send_block_sizes, ego->send_block_offsets, ++ FFTW_MPI_TYPE, ++ I, ego->recv_block_sizes, ego->recv_block_offsets, ++ FFTW_MPI_TYPE, ++ ego->comm); ++ ++ /* transpose locally to get non-transposed output */ ++ cld1->apply(ego->cld1, I, O); ++ } /* else TRANSPOSED_OUT is true and user wants O transposed */ ++ else { ++ /* transpose locally to get contiguous chunks */ ++ apply_pretranspose(ego, I, I); ++ ++ /* transpose chunks globally */ ++ if (ego->equal_blocks) ++ MPI_Alltoall(I, ego->send_block_sizes[0], FFTW_MPI_TYPE, ++ O, ego->recv_block_sizes[0], FFTW_MPI_TYPE, ++ ego->comm); ++ else ++ MPI_Alltoallv(I, ego->send_block_sizes, ego->send_block_offsets, ++ FFTW_MPI_TYPE, ++ O, ego->recv_block_sizes, ego->recv_block_offsets, ++ FFTW_MPI_TYPE, ++ ego->comm); ++ } ++} ++ ++static int applicable(const S *ego, const problem *p_, ++ const planner *plnr) ++{ ++ /* in contrast to transpose-alltoall this algorithm can not preserve the input, ++ * since we need at least one transpose before the (out-of-place) Alltoall */ ++ const problem_mpi_transpose *p = (const problem_mpi_transpose *) p_; ++ return (1 ++ && p->I != p->O ++ && (!NO_DESTROY_INPUTP(plnr)) ++ && ((p->flags & TRANSPOSED_OUT) || !ego->copy_transposed_out) ++ && ONLY_TRANSPOSEDP(p->flags) ++ ); ++} ++ ++static void awake(plan *ego_, enum wakefulness wakefulness) ++{ ++ P *ego = (P *) ego_; ++ X(plan_awake)(ego->cld1, wakefulness); ++ X(plan_awake)(ego->cld2, wakefulness); ++ X(plan_awake)(ego->cld2rest, wakefulness); ++ X(plan_awake)(ego->cld3, wakefulness); ++} ++ ++static void destroy(plan *ego_) ++{ ++ P *ego = (P *) ego_; ++ X(ifree0)(ego->send_block_sizes); ++ MPI_Comm_free(&ego->comm); ++ X(plan_destroy_internal)(ego->cld3); ++ X(plan_destroy_internal)(ego->cld2rest); ++ X(plan_destroy_internal)(ego->cld2); ++ X(plan_destroy_internal)(ego->cld1); ++} ++ ++static void print(const plan *ego_, printer *p) ++{ ++ const P *ego = (const P *) ego_; ++ p->print(p, "(mpi-transpose-alltoall-transposed%s%(%p%)%(%p%)%(%p%)%(%p%))", ++ ego->equal_blocks ? "/e" : "", ++ ego->cld1, ego->cld2, ego->cld2rest, ego->cld3); ++} ++ ++static plan *mkplan(const solver *ego_, const problem *p_, planner *plnr) ++{ ++ const S *ego = (const S *) ego_; ++ const problem_mpi_transpose *p; ++ P *pln; ++ plan *cld1 = 0, *cld2 = 0, *cld2rest = 0, *cld3 = 0; ++ INT b, bt, vn, rest_Ioff, rest_Ooff; ++ R *O; ++ int *sbs, *sbo, *rbs, *rbo; ++ int pe, my_pe, n_pes; ++ int equal_blocks = 1; ++ static const plan_adt padt = { ++ XM(transpose_solve), awake, print, destroy ++ }; ++ ++ if (!applicable(ego, p_, plnr)) ++ return (plan *) 0; ++ ++ p = (const problem_mpi_transpose *) p_; ++ vn = p->vn; ++ ++ MPI_Comm_rank(p->comm, &my_pe); ++ MPI_Comm_size(p->comm, &n_pes); ++ ++ bt = XM(block)(p->ny, p->tblock, my_pe); ++ ++ if (p->flags & TRANSPOSED_OUT) { /* O stays transposed */ ++ if (ego->copy_transposed_out) { ++ cld1 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)(X(mktensor_1d) ++ (bt * p->nx * vn, 1, 1), ++ p->I, O = p->O), ++ 0, 0, NO_SLOW); ++ if (XM(any_true)(!cld1, p->comm)) goto nada; ++ } ++ else /* first transpose is in-place */ ++ O = p->I; ++ } ++ else { /* transpose nx x bt x vn -> bt x nx x vn */ ++ cld1 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)(X(mktensor_3d) ++ (bt, vn, p->nx * vn, ++ p->nx, bt * vn, vn, ++ vn, 1, 1), ++ p->I, O = p->O), ++ 0, 0, NO_SLOW); ++ if (XM(any_true)(!cld1, p->comm)) goto nada; ++ } ++ ++ if (XM(any_true)(!XM(mkplans_pretranspose)(p, plnr, p->I, O, my_pe, ++ &cld2, &cld2rest, &cld3, ++ &rest_Ioff, &rest_Ooff), ++ p->comm)) goto nada; ++ ++ ++ pln = MKPLAN_MPI_TRANSPOSE(P, &padt, apply); ++ ++ pln->cld1 = cld1; ++ pln->cld2 = cld2; ++ pln->cld2rest = cld2rest; ++ pln->rest_Ioff = rest_Ioff; ++ pln->rest_Ooff = rest_Ooff; ++ pln->cld3 = cld3; ++ ++ MPI_Comm_dup(p->comm, &pln->comm); ++ ++ /* Compute sizes/offsets of blocks to send for all-to-all command. */ ++ sbs = (int *) MALLOC(4 * n_pes * sizeof(int), PLANS); ++ sbo = sbs + n_pes; ++ rbs = sbo + n_pes; ++ rbo = rbs + n_pes; ++ b = XM(block)(p->nx, p->block, my_pe); ++ bt = XM(block)(p->ny, p->tblock, my_pe); ++ for (pe = 0; pe < n_pes; ++pe) { ++ INT db, dbt; /* destination block sizes */ ++ db = XM(block)(p->nx, p->block, pe); ++ dbt = XM(block)(p->ny, p->tblock, pe); ++ if (db != p->block || dbt != p->tblock) ++ equal_blocks = 0; ++ ++ /* MPI requires type "int" here; apparently it ++ has no 64-bit API? Grrr. */ ++ sbs[pe] = (int) (b * dbt * vn); ++ sbo[pe] = (int) (pe * (b * p->tblock) * vn); ++ rbs[pe] = (int) (db * bt * vn); ++ rbo[pe] = (int) (pe * (p->block * bt) * vn); ++ } ++ pln->send_block_sizes = sbs; ++ pln->send_block_offsets = sbo; ++ pln->recv_block_sizes = rbs; ++ pln->recv_block_offsets = rbo; ++ pln->equal_blocks = equal_blocks; ++ ++ X(ops_zero)(&pln->super.super.ops); ++ if (cld1) X(ops_add2)(&cld1->ops, &pln->super.super.ops); ++ if (cld2) X(ops_add2)(&cld2->ops, &pln->super.super.ops); ++ if (cld2rest) X(ops_add2)(&cld2rest->ops, &pln->super.super.ops); ++ if (cld3) X(ops_add2)(&cld3->ops, &pln->super.super.ops); ++ /* FIXME: should MPI operations be counted in "other" somehow? */ ++ ++ return &(pln->super.super); ++ ++ nada: ++ X(plan_destroy_internal)(cld3); ++ X(plan_destroy_internal)(cld2rest); ++ X(plan_destroy_internal)(cld2); ++ X(plan_destroy_internal)(cld1); ++ return (plan *) 0; ++} ++ ++static solver *mksolver(int copy_transposed_out) ++{ ++ static const solver_adt sadt = { PROBLEM_MPI_TRANSPOSE, mkplan, 0 }; ++ S *slv = MKSOLVER(S, &sadt); ++ slv->copy_transposed_out = copy_transposed_out; ++ return &(slv->super); ++} ++ ++void XM(transpose_alltoall_transposed_register)(planner *p) ++{ ++ int cto; ++ for (cto = 0; cto <= 1; ++cto) ++ REGISTER_SOLVER(p, mksolver(cto)); ++} +diff -rupN fftw-3.3.4/mpi/transpose-pairwise.c fftw-3.3.4-patched/mpi/transpose-pairwise.c +--- fftw-3.3.4/mpi/transpose-pairwise.c 2014-03-04 19:41:03.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/transpose-pairwise.c 2015-09-05 06:00:05.715433709 +0200 +@@ -53,7 +53,6 @@ static void transpose_chunks(int *sched, + { + if (sched) { + int i; +- MPI_Status status; + + /* TODO: explore non-synchronous send/recv? */ + +@@ -74,7 +73,7 @@ static void transpose_chunks(int *sched, + O + rbo[pe], (int) (rbs[pe]), + FFTW_MPI_TYPE, + pe, (pe * n_pes + my_pe) & 0xffff, +- comm, &status); ++ comm, MPI_STATUS_IGNORE); + } + } + +@@ -92,7 +91,7 @@ static void transpose_chunks(int *sched, + O + rbo[pe], (int) (rbs[pe]), + FFTW_MPI_TYPE, + pe, (pe * n_pes + my_pe) & 0xffff, +- comm, &status); ++ comm, MPI_STATUS_IGNORE); + } + } + } +@@ -350,6 +349,7 @@ nada: + X(plan_destroy_internal)(*cld3); + X(plan_destroy_internal)(*cld2rest); + X(plan_destroy_internal)(*cld2); ++ *cld2 = *cld2rest = *cld3 = NULL; + return 0; + } + +diff -rupN fftw-3.3.4/mpi/transpose-pairwise-transposed.c fftw-3.3.4-patched/mpi/transpose-pairwise-transposed.c +--- fftw-3.3.4/mpi/transpose-pairwise-transposed.c 1970-01-01 01:00:00.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/transpose-pairwise-transposed.c 2015-09-05 06:00:07.280481042 +0200 +@@ -0,0 +1,510 @@ ++/* ++ * Copyright (c) 2003, 2007-11 Matteo Frigo ++ * Copyright (c) 2003, 2007-11 Massachusetts Institute of Technology ++ * Copyright (c) 2012 Michael Pippig ++ * ++ * This program is free software; you can redistribute it and/or modify ++ * it under the terms of the GNU General Public License as published by ++ * the Free Software Foundation; either version 2 of the License, or ++ * (at your option) any later version. ++ * ++ * This program is distributed in the hope that it will be useful, ++ * but WITHOUT ANY WARRANTY; without even the implied warranty of ++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++ * GNU General Public License for more details. ++ * ++ * You should have received a copy of the GNU General Public License ++ * along with this program; if not, write to the Free Software ++ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA ++ * ++ */ ++ ++/* Distributed transposes using a sequence of carefully scheduled ++ pairwise exchanges. This has the advantage that it can be done ++ in-place, or out-of-place while preserving the input, using buffer ++ space proportional to the local size divided by the number of ++ processes (i.e. to the total array size divided by the number of ++ processes squared). */ ++ ++#include "mpi-transpose.h" ++#include ++ ++typedef struct { ++ solver super; ++ int preserve_input; /* preserve input even if DESTROY_INPUT was passed */ ++} S; ++ ++typedef struct { ++ plan_mpi_transpose super; ++ ++ plan *cld1, *cld2, *cld2rest, *cld3; ++ INT rest_Ioff, rest_Ooff; ++ ++ int n_pes, my_pe, *sched; ++ INT *send_block_sizes, *send_block_offsets; ++ INT *recv_block_sizes, *recv_block_offsets; ++ MPI_Comm comm; ++ int preserve_input; ++} P; ++ ++static void transpose_chunks(int *sched, int n_pes, int my_pe, ++ INT *sbs, INT *sbo, INT *rbs, INT *rbo, ++ MPI_Comm comm, ++ R *I, R *O) ++{ ++ if (sched) { ++ int i; ++ ++ /* TODO: explore non-synchronous send/recv? */ ++ ++ if (I == O) { ++ R *buf = (R*) MALLOC(sizeof(R) * sbs[0], BUFFERS); ++ ++ for (i = 0; i < n_pes; ++i) { ++ int pe = sched[i]; ++ if (my_pe == pe) { ++ if (rbo[pe] != sbo[pe]) ++ memmove(O + rbo[pe], O + sbo[pe], ++ sbs[pe] * sizeof(R)); ++ } ++ else { ++ memcpy(buf, O + sbo[pe], sbs[pe] * sizeof(R)); ++ MPI_Sendrecv(buf, (int) (sbs[pe]), FFTW_MPI_TYPE, ++ pe, (my_pe * n_pes + pe) & 0xffff, ++ O + rbo[pe], (int) (rbs[pe]), ++ FFTW_MPI_TYPE, ++ pe, (pe * n_pes + my_pe) & 0xffff, ++ comm, MPI_STATUS_IGNORE); ++ } ++ } ++ ++ X(ifree)(buf); ++ } ++ else { /* I != O */ ++ for (i = 0; i < n_pes; ++i) { ++ int pe = sched[i]; ++ if (my_pe == pe) ++ memcpy(O + rbo[pe], I + sbo[pe], sbs[pe] * sizeof(R)); ++ else ++ MPI_Sendrecv(I + sbo[pe], (int) (sbs[pe]), ++ FFTW_MPI_TYPE, ++ pe, (my_pe * n_pes + pe) & 0xffff, ++ O + rbo[pe], (int) (rbs[pe]), ++ FFTW_MPI_TYPE, ++ pe, (pe * n_pes + my_pe) & 0xffff, ++ comm, MPI_STATUS_IGNORE); ++ } ++ } ++ } ++} ++ ++/* transpose locally to get contiguous chunks ++ this may take two transposes if the block sizes are unequal ++ (3 subplans, two of which operate on disjoint data) */ ++static void apply_pretranspose( ++ const P *ego, R *I, R *O ++ ) ++{ ++ plan_rdft *cld2, *cld2rest, *cld3; ++ ++ cld3 = (plan_rdft *) ego->cld3; ++ if (cld3) ++ cld3->apply(ego->cld3, O, O); ++ /* else TRANSPOSED_IN is true and user wants I transposed */ ++ ++ cld2 = (plan_rdft *) ego->cld2; ++ cld2->apply(ego->cld2, I, O); ++ cld2rest = (plan_rdft *) ego->cld2rest; ++ if (cld2rest) { ++ cld2rest->apply(ego->cld2rest, ++ I + ego->rest_Ioff, O + ego->rest_Ooff); ++ } ++} ++ ++static void apply(const plan *ego_, R *I, R *O) ++{ ++ const P *ego = (const P *) ego_; ++ plan_rdft *cld1 = (plan_rdft *) ego->cld1; ++ ++ if (cld1) { ++ /* transpose locally to get contiguous chunks */ ++ apply_pretranspose(ego, I, O); ++ ++ if(ego->preserve_input) I = O; ++ ++ /* transpose chunks globally */ ++ transpose_chunks(ego->sched, ego->n_pes, ego->my_pe, ++ ego->send_block_sizes, ego->send_block_offsets, ++ ego->recv_block_sizes, ego->recv_block_offsets, ++ ego->comm, O, I); ++ ++ /* transpose locally to get non-transposed output */ ++ cld1->apply(ego->cld1, I, O); ++ } /* else TRANSPOSED_OUT is true and user wants O transposed */ ++ else if (ego->preserve_input) { ++ /* transpose locally to get contiguous chunks */ ++ apply_pretranspose(ego, I, O); ++ ++ /* transpose chunks globally */ ++ transpose_chunks(ego->sched, ego->n_pes, ego->my_pe, ++ ego->send_block_sizes, ego->send_block_offsets, ++ ego->recv_block_sizes, ego->recv_block_offsets, ++ ego->comm, O, O); ++ } ++ else { ++ /* transpose locally to get contiguous chunks */ ++ apply_pretranspose(ego, I, I); ++ ++ /* transpose chunks globally */ ++ transpose_chunks(ego->sched, ego->n_pes, ego->my_pe, ++ ego->send_block_sizes, ego->send_block_offsets, ++ ego->recv_block_sizes, ego->recv_block_offsets, ++ ego->comm, I, O); ++ } ++} ++ ++static int applicable(const S *ego, const problem *p_, ++ const planner *plnr) ++{ ++ const problem_mpi_transpose *p = (const problem_mpi_transpose *) p_; ++ /* Note: this is *not* UGLY for out-of-place, destroy-input plans; ++ the planner often prefers transpose-pairwise to transpose-alltoall, ++ at least with LAM MPI on my machine. */ ++ return (1 ++ && (!ego->preserve_input || (!NO_DESTROY_INPUTP(plnr) ++ && p->I != p->O)) ++ && ONLY_TRANSPOSEDP(p->flags)); ++} ++ ++static void awake(plan *ego_, enum wakefulness wakefulness) ++{ ++ P *ego = (P *) ego_; ++ X(plan_awake)(ego->cld1, wakefulness); ++ X(plan_awake)(ego->cld2, wakefulness); ++ X(plan_awake)(ego->cld2rest, wakefulness); ++ X(plan_awake)(ego->cld3, wakefulness); ++} ++ ++static void destroy(plan *ego_) ++{ ++ P *ego = (P *) ego_; ++ X(ifree0)(ego->sched); ++ X(ifree0)(ego->send_block_sizes); ++ MPI_Comm_free(&ego->comm); ++ X(plan_destroy_internal)(ego->cld3); ++ X(plan_destroy_internal)(ego->cld2rest); ++ X(plan_destroy_internal)(ego->cld2); ++ X(plan_destroy_internal)(ego->cld1); ++} ++ ++static void print(const plan *ego_, printer *p) ++{ ++ const P *ego = (const P *) ego_; ++ p->print(p, "(mpi-transpose-pairwise-transposed%s%(%p%)%(%p%)%(%p%)%(%p%))", ++ ego->preserve_input==2 ?"/p":"", ++ ego->cld1, ego->cld2, ego->cld2rest, ego->cld3); ++} ++ ++/* Given a process which_pe and a number of processes npes, fills ++ the array sched[npes] with a sequence of processes to communicate ++ with for a deadlock-free, optimum-overlap all-to-all communication. ++ (All processes must call this routine to get their own schedules.) ++ The schedule can be re-ordered arbitrarily as long as all processes ++ apply the same permutation to their schedules. ++ ++ The algorithm here is based upon the one described in: ++ J. A. M. Schreuder, "Constructing timetables for sport ++ competitions," Mathematical Programming Study 13, pp. 58-67 (1980). ++ In a sport competition, you have N teams and want every team to ++ play every other team in as short a time as possible (maximum overlap ++ between games). This timetabling problem is therefore identical ++ to that of an all-to-all communications problem. In our case, there ++ is one wrinkle: as part of the schedule, the process must do ++ some data transfer with itself (local data movement), analogous ++ to a requirement that each team "play itself" in addition to other ++ teams. With this wrinkle, it turns out that an optimal timetable ++ (N parallel games) can be constructed for any N, not just for even ++ N as in the original problem described by Schreuder. ++*/ ++static void fill1_comm_sched(int *sched, int which_pe, int npes) ++{ ++ int pe, i, n, s = 0; ++ A(which_pe >= 0 && which_pe < npes); ++ if (npes % 2 == 0) { ++ n = npes; ++ sched[s++] = which_pe; ++ } ++ else ++ n = npes + 1; ++ for (pe = 0; pe < n - 1; ++pe) { ++ if (npes % 2 == 0) { ++ if (pe == which_pe) sched[s++] = npes - 1; ++ else if (npes - 1 == which_pe) sched[s++] = pe; ++ } ++ else if (pe == which_pe) sched[s++] = pe; ++ ++ if (pe != which_pe && which_pe < n - 1) { ++ i = (pe - which_pe + (n - 1)) % (n - 1); ++ if (i < n/2) ++ sched[s++] = (pe + i) % (n - 1); ++ ++ i = (which_pe - pe + (n - 1)) % (n - 1); ++ if (i < n/2) ++ sched[s++] = (pe - i + (n - 1)) % (n - 1); ++ } ++ } ++ A(s == npes); ++} ++ ++/* Sort the communication schedule sched for npes so that the schedule ++ on process sortpe is ascending or descending (!ascending). This is ++ necessary to allow in-place transposes when the problem does not ++ divide equally among the processes. In this case there is one ++ process where the incoming blocks are bigger/smaller than the ++ outgoing blocks and thus have to be received in ++ descending/ascending order, respectively, to avoid overwriting data ++ before it is sent. */ ++static void sort1_comm_sched(int *sched, int npes, int sortpe, int ascending) ++{ ++ int *sortsched, i; ++ sortsched = (int *) MALLOC(npes * sizeof(int) * 2, OTHER); ++ fill1_comm_sched(sortsched, sortpe, npes); ++ if (ascending) ++ for (i = 0; i < npes; ++i) ++ sortsched[npes + sortsched[i]] = sched[i]; ++ else ++ for (i = 0; i < npes; ++i) ++ sortsched[2*npes - 1 - sortsched[i]] = sched[i]; ++ for (i = 0; i < npes; ++i) ++ sched[i] = sortsched[npes + i]; ++ X(ifree)(sortsched); ++} ++ ++/* make the plans to do the pre-MPI transpositions (shared with ++ transpose-alltoall-transposed) */ ++int XM(mkplans_pretranspose)(const problem_mpi_transpose *p, planner *plnr, ++ R *I, R *O, int my_pe, ++ plan **cld2, plan **cld2rest, plan **cld3, ++ INT *rest_Ioff, INT *rest_Ooff) ++{ ++ INT vn = p->vn; ++ INT b = XM(block)(p->nx, p->block, my_pe); ++ INT bt = p->tblock; ++ INT nyb = p->ny / bt; /* number of equal-sized blocks */ ++ INT nyr = p->ny - nyb * bt; /* leftover rows after equal blocks */ ++ ++ *cld2 = *cld2rest = *cld3 = NULL; ++ *rest_Ioff = *rest_Ooff = 0; ++ ++ if (!(p->flags & TRANSPOSED_IN) && (nyr == 0 || I != O)) { ++ INT ny = p->ny * vn; ++ bt *= vn; ++ *cld2 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)(X(mktensor_3d) ++ (nyb, bt, b * bt, ++ b, ny, bt, ++ bt, 1, 1), ++ I, O), ++ 0, 0, NO_SLOW); ++ if (!*cld2) goto nada; ++ ++ if (nyr > 0) { ++ *rest_Ioff = nyb * bt; ++ *rest_Ooff = nyb * b * bt; ++ bt = nyr * vn; ++ *cld2rest = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)(X(mktensor_2d) ++ (b, ny, bt, ++ bt, 1, 1), ++ I + *rest_Ioff, ++ O + *rest_Ooff), ++ 0, 0, NO_SLOW); ++ if (!*cld2rest) goto nada; ++ } ++ } ++ else { ++ *cld2 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)( ++ X(mktensor_4d) ++ (nyb, b * bt * vn, b * bt * vn, ++ b, vn, bt * vn, ++ bt, b * vn, vn, ++ vn, 1, 1), ++ I, O), ++ 0, 0, NO_SLOW); ++ if (!*cld2) goto nada; ++ ++ *rest_Ioff = *rest_Ooff = nyb * bt * b * vn; ++ *cld2rest = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)( ++ X(mktensor_3d) ++ (b, vn, nyr * vn, ++ nyr, b * vn, vn, ++ vn, 1, 1), ++ I + *rest_Ioff, O + *rest_Ooff), ++ 0, 0, NO_SLOW); ++ if (!*cld2rest) goto nada; ++ ++ if (!(p->flags & TRANSPOSED_IN)) { ++ *cld3 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)( ++ X(mktensor_3d) ++ (p->ny, vn, b * vn, ++ b, p->ny * vn, vn, ++ vn, 1, 1), ++ I, I), ++ 0, 0, NO_SLOW); ++ if (!*cld3) goto nada; ++ } ++ } ++ ++ return 1; ++ ++nada: ++ X(plan_destroy_internal)(*cld3); ++ X(plan_destroy_internal)(*cld2rest); ++ X(plan_destroy_internal)(*cld2); ++ *cld2 = *cld2rest = *cld3 = NULL; ++ return 0; ++} ++ ++static plan *mkplan(const solver *ego_, const problem *p_, planner *plnr) ++{ ++ const S *ego = (const S *) ego_; ++ const problem_mpi_transpose *p; ++ P *pln; ++ plan *cld1 = 0, *cld2 = 0, *cld2rest = 0, *cld3 = 0; ++ INT b, bt, vn, rest_Ioff, rest_Ooff; ++ INT *sbs, *sbo, *rbs, *rbo; ++ int pe, my_pe, n_pes, sort_pe = -1, ascending = 1; ++ R *I, *O; ++ static const plan_adt padt = { ++ XM(transpose_solve), awake, print, destroy ++ }; ++ ++ UNUSED(ego); ++ ++ if (!applicable(ego, p_, plnr)) ++ return (plan *) 0; ++ ++ p = (const problem_mpi_transpose *) p_; ++ vn = p->vn; ++ I = p->I; O = p->O; ++ ++ MPI_Comm_rank(p->comm, &my_pe); ++ MPI_Comm_size(p->comm, &n_pes); ++ ++ bt = XM(block)(p->ny, p->tblock, my_pe); ++ ++ ++ if (ego->preserve_input || NO_DESTROY_INPUTP(plnr)) I = p->O; ++ ++ if (!(p->flags & TRANSPOSED_OUT)) { /* nx x bt x vn -> bt x nx x vn */ ++ cld1 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)(X(mktensor_3d) ++ (bt, vn, p->nx * vn, ++ p->nx, bt * vn, vn, ++ vn, 1, 1), ++ I, O = p->O), ++ 0, 0, NO_SLOW); ++ if (XM(any_true)(!cld1, p->comm)) goto nada; ++ ++ } ++ else { ++ if (ego->preserve_input || NO_DESTROY_INPUTP(plnr)) ++ O = p->O; ++ else ++ O = p->I; ++ } ++ ++ if (XM(any_true)(!XM(mkplans_pretranspose)(p, plnr, p->I, O, my_pe, ++ &cld2, &cld2rest, &cld3, ++ &rest_Ioff, &rest_Ooff), ++ p->comm)) goto nada; ++ ++ pln = MKPLAN_MPI_TRANSPOSE(P, &padt, apply); ++ ++ pln->cld1 = cld1; ++ pln->cld2 = cld2; ++ pln->cld2rest = cld2rest; ++ pln->rest_Ioff = rest_Ioff; ++ pln->rest_Ooff = rest_Ooff; ++ pln->cld3 = cld3; ++ pln->preserve_input = ego->preserve_input ? 2 : NO_DESTROY_INPUTP(plnr); ++ ++ MPI_Comm_dup(p->comm, &pln->comm); ++ ++ n_pes = (int) X(imax)(XM(num_blocks)(p->nx, p->block), ++ XM(num_blocks)(p->ny, p->tblock)); ++ ++ /* Compute sizes/offsets of blocks to exchange between processors */ ++ sbs = (INT *) MALLOC(4 * n_pes * sizeof(INT), PLANS); ++ sbo = sbs + n_pes; ++ rbs = sbo + n_pes; ++ rbo = rbs + n_pes; ++ b = XM(block)(p->nx, p->block, my_pe); ++ bt = XM(block)(p->ny, p->tblock, my_pe); ++ for (pe = 0; pe < n_pes; ++pe) { ++ INT db, dbt; /* destination block sizes */ ++ db = XM(block)(p->nx, p->block, pe); ++ dbt = XM(block)(p->ny, p->tblock, pe); ++ ++ sbs[pe] = b * dbt * vn; ++ sbo[pe] = pe * (b * p->tblock) * vn; ++ rbs[pe] = db * bt * vn; ++ rbo[pe] = pe * (p->block * bt) * vn; ++ ++ if (db * dbt > 0 && db * p->tblock != p->block * dbt) { ++ A(sort_pe == -1); /* only one process should need sorting */ ++ sort_pe = pe; ++ ascending = db * p->tblock > p->block * dbt; ++ } ++ } ++ pln->n_pes = n_pes; ++ pln->my_pe = my_pe; ++ pln->send_block_sizes = sbs; ++ pln->send_block_offsets = sbo; ++ pln->recv_block_sizes = rbs; ++ pln->recv_block_offsets = rbo; ++ ++ if (my_pe >= n_pes) { ++ pln->sched = 0; /* this process is not doing anything */ ++ } ++ else { ++ pln->sched = (int *) MALLOC(n_pes * sizeof(int), PLANS); ++ fill1_comm_sched(pln->sched, my_pe, n_pes); ++ if (sort_pe >= 0) ++ sort1_comm_sched(pln->sched, n_pes, sort_pe, ascending); ++ } ++ ++ X(ops_zero)(&pln->super.super.ops); ++ if (cld1) X(ops_add2)(&cld1->ops, &pln->super.super.ops); ++ if (cld2) X(ops_add2)(&cld2->ops, &pln->super.super.ops); ++ if (cld2rest) X(ops_add2)(&cld2rest->ops, &pln->super.super.ops); ++ if (cld3) X(ops_add2)(&cld3->ops, &pln->super.super.ops); ++ /* FIXME: should MPI operations be counted in "other" somehow? */ ++ ++ return &(pln->super.super); ++ ++ nada: ++ X(plan_destroy_internal)(cld3); ++ X(plan_destroy_internal)(cld2rest); ++ X(plan_destroy_internal)(cld2); ++ X(plan_destroy_internal)(cld1); ++ return (plan *) 0; ++} ++ ++static solver *mksolver(int preserve_input) ++{ ++ static const solver_adt sadt = { PROBLEM_MPI_TRANSPOSE, mkplan, 0 }; ++ S *slv = MKSOLVER(S, &sadt); ++ slv->preserve_input = preserve_input; ++ return &(slv->super); ++} ++ ++void XM(transpose_pairwise_transposed_register)(planner *p) ++{ ++ int preserve_input; ++ for (preserve_input = 0; preserve_input <= 1; ++preserve_input) ++ REGISTER_SOLVER(p, mksolver(preserve_input)); ++} 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 new file mode 100644 index 0000000000000000000000000000000000000000..d88b64d96a2da3e6b80862b404dd8d9b8273843d --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-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': 'intel', '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/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-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb similarity index 63% rename from easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb index 4bf3f06a01c7f2354475e33278012988fdedfe70..54414776644f3c32312b3620166bae190955a90d 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb @@ -6,7 +6,7 @@ # License:: MIT/GPL # ## -easyblock = "PackedBinary" +easyblock = 'PackedBinary' name = 'FastQC' version = '0.10.1' @@ -17,22 +17,26 @@ description = """FastQC is a quality control application for high throughput seq 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': 'goolf', 'version': '1.4.10'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s_v%(version)s.zip'] source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +patches = ['FastQC_shebang.patch'] + java = 'Java' javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] -dependencies = [('Java', '1.7.0_80', '', True)] - -install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc" +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] sanity_check_paths = { - 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.32.jar"], - 'dirs': ["Contaminants", "Help", "Templates", "uk"], + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.32.jar'], + 'dirs': ['Contaminants', 'Help', 'Templates', 'uk'], } +sanity_check_commands = [('fastqc', '-v')] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb new file mode 100644 index 0000000000000000000000000000000000000000..89f6650b3ca94f65c0b85da197dcb90d635e8bcb --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb @@ -0,0 +1,34 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.2' + +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'] + +java = 'Java' +javaver = '1.7.0_60' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] + +sanity_check_paths = { + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd7fff1b1628fb2644597b5e492b4e16b5936610 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb @@ -0,0 +1,34 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.3' + +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'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +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-0.11.4-Java-1.8.0_66.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb new file mode 100644 index 0000000000000000000000000000000000000000..7c531942b3fe65842f5ca358312390a3b684112f --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb @@ -0,0 +1,34 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.4' + +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'] + +java = 'Java' +javaver = '1.8.0_66' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +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-0.11.4-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b6a4d51e97337caeefb2ec1e2c5e56c611d8743 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb @@ -0,0 +1,34 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.4' + +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'] + +java = 'Java' +javaver = '1.8.0_74' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +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-1.7.0_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/FastQC/FastQC_shebang.patch b/easybuild/easyconfigs/f/FastQC/FastQC_shebang.patch new file mode 100644 index 0000000000000000000000000000000000000000..8e9733bfcedf8272177eacc314b642c88d66052f --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC_shebang.patch @@ -0,0 +1,11 @@ +Fix hardcoding of /usr/bin/perl, use perl available through $PATH +author: Nathan S. Watson-Haigh (ACPFG) +--- fastqc.orig 2016-03-01 10:53:17.433849105 +1030 ++++ fastqc 2016-03-01 10:53:44.850579745 +1030 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + use warnings; + use strict; + use FindBin qw($RealBin); + diff --git a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..21da1fddad55a1d15559dcf2430a828f3becf94e --- /dev/null +++ b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.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 = 'Tarball' + +name = 'Firefox' +version = '44.0.2' + +homepage = 'https://www.mozilla.org/en-US/firefox/new/' +description = """Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code + base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy + and security measures, smart searching, and RSS live bookmarks.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://ftp.mozilla.org/pub/firefox/releases/%(version)s/linux-x86_64/en-US/'] +sources = [SOURCELOWER_TAR_BZ2] + +sanity_check_paths = { + 'files': ['firefox'], + 'dirs': [] +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': "", +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb deleted file mode 100644 index 9ff730ebeda8b1096f7e370f983285c321dcc2c4..0000000000000000000000000000000000000000 --- a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'EB_Java' - -name = 'fastqc' -version = '0.11.2' - -homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' -description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] -sources = ['%(name)s_v%(version)s.zip'] - -dependencies = [('Java', '1.7.0_60')] - -postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] - -modextrapaths = {'PATH': ['']} - -sanity_check_paths = { - 'files': ['fastqc'], - 'dirs': [], -} - -sanity_check_commands = [('fastqc', '-v')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb deleted file mode 100644 index c5f20b91654926eb90d7d61fbb9671bdbc67d835..0000000000000000000000000000000000000000 --- a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'EB_Java' - -name = 'fastqc' -version = '0.11.3' - -homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' -description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] -sources = ['%(name)s_v%(version)s.zip'] - -dependencies = [('Java', '1.7.0_80')] - -postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] - -modextrapaths = {'PATH': ['']} - -sanity_check_paths = { - 'files': ['fastqc'], - 'dirs': [], -} - -sanity_check_commands = [('fastqc', '-v')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb deleted file mode 100644 index a4d75eb501de26f23f1b9e9442e1a83c20f55680..0000000000000000000000000000000000000000 --- a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'EB_Java' - -name = 'fastqc' -version = '0.11.4' - -homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' -description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] -sources = ['%(name)s_v%(version)s.zip'] - -dependencies = [('Java', '1.7.0_80')] - -postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] - -modextrapaths = {'PATH': ['']} - -sanity_check_paths = { - 'files': ['fastqc'], - 'dirs': [], -} - -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 new file mode 100644 index 0000000000000000000000000000000000000000..1deb262347d6cec0b6b1daa4ce3fad21644c23d8 --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-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-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb similarity index 87% rename from easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb index d9b2e6f439e250edaa5289424a7ce6e72e2e70c2..24e3dfb5dc336b8cad4e650054195077c7496dce 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb @@ -5,7 +5,7 @@ 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': 'CrayGNU', 'version': '2015.06-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb similarity index 87% rename from easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb index 7fbee438c59e031b996a89299a9df25c06ad93e5..8c57faa30991446979874b6897cd22216ae6b6b3 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb @@ -5,7 +5,7 @@ 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': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] 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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb index bd9f2b71e7df2fca1cb02cd29fae60e4fc95f066..32dffb057fd38fb79e7dfdf93bb6fe6652af369e 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb @@ -11,6 +11,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +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-2.5.39.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb index 53eb8f6c785226d322419e2e7a2711bce275b9a1..e4d83f163cb9c7b974e70a586251f06ef412e697 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb @@ -5,10 +5,12 @@ 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': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +builddependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..4015f4129186587d66c5fad9158d35c5a271c6c4 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.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': '4.9.3'} +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', '2.25', '', True)] + +parallel = 1 + +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-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..c2677565b597dedb7ead661f16ed06c8aa7aafb0 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} +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/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 new file mode 100644 index 0000000000000000000000000000000000000000..8e577e277b2e6ff595f523fe19ef4eed3facb7c9 --- /dev/null +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} +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-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/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="$EBROOTLIBXI/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe4a731eff1482dd4507ef6d199073fc6a07febf --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', '11.1.2'), +] + +configopts = ' -DX11_X11_LIB="$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/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-2.6.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..fec100e1f022981fcb70f63b03281d3b18ca28ae --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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/GATE/GATE-6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb index f6983e6ed65b375371b6f5a8d3c8b61d71f13a1f..24800cedc71596854a2ba324355eb8dc147515b8 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb @@ -4,7 +4,7 @@ version = '6.1' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'ictce', 'version': '4.0.6'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb index 8cd12c59aae644f6ed8f86207ecdebe71482e5ea..b344b3f548cf3ac344fb39c1b17b750725ec7d5c 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb @@ -4,7 +4,7 @@ version = '6.2' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb index 3bac12bc2cf8496c77ad46e15a055f0a924bee25..89a8046f2fe93f2a32562e62252e98c15ca4a0a6 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb @@ -4,7 +4,7 @@ version = '6.2' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb index cf9f93f19824db826c53044dbf07efaf9576eb45..2c2c954a1ca1f255f209906a393ef8a2d251ba19 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb @@ -4,7 +4,7 @@ version = '6.2' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'ictce', 'version': '4.0.6'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb index b6ef9ed9c17c336a3f0684bb7c90f8f8c668286f..1a6ef28db96f3ad8f904b8ecc2288950d3a4c709 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb @@ -4,7 +4,7 @@ version = '6.2' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..d237afef62bb79119ed24d9c2319dd33d2bf2095 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +name = 'GATE' +version = '6.2' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [('%%(namelower)s_v%s_tar_gz_15843.gz' % '_'.join(version.split('.')), "tar xfvz %s")] +source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/gate_release/2012/08/'] + +patches = [ + 'GATE-%(version)s_Makefile-prefix.patch', + 'GATE-%(version)s_GCC-4.7.patch', +] + +dependencies = [ + ('Geant4', '9.5.p02'), + ('CLHEP', '2.1.1.0'), + ('ROOT', 'v5.34.34', versionsuffix), +] +builddependencies = [('CMake', '3.4.3')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb index e93ce7917511e1e253587bed2307978509a36f74..85541021f4d1db7119ee74c0897e4570c1bf8440 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb @@ -4,7 +4,7 @@ version = '7.0' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..ddcd9aaa7c1a10c1f2eba08bde6f21bd8eb79ffa --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +name = 'GATE' +version = '7.1' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [('%(namelower)s_v%(version)s.tar.gz', "tar xfvz %s")] +source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/'] + +patches = [ + 'GATE-7.0_Makefile-prefix.patch', + 'GATE-7.0_unistdh.patch', + 'GATE-7.1_std-isnan.patch', +] + +dependencies = [ + ('Geant4', '10.01.p03'), + ('CLHEP', '2.2.0.8'), + ('ROOT', 'v5.34.34', versionsuffix), +] +builddependencies = [ + ('CMake', '3.4.3'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch b/easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch new file mode 100644 index 0000000000000000000000000000000000000000..b8d39150f4be4ce7ca5a742e4430fc24b98b1f6d --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch @@ -0,0 +1,13 @@ +fix for compiler error ""error: more than one instance of overloaded function isnan matches the argument list" +author: Kenneth Hoste (HPC-UGent) +--- gate_v7.1/source/digits_hits/src/GateToRoot.cc.orig 2016-03-03 19:41:50.569854028 +0100 ++++ gate_v7.1/source/digits_hits/src/GateToRoot.cc 2016-03-03 19:43:09.370590639 +0100 +@@ -765,7 +765,7 @@ + if (dzg1 > dzg2) {dev = acos(-dev)*180/Pi;} + else {dev = acos(dev)*180/Pi - 180;} + +- if (isnan(dev) ) dev = 0.; ++ if (std::isnan(dev) ) dev = 0.; + + // G4cout<< " dev = " << dev << G4endl; + diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..91e8c30f8c12ee523d753bd559d261effcb0a17d --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +name = 'GATE' +version = '7.2' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [('%(namelower)s_v%(version)s.tar.gz', "tar xfvz %s")] +source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/'] + +patches = [ + 'GATE-7.0_Makefile-prefix.patch', + 'GATE-7.0_unistdh.patch', +] + +dependencies = [ + ('Geant4', '10.02.p01'), + ('CLHEP', '2.3.1.1'), + ('ROOT', 'v5.34.34', versionsuffix), +] +builddependencies = [ + ('CMake', '3.4.3'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb index ddd5712d6f0345760c31665553c81f5bae9d76c9..dd2c25a6273d5f3bf74e63a40a1908768e78421c 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb @@ -9,7 +9,7 @@ description = """The GATK is a structured software library that makes writing ef medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb index daf52209028c60e3c5b5a07678f041e95b6f8ec8..ee70681358adac604a926d72c27e42aef1f0a9b0 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb index 0c9ece0c956dd82d1040226b8a0b33c9133f979d..dde93eb10a0faf69de36703c1517e0c0fa89eb00 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb index 12fe8dadb4ffcaa0a9dd9e48e8a65179b462994f..a45cb4ec3bdc1a0bfe22c1c04b29950175d0c060 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb index 98e7df7db87bfa06850ed5deadbe7047feb43e12..1bdef83c68fbaec7972033a6924a21a41e7a3269 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb @@ -9,7 +9,7 @@ description = """The GATK is a structured software library that makes writing ef medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb index aa6e7fe2329812a0b0fe2e81e6f94d6609924724..21448792b2586cf3b6533b9d18d1ded0ecf8e58a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb index 13de380c1b550861e16910f07b1fcfe65ac645ae..a6fc22eedf1e257ac4834471f582160989a3dda7 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb index 065919e6f31fd1d5f743a679aec1296f3d5e4ecd..38e7ae6db1890778b73f7ac995af9aea865a3ed4 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb index f53b54862bc930abd62012dac47fed1012790893..689accfbd9d1a55c8e429cb48c8d8cd60ea29a6b 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb index 00459becfc657117baa26a7f178e3ddfe96997c0..520cb6b37a67786ee3d4a0181fc388fb8b26563a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb index 2dc9a277e24b16f51714356772dc9dc1cd01abf1..adf96fa7cf2133ef49c2dcc7b77056ce4fc16493 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb new file mode 100644 index 0000000000000000000000000000000000000000..c52824dc923673d3c41c8a119ce49b1e28ac8fa0 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '3.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] + +dependencies = [('Java', '1.8.0_74')] + +modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index 3b725d6c3c0e1437e95f65b23edbe8e231a195a2..a6eca83b67fce672084ff2f27f46bed0f56700a8 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 662fb134c28a876be1cd49172e1f53943cdf423c..84677a51423eb42376059f32ed600acc1a4b3acd 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index b08b112eb7d5032d1720f3abefc858ed8f45dbef..55217f87b712186b917315b4e0b6a3decde47e2e 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 92f6d885db252e11fa3d669838d30832eb0b7ce5..dbc732d1791f5df3629f7d962b8f9518f1d7bdbf 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index e5720c5610cff3f8dfcf833c52d6ffcb2f8e6541..0e7690c9c0d9995445f6a93dea23d58e755e9e27 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] 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/GDAL/GDAL-2.0.2-foss-2016a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..80039ca35021ea0536cf83a585b97ffb4ed15fef --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.2' + +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': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.3.3.1'), + ('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/GDAL/GDAL-2.0.2-intel-2016a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..203a2ae45413612353482252862916cf6a01f571 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.2' + +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': 'intel', 'version': '2016a'} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.3.3.1'), + ('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/GEOS/GEOS-3.5.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..b8bf09f57e16ef171d44d146ae97332f129e0ab3 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('Python', '2.7.11')] + +builddependencies = [('SWIG', '3.0.8', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' 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/GL2PS/GL2PS-1.3.9-intel-2016a.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b004cefeffec9d6668955e911f7d0f53556dd69 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-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': 'intel', '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/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/GLPK/GLPK-4.58-intel-2016a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..07ed2e7997e4168479261f7ee12a4c23546b51e7 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-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': 'intel', '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-2.34.3-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..04873f8e5c29cc3b399ed6a108f9f7bb6fb35515 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.34.3' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.0.13'), + ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), +] +builddependencies = [('Python', '2.7.10')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb index 8949f8ac3aa52ecbf85715cb7631702a9c78b20a..d5179c2d3fef23e02861142d818338a7174ef283 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb index 30174bd67f75115ef4d97752b04882cdaba76500..8a3283f98f40728afb287d979bfa303a7cfc1976 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb @@ -14,6 +14,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015b.eb index b79abecbd35daced6f9aea0c06e314fe00cd2656..f78f7979674b5755a29be262d1658ef02f0ba0a8 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015b.eb @@ -14,6 +14,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.10')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb index 08bf6bb8cb88fbdac46b27df2587aa976cc0d861..94d03a2c3da6a68f655bc14a74a95a9c8ec79dc3 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb index e2971ec78cf81b2d2c3a569c726b43ec75201bfa..1320160d1a592f5991d5ec3b7041296ebf9167e8 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb @@ -15,6 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb index 224be4393680a827389d6a5c1c67967151253bce..09e94d7c70f2bc36a76a3cc12ae88d8abc98ec6a 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb @@ -15,6 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb index c6424b3f539a59c37b2a765ffb3859512f6586aa..9b0db5c7d4ef03695435a95e6b4468ce19739f42 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb index 9f4e52261e8e0a1a79eb532dd2f344a1c326204b..e1f3dc6096522da991ccb20522f532c07e05dee9 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] python = 'Python' pyver = '2.7.10' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb index ea740d47cab510dedc1ab0c08fefe8795630a282..6aacfaecc2284296d771b8b82a17ea2aab41357f 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..a273876d40359908e0b5ac7cf1991fcfdf916a64 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.46.0' +pyver = '2.7.11' +versionsuffix = '-Python-%s' % pyver + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3', versionsuffix), +] +builddependencies = [('Python', pyver)] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb index 56025316ff1738f7630a851bd2b8e33c66836ad8..1a6974652c3a5a3ac9fdbd7b9d69b87c746628e7 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb @@ -15,6 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.10')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2d418a45be4304ecabffcd9e6522ce891a9a84b7 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.46.2' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.2'), +] +builddependencies = [('Python', '2.7.10')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb index d5db1754d15a286b2eb9f8e9bb6b48eb4f27429a..90389b48f3247fd50425be93ef845069db2d5755 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb @@ -15,6 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.10')] 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-2.47.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..8580a33ef19a70c343752e88e8c3525b8218947a --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} +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-2.47.5-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb index 3dcfe3ad198e2c99348c2dda70f7c265156fab72..2b30216f8cba3e294c1d02b3f950835c6be51456 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb @@ -12,18 +12,14 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) -pysuffix = '-Python-%s' % pyver - dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), - ('libxml2', '2.9.3', pysuffix), + ('libxml2', '2.9.3'), ('PCRE', '8.38'), ] -builddependencies = [('Python', pyver)] +builddependencies = [('Python', '2.7.11')] configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" 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-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..3a93d0ea86a889b4a628d35d322241da9089c7ba --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} +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/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-4.6.7-CrayGNU-2015.06-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb similarity index 96% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb index eb693a5ca3329e8ad9285c1d5d47d2ee259d3010..7fae7e2b3ff44714c71a681f1b90bfd8263ee240 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb @@ -18,7 +18,7 @@ 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': 'CrayGNU', 'version': '2015.06-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb similarity index 96% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb index 7d022ac778da22d274698a051f8f1ee6b38500c7..83b2732fb5a3c0509fdce3a3fb7e147696885b2b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb @@ -18,7 +18,7 @@ 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': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb new file mode 100644 index 0000000000000000000000000000000000000000..350a3d6cfac172ec6e9c4867fa56480d697124d1 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb @@ -0,0 +1,45 @@ +## +# 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 +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +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': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " + +dependencies = [ + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' 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-1.15-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb index 85ec8681aa7fcd1f7874900bf7cdb7b624171eab..f4197820e570274320e98241509377448592e06b 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb @@ -5,7 +5,8 @@ version = '1.15' 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb index 2bc7e232eb602992cf83ea526e238fe9b7773076..d9295adc89e6bbc5c3c72862949a1504e85286c7 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb @@ -5,7 +5,8 @@ version = '1.15' 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.""" +The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb index d19efed940179e6b5f19286e9095e300a9dbddc9..3230d895d12e31362857f264ab7e8abe2677f39d 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb @@ -5,7 +5,8 @@ version = '1.15' 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb index 3ee18f98a213b915b001e4d1b645582d7e06890a..93b875b8e7ab61bf07d3e3bea852b0ffcb9df977 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb @@ -5,7 +5,8 @@ version = '1.15' 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb index a0f704520931317bc1ad442f149120655de843c7..3e17c8b5d6d8cf45482279285fbe1320af2cb6f0 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb @@ -5,7 +5,8 @@ version = '1.15' 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb index 3d34fbf06f55ceeb2fca5732ba4ef16d5c7a768b..9ef4e74b993f8ff438bc668c7b2d7ceedf01f917 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb @@ -5,7 +5,8 @@ version = '1.15' 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb index 9cfba7ecd1ab82dc738d56bf4995b338df098946..2c856c0c22afa523e7c550b932bf4c5f0d544ec9 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb @@ -5,7 +5,8 @@ version = '1.15' 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb index b20d7731f8b8ec54fc8b1ae0b2cfecafe7396303..426a5fa7025dde868de4b9716218dd8ef3c37527 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb index ed67148304a69a9965928bf6217ad27a0305af06..681aa2648bc1f8ea044ed5c29d3b975d6949c556 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2cce073a650a76dba30685a7620c0d3a02b0c43f --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.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': 'foss', 'version': '2016a'} +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/GSL/GSL-1.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb index 108a2f3dc54cd63352a14bf8aabf0d2b43f1fbee..7481f9558261c3db9097e59c82948b7cf9aca26b 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb index ffcd9e480449ad3fd029a9195a54f10bc3dda8a7..493418d2594b52c8e70cc5a17825b1c62aead62f 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} 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-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb index 875d7306f51a7de44c70c56266e337b481b166a7..0336ef456fd718d1dd4003a826a05e497b7d1035 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolfc', 'version': '1.3.12'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb index 9d9ca828127cfc1a3fcf22bee3865713a1331f15..0e558d56442f28d04b34e8921a9246562dd04777 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolfc', 'version': '2.6.10'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb index 7005ed5e6ab8d18340cb53ca1e1fee7548b58de6..e3cf37d1e505e6dc131862bc43a231d3faca875b 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb index 9d1699e64d8d711de212654c0c50284a43a6b017..1ee8967b14eb5f68a48a28c00fcfa2dc241e4452 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb index 1291647435089335a51cdbbc62d564e34882778b..cc561c1cbf7a463df3f251af1ed1de5b6b515c02 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb index 958500b4dd9c7ab76f8ca3f39b43aace393ad432..e1a049a993233a34c1df89b928b1345b61d4870d 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '6.2.5'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb index 3587bf11b973c2665c51c7c105808be910629923..f93fbb10905837d92d59844c947932ebf155e75d 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb index 79f876ac1d11aac1ed5637239d8a01f0dc65e01f..207992d0ebd455b305eca19d5040e82dc7184453 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb index f9f59f712ba8cb4c758f1063718a4e509b3d9374..33c068c25d68560d79b19538bb85e8eb0a596a9b 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..aaffd974f5fa4a19d9818cf2c976d7c02cf5554c --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.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': 'intel', 'version': '2016a'} +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/GSL/GSL-2.1-foss-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb index 812faf4e0f961d12935b387256830af9b24f28af..64966f00239781cec21f368057ca1daed928901b 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'version': '2015b', 'name': 'foss'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} 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/GSL/GSL-2.1-intel-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb index cae4fccd47ea15e135f6adc41acce5be4725c1d2..d363055a950c18339c9736ac7ee00d3b56b38927 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb @@ -5,7 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb index 418483081374507a1cf8132a955b69e1eaa8ce1a..6ff19555c345cf23b42dd47073b675bdd5bbf031 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb @@ -5,8 +5,8 @@ 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.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} 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 412c19225c040f5f5683c04e7a060fc2f3994e44..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 @@ -13,12 +13,13 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.10.1.html#2. ('CLHEP', '2.2.0.5'), ] 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 new file mode 100644 index 0000000000000000000000000000000000000000..60a8b5c5407b98d0757df863e598fcb6572eaf63 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb @@ -0,0 +1,25 @@ +name = 'Geant4' +version = '10.01.p03' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.10.1.html#2. + ('CLHEP', '2.2.0.8'), +] + +builddependencies = [('CMake', '3.4.3')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +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 new file mode 100644 index 0000000000000000000000000000000000000000..9f9a3a4002cda0ba837dd004bb71173968ecc8d1 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb @@ -0,0 +1,25 @@ +name = 'Geant4' +version = '10.02.p01' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.10.2.html#2. + ('CLHEP', '2.3.1.1'), +] + +builddependencies = [('CMake', '3.4.3')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +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 dd53f8508842ddf78dae7f69fb94826d1d06a1a2..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 @@ -13,12 +13,13 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.4.html#2. ('CLHEP', '2.1.1.0'), ] 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 fbf3b03c0b5b104cb2e5bfb3add6a19ed005060d..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 @@ -13,12 +13,13 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. ('CLHEP', '2.1.1.0'), ] 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 7db2e910b247cfd981c576eb5b685abf9fa847da..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 @@ -13,12 +13,13 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. ('CLHEP', '2.1.1.0'), ] 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 8eb3941ded72027456217a433e3c5f9acdf94341..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 @@ -13,12 +13,13 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. ('CLHEP', '2.1.1.0'), ] 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 cbe91d153a165e97b00e191efbb922be05943a2f..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 @@ -13,12 +13,13 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. ('CLHEP', '2.1.1.0'), ] 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 bfe0be4aaf8f564bf2e78b465e292b68adcf1c09..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 @@ -13,12 +13,13 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. ('CLHEP', '2.1.1.0'), ] 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 new file mode 100644 index 0000000000000000000000000000000000000000..cfa9e5761c52495ebde37a74dc7bbe21a736176b --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb @@ -0,0 +1,25 @@ +name = 'Geant4' +version = '9.5.p02' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. + ('CLHEP', '2.1.1.0'), +] + +builddependencies = [('CMake', '3.4.3')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +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 791ce6652ffc04ceeb117eaf9f5490ae2597bf9a..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 @@ -13,12 +13,13 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.6.html#2. ('CLHEP', '2.1.3.1'), ] 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 new file mode 100644 index 0000000000000000000000000000000000000000..ca80a8a174baf00fb7c990a4ce2b888bd8e23d7e --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb @@ -0,0 +1,26 @@ +name = 'Geant4' +version = '9.6.p04' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.6.html#2. + ('CLHEP', '2.1.3.1'), +] +builddependencies = [ + ('CMake', '3.4.3'), +] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += " -DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index df30b5f05b3a93b20e3da108345ec34738472f27..935c3f665fc3db29ad6446b328095bc6eab7f87b 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} java = 'Java' javaver = '1.7.0_80' 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/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7b4701d28d5d65530b9524f9041149f56493fc41 --- /dev/null +++ b/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Glade' +version = '3.8.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://glade.gnome.org/' +description = """Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit + and the GNOME desktop environment.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s%(version_major)s/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version_major)s-%(version)s.tar.xz'] + +dependencies = [ + ('Python', '2.7.11'), + ('GTK+', '2.24.28'), + ('PyGTK', '2.24.0', versionsuffix), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3'), +] +builddependencies = [ + ('intltool', '0.51.0', '-Perl-5.20.3'), + ('pkg-config', '0.29'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('renderproto', '0.11'), +] + +sanity_check_paths = { + 'files': ['bin/glade-%(version_major)s', 'lib/libgladeui-1.%s' % SHLIB_EXT, 'lib/pkgconfig/gladeui-1.0.pc', + 'lib/glade%%(version_major)s/modules/libgladegtk.%s' % SHLIB_EXT, + 'lib/glade%%(version_major)s/modules/libgladepython.%s' % SHLIB_EXT], + 'dirs': ['include/libgladeui-1.0/gladeui', 'share'], +} + +moduleclass = 'vis' 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=$EBROOTGUILE" diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.3.21-intel-2016a.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.3.21-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..dcf1712871080bd2bba6fbfbadbc11ccafdb58a6 --- /dev/null +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.3.21-intel-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GnuTLS' +version = '3.3.21' + +homepage = 'http://www.gnutls.org/' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +guilever = '1.8.8' +guileshortver = '.'.join(guilever.split('.')[:2]) +dependencies = [ + ('GMP', '6.1.0'), + ('nettle', '3.1.1'), + ('Guile', guilever), + ('libtasn1', '4.7'), + ('libidn', '1.32'), + ('p11-kit', '0.23.2'), +] + +configopts = "--with-guile-site-dir=$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-3.4.11-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 new file mode 100644 index 0000000000000000000000000000000000000000..de4cfae31e016e49ff0181de1e9411b85f41fd18 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-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': 'intel', '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/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 new file mode 100644 index 0000000000000000000000000000000000000000..a7b2c1f8edec0f0746651bee1c85156212b989c1 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-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': 'intel', '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-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-0.18.2-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e7d30bfac735bde0a37a1e05bc5868106eb62311 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.18.2' + +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': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' 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-0.19.6-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..4aed92d350e6c1ccc8f7f2248deb7c3cb1578cca --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..690872c686f14da3d5a18923ded8d5ea5130107e --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.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': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.2'), + ('ncurses', '5.9'), +] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..8a7667c002f7e1cc6de3be36825de2e2de99bdcb --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..5dd250fddb83cb74bdcd9c77717b510b4121f241 --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-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': 'intel', '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/gmpich/gmpich-2016a.eb b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..45cf27aa8b39682528f7556cc3938071e52554b7 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb @@ -0,0 +1,22 @@ +easyblock = "Toolchain" + +name = 'gmpich' +version = '2016a' + +homepage = '(none)' +description = """gcc and GFortran based compiler toolchain, + including MPICH for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.9.3-2.25' +comp = (compname, compver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('MPICH', '3.2', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d81b50276db3da4e894fbf1ae7cf63ffab437851 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb @@ -0,0 +1,35 @@ +easyblock = "Toolchain" + +name = 'gmpolf' +version = '2016a' + +homepage = '(none)' +description = """gcc and GFortran based compiler toolchain, + MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.3-2.25' + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gmpich' +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), + ('MPICH', '3.2', '', ('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/g/gmvapich2/gmvapich2-2016a.eb b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..80a9588d018d3330d0074119be07dd698d149904 --- /dev/null +++ b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb @@ -0,0 +1,22 @@ +easyblock = "Toolchain" + +name = 'gmvapich2' +version = '2016a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including MVAPICH2 for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.9.3-2.25' +comp = (compname, compver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('MVAPICH2', '2.2b', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb b/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b9a63b2c7c98b80b64485f908204bdedae887795 --- /dev/null +++ b/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'gmvolf' +version = '2016a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + MVAPICH2 for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.3-2.25' + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gmvapich2' +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), + ('MVAPICH2', '2.2b', '', ('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/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/gnuplot/gnuplot-5.0.3-intel-2016a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..131131cfee1f615ebfdb3a5235ade2e278bd1b4a --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-intel-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': 'intel', '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/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/gperf/gperf-3.0.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..53134ddab6e6401aee7c6d2a83521c2381fbe6bd --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-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-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..84580d9ba86a137adc09e2eeb6ca968d413db2b9 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.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': 'foss', 'version': '2016a'} +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="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..d1c17ce30e587c89343aa470163633f0c3eba61a --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.16' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$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-CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb similarity index 91% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb index 845802b50453459a0037378e23af09ca6ad9405d..934cc8d3eba6ae6200d69b2ef55398b3975cb5f8 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s 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': 'CrayCCE', 'version': '2015.06-XC'} +toolchain = {'name': 'CrayCCE', 'version': '2015.06'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb similarity index 91% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb index f4a0256f792ccb59850cab642b040dcce744c346..7a8e5a0800a1066a62c4d21c3218e1ef6c225782 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s 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': 'CrayCCE', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayCCE', 'version': '2015.11'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb similarity index 91% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb index fe0de8812c09e89270bcd9e93f493d9b8d9857a9..4f4dbfc813e7bb2c067516570a5e6a6b23b7002c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s 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': '2015.06-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb similarity index 91% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb index ecd5998b8d6a52014e0fb7fed6fd9d0e03cae82d..455f495e6effbee37ed41d4de3bd31a548ab2196 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s 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': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb similarity index 91% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb index 32e943a8d6e9be4c4dad2d6db3c6c23d6857d5ef..f64bec348b182077ae3001f5fb4b62469e7948e9 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s 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': 'CrayIntel', 'version': '2015.06-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2016.03'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb similarity index 91% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb index 370ce49b4cf7cb051b02d4f1763140117941e9ce..00ee4facc9deb07e6e72a87f7a53cdfe19e45f36 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s 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': 'CrayIntel', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayIntel', 'version': '2015.06'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..651ae824ba838e35c74049fb2a3e6ef2a1b29fa0 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.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': 'CrayIntel', 'version': '2015.11'} +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-gmpolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ae8a971cbf82e4e5053e35466e3bbdde03f12219 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.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': 'gmpolf', 'version': '2016a'} +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-gmvolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d581afc6f7e9572c10e24cb327bcbc8c4a82c106 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.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': 'gmvolf', 'version': '2016a'} +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-4.9.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..977c7d487d17b2770aec1bfd1f5449799864b0b8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-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': '2016.02-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-2016.02-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/HTSlib/HTSlib-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb index d99049bc6c6b2d0c0ff6f3798968d1918a9c7405..2f2abef4e6730210c5180cb11d88aadb90dd0e49 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb @@ -9,8 +9,8 @@ name = 'HTSlib' version = '1.1' homepage = 'http://www.htslib.org/' -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb index b9abe470f01314d4d14ed54ada177e3931e97f7f..36facf37a3ef9b2c65348ee18dde0f7af6878cde 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb @@ -9,8 +9,8 @@ name = 'HTSlib' version = '1.2.1' homepage = "http://www.htslib.org/" -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb index 742be3ddc090196a80f5e4a034465aeba6999456..7f25a2acfbdbdb35e19dce92a5250eefa82df132 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb @@ -11,8 +11,8 @@ name = 'HTSlib' version = '1.2.1' homepage = "http://www.htslib.org/" -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'goolf', 'version': '1.7.20'} diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb index a5f315ea84f911674974c9461b006892f5cddf0f..258f48d92ee736ca140bfea003d76557916b5220 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb @@ -9,8 +9,8 @@ name = 'HTSlib' version = '1.2.1' homepage = "http://www.htslib.org/" -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb index ced9e05617be9c6f7e523b05b5262209e64dab5b..8c0f7d5ac6f056394b9053626ab410b7fc1ac82a 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb @@ -9,8 +9,8 @@ name = 'HTSlib' version = '1.2.1' homepage = "http://www.htslib.org/" -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'intel', 'version': '2015b'} 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-intel-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7b22333e99d996afb643dd7358c076ef67ce7b08 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-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': 'intel', '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/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index c839cbc2dd879a0fc9f19e6f9bc77b318b1ef396..12d6705dfac95ef61ec59f529f9a3e3e14052470 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -19,11 +19,15 @@ pythonver = '2.7.9' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s-serial' % (python, pythonver) +prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' + dependencies = [ (python, pythonver), ('HDF5', '1.8.14', '-serial'), ] +builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] + sanity_check_paths = { 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], 'dirs': [], diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b6bd52a313b118ebdcee8008a404080568a7dee --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': False} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.16' +hdf5versuffix = '-serial' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s%s' % (hdf5ver, hdf5versuffix) + +prebuildopts = ' python setup.py configure --hdf5=$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=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.11'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb index f070e8c2260357de11cfbdabe63ef51e5e89f9c6..7cd0e1723212809d2e7706055c3188b74db0c6ca 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -19,12 +19,15 @@ pyver = '%s.10' % py_maj_min hdf5ver = '1.8.15-patch1' versionsuffix = '-Python-%s-HDF5-%s-serial' % (pyver, hdf5ver) +prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' + dependencies = [ ('Python', pyver), ('HDF5', hdf5ver), - ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), ] +builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%s/site-packages/' % py_maj_min], diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..2f905991c2e85311ef4860985e3413ee3c190913 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-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': 'intel', '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/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-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-3.2.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb index 4c966b0d8aa55b12cf8fad541c67d26de4513414..92dcaa700c62d90dbe1ba3fe6d630d4bd779eb1e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb @@ -25,7 +25,6 @@ dependencies = [ # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('pysqlite', '2.7.0', { 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 6a2901ff52a1797d22ba3a8af5a5ae668b2fb4d5..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: @@ -13,19 +14,13 @@ 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), ] # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('pysqlite', '2.8.1', { @@ -53,9 +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/'], }), @@ -74,11 +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 fd3e839da8d3eb686b8b3de324ca76daf1b04802..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: @@ -13,19 +14,13 @@ 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), ] # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('pysqlite', '2.8.1', { @@ -53,9 +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/'], }), @@ -74,11 +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-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb index 23b5d632b056950be2a140e46945cd265f8f3c0f..446396ee03bca9646ad8dc1b95f4e1ecd10deb25 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb @@ -4,7 +4,7 @@ version = '2013.5.192' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb index 1c9509e4eddf61c8ff69d179a19edaf32013882a..d02dca7d2281aaedc0546b3524d6173c5d37f562 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.0.090' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb index b54726809800307d62205b10bb84334e340ae16d..368b594177c120009bb61d4e425661a0b21dd4a1 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.1.133' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb index 6ae91f49df63f353e37bb71fcd6de370f3d85fab..8439c044f45586a1956d414446ce6cdeaa1d896d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.2.164' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb index 5d89d21731d4988c4212a5e5ee3837df13021199..37331a148806eae1f491109ae7e963dd503e9318 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '2015.3.187' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb index 3a9d4088aee0c036ec6a4522167fbdbb75fe1c94..1ca6568cb7049f00c1696a87484efb06caaf1028 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '2015.5.223' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] 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 7354472c7ec882d2363fbbdcfce80a8f9425dbc0..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 @@ -6,7 +6,7 @@ version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] @@ -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 0748e2d4000b52a9699fdbddd005d5f74a4a11bd..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 @@ -6,7 +6,7 @@ version = '2016.1.150' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] @@ -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-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..4d0d75afae2914f5acf4739922f5a6cff60b7b99 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-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 = '2016.2.181' + +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 = '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-2016.2.181-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-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..871fae395a716b77de72c776de28e2125b8f5f7d --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-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 = '2016.2.181' +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-2016.2.181-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-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb index cba97b45a2ca9094278809183f3bf838fe62b109..901fc019cc7f3ba3dc4097b62266d151ff9a4297 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb @@ -4,7 +4,7 @@ version = '2013.5.192' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb index 6f1139a94c33e3ceeadb501d842063a6ee29c779..a94df9884bd0363204bda12daba89bf92a9dd2cb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.0.090' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb index b653c4f8582b152d712ff61bb3e36bdd92730358..419e0257c0918bc09851082a152b1a35a3cf4cfb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.1.133' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb index 4f376249d8f9c0f98cc9237ea557ef87d07bd90e..5767d1400f2405ac64a1aa5fcc1520ec39404aa3 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.2.164' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb index f944202e890a53a19f790165d933071c3bb78cc6..0f54df3a82e9919122dd17cf8d1cdcc8a7c74f83 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '2015.3.187' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb index faee88adb1dbf888676eeaaae52029a34a2654a8..2fd9b5a9467ab1b0bf0b4a2f56bbf539d2d3863a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '2015.5.223' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] 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 c188753ac5274d0fe96de44d731c5e5f5049528c..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 @@ -6,7 +6,7 @@ version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] @@ -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 f961cef224fc6092654905862e8fd7afc6b55f4e..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 @@ -6,7 +6,7 @@ version = '2016.1.150' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] @@ -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-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..ffe995c4ac47d86db8e0533cf7a81485c97c4801 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-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 = '2016.2.181' + +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 = '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-2016.2.181-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-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..3d1b98171457ee844aefd8a184fffccbde677e37 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.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-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'} + +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-2016.02-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-10.2.6.038-32bit.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb index 4619863d5f6fa7ed01867589d4e2ccc329137a7a..39b3d7cf7b3c595141c73d338fa030958053b505 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb @@ -8,10 +8,12 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_p_%(version)s.tar.gz'] +patches = ['imkl-%(version)s_fix-install-double-dash.patch'] + dontcreateinstalldir = 'True' # deps for interface build diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb index a693a15b86e5bea1a74d8f001c0ca55265aa5f78..b1eb6ee6e39a4eb88b1bebf927538eb0614aa1c2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_p_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038_fix-install-double-dash.patch b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038_fix-install-double-dash.patch new file mode 100644 index 0000000000000000000000000000000000000000..929b9c706900e95be3a7735bdc888236cd209377 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038_fix-install-double-dash.patch @@ -0,0 +1,14 @@ +fix regex that doesn't handle directory names with a double dash (--) in them correctly +this fix is specific to using '-32bit' as versionsuffix +author: Kenneth Hoste (HPC-UGent) +--- l_mkl_p_10.2.6.038/pset/install.sh.orig 2016-03-04 15:28:03.092055076 +0100 ++++ l_mkl_p_10.2.6.038/pset/install.sh 2016-03-04 15:27:44.071603046 +0100 +@@ -1281,7 +1281,7 @@ + + [ $err -eq ${ERR_OK} ] || return 1 + +- RS=$(echo $CMD_STR | sed s/.*--$cmd[[:blank:]]*//g | sed 's/[[:blank:]]*--.*$//g') ++ RS=$(echo $CMD_STR | sed s/.*--$cmd[[:blank:]]*//g | sed 's/[[:blank:]]*--[^3].*$//g') + [[ -z "$RS" ]] && return 1 + echo $RS + diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb index b3d47b810d819ea6215aa3ac419b9787dae38bdc..91c64cfa0d5e70274c1d330775139846049a4c00 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s_intel64.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb index 078c8848d8acf44b3b6f12d9bee16aa32ce0773e..4d5ef42fcf1ae19862198e6890807257f9e08ad7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb @@ -6,7 +6,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, ext 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': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb index 725bb2b396fbafc7d4beb94cd82ea146f0c4fb69..2bd88ac625c46afa75b23783cd16177323c9645e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb @@ -6,7 +6,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, ext 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': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index 0db4c8f64f6c6056b4f60e2cbc0eba91bd806a6a..b8769ef805f7da0f9c00d64151c423d5b5d01b04 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb index c3fb0d1e8e6395e28e82ca47fc659f2a77c6bfc4..b5b58cc1885370919e49fdb7da5a54164cf8788e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s_intel64.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb index 209f8143d8827a7dd885b295d02ad019628091a7..8adf971a63b6e0daa8529ac8eeab1d4ac589732d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb index 94a66c877fd17be0c8f8ba015b6f4d519638f436..ccd95b2a7ac92e3db34fd79f9d813a4f47c88b27 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb index 14cee4947923aa4506f96de31f0cdd02fa7bd78f..8b97b3ff265166f10c5fac0f5854499a4144c1d9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb index 339abe07e2a548331a9dc404764c96c5c438b72f..98e5ffd25fb55b8a5289f64b0d79f61743c64c10 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb index 5b2f5de9a8c79590be954a87f0a5a04ed1fad6dd..0fe1b14e46ecd70eecb2ac8446a47d8c0688d434 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb index ca26f636cc8ff29112a43c276fdd0fab49f4bf5b..7b7f159547c27c6f4dba8d1e67410c708ddb1792 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb index 6c2f677c6cf499b7e6cc79da525d4ad0ad99850c..cc9f1d89b5d1922fc0ab58e82a75f98c59dd4d5b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb index 716cd4b3dded05f3b681cb161d69e4289b4f64b8..3b9cb14613ed640f57ef0823ffa3bb005afc27dc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb index d1128e779927c19929a355da72ec7daf894a1dc3..4843fd2442624f5d51bf92e118acbad744d00de2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb index 7c293cda0abd7751a7fb4af5ef646884a0d64b9a..3ad520461af4c20ceb2643c59e868d02ce774cd7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb @@ -6,7 +6,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, ext 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': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb index 03e70ed442f9e0a1156f3b1efa826b377b2915cc..47e59ba9fcd62671a8c558d951bed0558d1e4f9f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb index 3f03a3bd36f01702d5463dee76c423f14469ece5..bd599cfe0d4df98d14fa27f7b33de0e9871f276f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..91dcce3df94b6e4ee8feecb70628d5940be2877a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-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 = '11.3.2.181' + +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-4.9.3-2.25'} + +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-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-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..845f7631f8464ecaf93c49c7ece224008c0897ec --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-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': '2016.2.181-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-2016.2.181-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 new file mode 100644 index 0000000000000000000000000000000000000000..b26cb202221b665bd81f703f70d0661012e528d9 --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-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-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..41552f25a96abc21a8c1ddb116a54f7dc59303b0 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.02' +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 = '2016.2.181' +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', '11.3.2.181', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' 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-5.20.3.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..8fd4cb48f890bfd83f5b2fbede260b484fd10d36 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.20.3' + +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', '2.41', 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/i/itac/itac-9.0.3.051.eb b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb new file mode 100644 index 0000000000000000000000000000000000000000..42551d67c61cbe07655d8e131ffebaf6c7cf032c --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb @@ -0,0 +1,21 @@ +name = 'itac' +version = '9.0.3.051' + +homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_itac_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +preferredmpi = 'impi5' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'tools' 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-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb similarity index 90% rename from easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb index 057b6423c3e3539141a6b95ce97c57bba6bcfaa1..274dc4609367291579a08b08d75d91d28ab4e8e5 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb @@ -7,7 +7,7 @@ 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': 'CrayGNU', 'version': '2015.06-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'pic': True} sources = [SOURCELOWER_ZIP] diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb similarity index 90% rename from easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb index b3d235faba5503d382fbb74229d517b70325e45c..1a379efce9dd944327171300a09d95e55ab69c02 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb @@ -7,7 +7,7 @@ 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': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} sources = [SOURCELOWER_ZIP] diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..3cd71b46bfdd32e92b5f847dcdb48bad18396e92 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.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': 'CrayIntel', 'version': '2015.11'} +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/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 new file mode 100644 index 0000000000000000000000000000000000000000..a2add0de300401cf9e5aae6aae4e4adf5f6ad8c5 --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-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-3.7.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..6ad72252961cb4d6c6cb41a1f683c6a541bc1bac --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.7.1' + +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': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.4.3'), + ('Python', '2.7.11'), +] + +dependencies = [ + ('ncurses', '5.9'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' 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-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb similarity index 93% rename from easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb index 8c50a3c76663a9a59af1e22330ab069ae7131e94..173c7dbd1eabf1c02320c0a86e2eb4978944a812 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb @@ -5,7 +5,7 @@ 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': 'CrayGNU', 'version': '2015.06-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'opt': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb similarity index 93% rename from easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb index ba7eabefb47f123a89805401b19bb9da7ec00c43..ef47d32bbf871beac14ce45ed1a199c5eb653442 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb @@ -5,7 +5,7 @@ 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': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'opt': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] 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/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/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-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..2efc0a1d43514ced069713ca7d91e597edad4e68 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} +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/libGLU/libGLU-9.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..46c9710adc6dfd497fa3facaac53d0306b6a462a --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-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': 'intel', '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/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 new file mode 100644 index 0000000000000000000000000000000000000000..b63222e9d8bccccab6121f685160a848907fb9a7 --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..bd5ecc8bcd8f1d04a11ffc308d7a8573d32fe62d --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-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': 'intel', '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/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 new file mode 100644 index 0000000000000000000000000000000000000000..a8d0c1fc5507025fcb002a8f4e74f6c20d7a55ca --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..1bab5701feb9f0dd86b8630edad1b63106a22873 --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-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': 'intel', '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/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/libX11/libX11-1.6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..52b296562ea4532b4c676c3aac19a868251810b3 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..934e207665c7f6f71fbdd4162db4783b19c40130 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb @@ -0,0 +1,25 @@ +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': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('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-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/libXcursor/libXcursor-1.1.14-intel-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e7e9608bd8a46029604e707f99994f39dc8bea0d --- /dev/null +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-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': 'intel', '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/libXdamage/libXdamage-1.1.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..e140118bf0941e39e32445bb2ceccfabc6d8d04d --- /dev/null +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..395760652d78ee240234c25ab2d2f1228415029e --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb @@ -0,0 +1,25 @@ +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': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('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-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 new file mode 100644 index 0000000000000000000000000000000000000000..388076a4983eadc943f7bfe5e05f8aca4713c82e --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +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-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/libXfixes/libXfixes-5.0.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..7f710e144ecfbb8bd9f95cca637b558a1be61213 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..9695dfd53a3203f4240a66cca77f3c4596b09e7f --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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/libXft/libXft-2.3.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..17ddfd09d93227633ebd4817091fa53002d6330a --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-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': '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', '2.6.2'), + ('fontconfig', '2.11.94'), +] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..5e9d4cb87a9181d5ba3d50c5a01659c2484d6181 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-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': 'intel', '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/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/libXinerama/libXinerama-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..59633745894cf15d8d270872106bacbd247724e6 --- /dev/null +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-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': 'intel', '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/libXmu/libXmu-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5611aadb4b8fc0c4e14dd646b4db8e284183ee82 --- /dev/null +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-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': 'intel', '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/libXpm/libXpm-3.5.11-intel-2016a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..80b08e79227d1867066164bf747c20ee3e3ea2f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-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': 'intel', '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/libXrandr/libXrandr-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7c99042a39ce2e1b271f3274d45aecd7dc59829 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-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': 'intel', '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/libXrender/libXrender-0.9.9-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba222c9ba7b0caaf9b9966430b7571bdf627f2e5 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-gimkl-2.11.5.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fefc99f4eb0a28753443a0b2e9d580846b0f7439 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +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'), +] + +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/libXt/libXt-1.1.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..79ad76f252dd0a4ed887f42ccb036353f258c950 --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} +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/libXt/libXt-1.1.5-intel-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..66391ee4ad35f010f7de8221ad303f5a73d9b9dd --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-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': 'intel', '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/libcerf/libcerf-1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0a93e776ce695d2ef4539baa8ec8dc271b28db9 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-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': 'intel', '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-2.4.67-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..caf76a0cf51b18de9b5f2646f160d3a96df17d3a --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-2.4.67-intel-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f4e9adac9a11a5598a9211ed452e655f87e123de --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-intel-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': '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/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-2015b.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d516d79d6d7f9500a305a2ba948352befae7d253 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015b.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': '2015b'} + +source_urls = [ + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', + 'ftp://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/libffi/libffi-3.2.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..7436f22a768d7ff899a51987a9dd2ba5ec47fd62 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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/libfontenc/libfontenc-1.1.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..7e68f166358ce16f3a7b43f02c30f6f5510e3a26 --- /dev/null +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..437c5cc9a2b865ce84aecc1bac11054748860821 --- /dev/null +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'libgcrypt' +version = '1.6.5' + +homepage = 'https://gnupg.org/related_software/libgcrypt/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] + +dependencies = [('libgpg-error', '1.21')] + +sanity_check_paths = { + 'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/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/libgd/libgd-2.1.1-intel-2016a.eb b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6e0e81725193f65f6a3db281b3c81ca74a46aab7 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-intel-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': 'intel', '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/libglade/libglade-2.6.4-intel-2016a.eb b/easybuild/easyconfigs/l/libglade/libglade-2.6.4-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..479f939d5a2f3924741f83e90f04c2fd3e53cd44 --- /dev/null +++ b/easybuild/easyconfigs/l/libglade/libglade-2.6.4-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libglade' +version = '2.6.4' + +homepage = 'https://developer.gnome.org/libglade/' +description = """Libglade is a library for constructing user interfaces dynamically from XML descriptions.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/libglade/%(version_major_minor)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('ATK', '2.18.0'), + ('GTK+', '2.24.28'), + ('GLib', '2.47.5'), + ('libxml2', '2.9.3'), +] + +sanity_check_paths = { + 'files': ['bin/libglade-convert', 'lib/libglade-2.0.a', 'lib/libglade-2.0.%s' % SHLIB_EXT, + 'lib/pkgconfig/libglade-2.0.pc'], + 'dirs': ['include/libglade-2.0/glade', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.21-intel-2016a.eb b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.21-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a3d7d6c682aa62816d415468a420a759e36099e4 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.21-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libgpg-error' +version = '1.21' + +homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] + +sanity_check_paths = { + 'files': ['bin/gpg-error-config', 'include/gpg-error.h', 'lib/libgpg-error.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/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/libidn/libidn-1.32-intel-2016a.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..92af944d43a5b5b62c46fd07919d1855b46bb27c --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-intel-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': 'intel', '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-foss-2016a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe5eb900db2090044108ea741a8f6977ce8e9bfb --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a.eb @@ -0,0 +1,30 @@ +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': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +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/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 new file mode 100644 index 0000000000000000000000000000000000000000..ea05edccedb37f6684b81ce4d5d747cad15b573e --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..c0a23d9702e9d266c112a6df21943bc50ac9877c --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-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': 'intel', '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/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/libpng/libpng-1.6.21-foss-2016a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8cfac2c6e9ad2eaeddf5693c5012ea242b0bbcef --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2016a.eb @@ -0,0 +1,26 @@ +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': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +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/libpng/libpng-1.6.21-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b5b14067aaa01849bafa9d55e27cc811dc255a2 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-gimkl-2.11.5.eb @@ -0,0 +1,26 @@ +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': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +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/libpthread-stubs/libpthread-stubs-0.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..b29ddd60998b8dd2517bfa02f874855803dac2c9 --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..9a9c4dd1a0957579f22127b048218cc88d6b3a0f --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.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': 'foss', 'version': '2015b'} +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 = "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-6.2-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-6.3-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb similarity index 93% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb index 86d953546093074483e92d1bdae54f37a3b5ece0..be707f2f9def765fb3b3eaa50dadf0498be34a17 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libreadline' -version = '6.3' +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 @@ -9,7 +9,7 @@ description = """The GNU Readline library provides a set of functions for use by 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': '2015.06-XC'} +toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] 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-2015.11-XC.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb similarity index 88% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb index 9f6f591568a4b93d96818b3004837bcc5e0c9ab4..1710b5c8bc4dce739def12e8db8ced5fa616e208 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb @@ -9,16 +9,18 @@ description = """The GNU Readline library provides a set of functions for use by 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': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} 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 new file mode 100644 index 0000000000000000000000000000000000000000..a4fb8619cbc8911dff1da7a7048eedddd9ab2804 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.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': '2015.11'} +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-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/libspatialite/libspatialite-4.3.0a-foss-2015a.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9c107ea9d929aa43d0f933b34aeb765f88416769 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.3.0a' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = """SpatiaLite is an open source library intended to extend the SQLite core to support + fully fledged Spatial SQL capabilities.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('FreeXL', '1.0.2'), + ('GEOS', '3.5.0', '-Python-2.7.11'), + ('SQLite', '3.10.0'), + ('PROJ', '4.9.1'), +] + +builddependencies = [('CMake', '3.4.1')] + +configopts = '--disable-geosadvanced' + +sanity_check_paths = { + 'files': ['include/spatialite.h', 'lib/libspatialite.a', 'lib/libspatialite.%s' % SHLIB_EXT], + 'dirs': ['include/spatialite'], +} + +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/libtasn1/libtasn1-4.7-intel-2016a.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4bb22e3a8fe1ffb307c919603be93e950491d447 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-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': 'intel', '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-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..03bf53f3959aba9772a5d864ad53da2afbb573fa --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +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/libunistring/libunistring-0.9.3-intel-2016a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b6d4e58c52e78221b1cfd3cf58bd4d5c9bb9176 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-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': 'intel', '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-2.2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb similarity index 94% rename from easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb index 3ef89d660d2d5a6551a9e70c17adc39118ef5380..d9d2ff8c6b3e99c6d19cdb9a8fb77093735737b4 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb @@ -7,7 +7,7 @@ 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': 'CrayGNU', 'version': '2015.06-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'opt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb similarity index 94% rename from easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb index bfd88b3c4bccb65f094283d7fe96624aa6c7f4ae..254367cee7edc335d841ccf23272bf1a76b38851 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb @@ -7,7 +7,7 @@ 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': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'opt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..ae74d150b04e7c568340754278cadc07372aee73 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb @@ -0,0 +1,33 @@ +# contributed by Luca Marsella (CSCS) +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +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': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f8d72a6348448066ad51e5093f386222e0a0904 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$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/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab5bcf6b3802c02764b317254c390d338dbecca0 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb @@ -0,0 +1,33 @@ +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': 'gimkl', 'version': '2.11.5'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('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-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..03c075bd1ad120d75cf42b76c40171a8fbadd5f4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +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': '2015b'} +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/libxml2-2.9.1-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/libxml2/libxml2-2.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9f21eb1b663320556b4e5a4ce63eb3cd42a74085 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb @@ -0,0 +1,29 @@ +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': '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 --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..1f39ac3f7d499c91a45b4cba2d5e7ed9b663af26 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$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-intel-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b762d969015cee07367d5f5be54962ad7912cfe8 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb @@ -0,0 +1,29 @@ +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': 'intel', '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 --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/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-XC.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb similarity index 84% rename from easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb index 68ee7aa23b8022ae263d903304f4dfe632fd4dec..8398e40d0665ca4cb92593c45b2d9755f0ab75a4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb @@ -8,12 +8,12 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce 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': 'CrayGNU', 'version': '2015.06-XC'} +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-XC.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb similarity index 84% rename from easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb index fd7cafa798b0b63429f10cb06e6623ec2c0599d3..b84761b60206ddb7270a05110e8911573dff7510 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb @@ -8,12 +8,12 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce 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': 'CrayGNU', 'version': '2015.11-XC'} +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/MATLAB/MATLAB-2012b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb index ba3d36b9c7159b8d6dc38e2e7089dbba6a2aa404..b0b8036c47660933fa83884b8e72ebff20c604e8 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb @@ -6,7 +6,7 @@ description = """MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb index acdae43db5801fa2c7705d9c7068144a62839aa9..65e39e18726fcae599612fd9e26f0cf39a311481 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb @@ -6,7 +6,7 @@ description = """MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb index 1c593f743064a381b10e8dcd361abe240ef475d4..67a1f3909647f72a0a1cf75ccb8b6f65cd0ca5e4 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb index f459048eeb9810e2dfc7df43184553eef0974fe7..ccbd003e89a51cd9c7dbb0f8771aaa9ccc6091fe 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', 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/METIS/METIS-5.1.0-intel-2016a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b79e95dce7174128230b45e7332c8163abe38895 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, + and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the + multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, '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', '3.4.3')] + +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/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb index ecc1ac48366107246160b4e4ea55b90b379bb9ca..e96f02635c0fad1f00702cc220e8c9d4d5ac0f5f 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'MPICH' version = '3.0.3' @@ -10,19 +8,9 @@ It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).""" toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.mpich.org/static/tarballs/%s' % version] - -# MPICH configure wants F90/F90FLAGS to be renamed to FC/FCFLAGS. -preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset F90FLAGS; ' - -# Build shared libraries -configopts = '--enable-shared' +source_urls = ['http://www.mpich.org/static/tarballs/%(version)s'] -sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', - 'bin/mpiexec', 'bin/mpirun', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h'], - 'dirs': [], -} +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['ee2b8a8b88e3915804df0efcc747c48b'] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb index f81230a16b43a7d071a58fac0cb37ae55a563fdb..cf4928e5640f64f2b3eddcbd308edb15bc672175 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'MPICH' version = '3.0.4' @@ -9,21 +7,10 @@ It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).""" toolchain = {'name': 'GCC', 'version': '4.8.1'} -sources = ['mpich-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.mpich.org/static/tarballs/%(version)s'] -# MPICH configure wants F90/F90FLAGS to be renamed to FC/FCFLAGS. -preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset F90FLAGS; ' - -# Build shared libraries -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', 'bin/mpiexec', 'bin/mpirun', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', 'lib/libfmpich.a', 'lib/libfmpich.%s' % SHLIB_EXT, - 'lib/libmpich.a', 'lib/libmpich.%s' % SHLIB_EXT, 'lib/libmpichcxx.a', 'lib/libmpichcxx.%s' % SHLIB_EXT, 'lib/libmpichf90.a', - 'lib/libmpichf90.%s' % SHLIB_EXT], - 'dirs': [], -} +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['9c5d5d4fe1e17dd12153f40bc5b6dbc0'] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..06251f71e8e042cd47c7ff69ff314dcb168ce242 --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,16 @@ +name = 'MPICH' +version = '3.2' + +homepage = 'http://www.mpich.org/' +description = """MPICH v3.x is an open source high-performance MPI 3.0 implementation. +It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.mpich.org/static/tarballs/%(version)s'] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['f414cfa77099cd1fa1a5ae4e22db508a'] + +moduleclass = 'mpi' 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